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G. J. Kleywegt J. L. Markley C. Gloom H. M. Berman H. Nakamuraat EBI on September 29, 2011

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(Berman, Henrick & Nakamura (2003) Nat. Struct. Biol. 10, 980)

検 、 開発す 期待 。

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Issue about PDB formatIssue about PDB format1) PDB format is still the most widely used ) y

format

2) H h l li i i2) However, there are several limitations, which become problematic more and more

・For Large and Complex moleculesFor Large and Complex molecules・For Meta-data description・・ …..3) PDBx (mmCIF) or PDBML are for 3) ( C ) o a e omachines, and not very human readable.

Size Matters• PDB column format limitations

1 character for polymer chain labels– 1-character for polymer chain labels – 5-characters for atom serial numbers– 3-characters for monomers and ligand identifiers

5 characters for atom names– 5-characters for atom names – F8.3 for model coordinates

• Implications –– Maximum of 62 chains (upper and lower case!)– Maximum of 99,999 atoms

• Requires splitting structures across multiple entries (5Requires splitting structures across multiple entries (5 ribosomes in ASU stored in 10 PDB entries!)

• Map and experimental validation are difficult for split entries– Cannot use standard monomer & ligand nomenclaturesCannot use standard monomer & ligand nomenclatures

(e.g. carbohydrates & protonation variants)– Cannot use conventional atom names in large ligands

Limits molecular dimension (< 9999 999 Angstroms)– Limits molecular dimension (< 9999.999 Angstroms)

Example: Vault by Kato et al. (2zuo, 2zv4, 2zv5)

Example: Vault by Kato et al. (2zuo, 2zv4, 2zv5)

Example: Vault by Kato et al. (2zuo, 2zv4, 2zv5)

Refinement Details ExampleREMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000

PDB( ( ))

REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 43316 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULLREMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2189 REMARK 3

_refine.entry_id 1XBB _refine.ls_d_res_high 1.57 refine.ls d res low 23.00

mmCIF_refine.ls_d_res_low 23.00 _refine.pdbx_ls_sigma_F 0.0_refine.ls_percent_reflns_obs ? _refine.ls_number_reflns_obs 43316

_refine.pdbx_ls_cross_valid_method ? fi db R F l ti d t il ?_refine.pdbx_R_Free_selection_details ?

_refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.191 _refine.ls_R_factor_R_free 0.221 _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 2189 _ _ _ _ _

New PDB format• Internal data architecture of the wwPDB

New PDB formatInternal data architecture of the PDB is built on mmCIF dictionary technology

wwPDBAnnotation

• There will be continued support for mmCIF/PDBx and PDBML

PDBx/mmCIF

archival formats• There is a critical need to adopt

i l lt ti t th t

SimplifiedFormat

NewFormat PDBML

Current PDB Format

a simple alternative to the current PDB format

Format

Method Specific Atom Records Atom Records Retain Familiar Look and Feel!!BEGIN TABLE DATA atom site xray (record name atom id atom name element residue name chain id residue sequence number ¥!!BEGIN TABLE DATA atom site xray (record name atom id atom name element residue name chain id residue sequence number ¥!!BEGIN_TABLE_DATA atom_site_xray (record_name,atom_id,atom_name,element,residue_name,chain_id,residue_sequence_number,¥insertion_code,Cartn_x,Cartn_y,Cartn_z,formal_charge,model_number,group_id,occupancy,alternate_location,B_isotropic)

ATOM 1 N N ARG A 4 _ 16.757 8.703 13.450 0 1 1 0.620 _ 21.740ATOM 2 CA C ARG A 4 _ 17.014 7.699 12.351 0 1 1 0.620 _ 18.890ATOM 3 C C ARG A 4 _ 16.929 8.224 10.937 0 1 1 0.620 _ 18.590ATOM 4 O O ARG A 4 17.177 7.506 9.922 0 1 1 0.620 16.720

!!BEGIN_TABLE_DATA atom_site_xray (record_name,atom_id,atom_name,element,residue_name,chain_id,residue_sequence_number,¥insertion_code,Cartn_x,Cartn_y,Cartn_z,formal_charge,model_number,group_id,occupancy,alternate_location,B_isotropic)

ATOM 1 N N ARG A 4 _ 16.757 8.703 13.450 0 1 1 0.620 _ 21.740ATOM 2 CA C ARG A 4 _ 17.014 7.699 12.351 0 1 1 0.620 _ 18.890ATOM 3 C C ARG A 4 _ 16.929 8.224 10.937 0 1 1 0.620 _ 18.590ATOM 4 O O ARG A 4 17.177 7.506 9.922 0 1 1 0.620 16.720_ _ATOM 5 CB C ARG A 4 _ 16.060 6.546 12.613 0 1 1 0.620 _ 20.010ATOM 6 CG C ARG A 4 _ 16.429 5.815 13.916 0 1 1 0.620 _ 22.740ATOM 7 CD C ARG A 4 _ 15.282 4.910 14.340 0 1 1 0.620 _ 24.130ATOM 8 NE N ARG A 4 _ 15.103 3.825 13.351 0 1 1 0.620 _ 22.450ATOM 9 CZ C ARG A 4 _ 14.137 2.914 13.579 0 1 1 0.620 _ 24.510

_ _ATOM 5 CB C ARG A 4 _ 16.060 6.546 12.613 0 1 1 0.620 _ 20.010ATOM 6 CG C ARG A 4 _ 16.429 5.815 13.916 0 1 1 0.620 _ 22.740ATOM 7 CD C ARG A 4 _ 15.282 4.910 14.340 0 1 1 0.620 _ 24.130ATOM 8 NE N ARG A 4 _ 15.103 3.825 13.351 0 1 1 0.620 _ 22.450ATOM 9 CZ C ARG A 4 _ 14.137 2.914 13.579 0 1 1 0.620 _ 24.510ATOM 10 NH1 N ARG A 4 _ 13.382 3.040 14.677 0 1 1 0.620 _ 24.220ATOM 11 NH2 N ARG A 4 _ 13.920 1.913 12.748 0 1 1 0.620 _ 24.130ATOM 12 N N LYS A 5 _ 16.357 9.426 10.835 0 1 1 0.620 _ 19.660ATOM 13 CA C LYS A 5 _ 16.206 10.152 9.575 0 1 1 0.620 _ 21.670ATOM 14 C C LYS A 5 _ 15.607 9.229 8.538 0 1 1 0.620 _ 20.880

ATOM 10 NH1 N ARG A 4 _ 13.382 3.040 14.677 0 1 1 0.620 _ 24.220ATOM 11 NH2 N ARG A 4 _ 13.920 1.913 12.748 0 1 1 0.620 _ 24.130ATOM 12 N N LYS A 5 _ 16.357 9.426 10.835 0 1 1 0.620 _ 19.660ATOM 13 CA C LYS A 5 _ 16.206 10.152 9.575 0 1 1 0.620 _ 21.670ATOM 14 C C LYS A 5 _ 15.607 9.229 8.538 0 1 1 0.620 _ 20.880ATOM 15 O O LYS A 5 _ 16.057 8.995 7.416 0 1 1 0.620 _ 20.640ATOM 16 CB C LYS A 5 _ 17.506 10.742 9.045 0 1 1 0.620 _ 23.450ATOM 17 CG C LYS A 5 _ 17.959 11.915 9.911 0 1 1 0.620 _ 26.960ATOM 18 CD C LYS A 5 _ 19.253 12.533 9.415 0 1 1 0.620 _ 30.300ATOM 19 CE C LYS A 5 _ 20.441 11.595 9.492 0 1 1 0.620 _ 31.990ATOM 20 NZ N LYS A 5 21 676 12 193 8 914 0 1 1 0 620 33 340

ATOM 15 O O LYS A 5 _ 16.057 8.995 7.416 0 1 1 0.620 _ 20.640ATOM 16 CB C LYS A 5 _ 17.506 10.742 9.045 0 1 1 0.620 _ 23.450ATOM 17 CG C LYS A 5 _ 17.959 11.915 9.911 0 1 1 0.620 _ 26.960ATOM 18 CD C LYS A 5 _ 19.253 12.533 9.415 0 1 1 0.620 _ 30.300ATOM 19 CE C LYS A 5 _ 20.441 11.595 9.492 0 1 1 0.620 _ 31.990ATOM 20 NZ N LYS A 5 21 676 12 193 8 914 0 1 1 0 620 33 340ATOM 20 NZ N LYS A 5 _ 21.676 12.193 8.914 0 1 1 0.620 _ 33.340!!END_TABLE_DATAATOM 20 NZ N LYS A 5 _ 21.676 12.193 8.914 0 1 1 0.620 _ 33.340!!END_TABLE_DATA

StandardMethod Specific

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