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- PDB-4ar8: Crystal structure of the peptidase domain of collagenase T from C... -

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Basic information

Entry
Database: PDB / ID: 4ar8
TitleCrystal structure of the peptidase domain of collagenase T from Clostridium tetani complexed with the peptidic inhibitor isoamyl- phosphonyl-Gly-Pro-Ala at 2.05 angstrom resolution.
Components
  • COLLAGENASE COLT
  • ISOAMYL-PHOSPHONYL-GLY-PRO-ALA
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / COLLAGENOLYSIS / METALLOPROTEASE / PEPTIDASE / HYDROLASE
Function / homology
Function and homology information


microbial collagenase / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Threonyl-tRNA Synthetase; Chain A, domain 2 / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal ...Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Threonyl-tRNA Synthetase; Chain A, domain 2 / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Neutral Protease; domain 2 / Glutaredoxin / Neutral zinc metallopeptidases, zinc-binding region signature. / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM TETANI (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsEckhard, U. / Brandstetter, H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T.
Authors: Eckhard, U. / Schonauer, E. / Brandstetter, H.
History
DepositionApr 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Derived calculations / Other
Revision 1.3Dec 21, 2016Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLLAGENASE COLT
B: COLLAGENASE COLT
C: ISOAMYL-PHOSPHONYL-GLY-PRO-ALA
D: ISOAMYL-PHOSPHONYL-GLY-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4958
Polymers92,2844
Non-polymers2114
Water5,044280
1
A: COLLAGENASE COLT
C: ISOAMYL-PHOSPHONYL-GLY-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2484
Polymers46,1422
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-5.1 kcal/mol
Surface area19640 Å2
MethodPISA
2
B: COLLAGENASE COLT
D: ISOAMYL-PHOSPHONYL-GLY-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2484
Polymers46,1422
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-4.8 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.420, 102.080, 102.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COLLAGENASE COLT


Mass: 45750.816 Da / Num. of mol.: 2 / Fragment: PEPTIDASE DOMAIN, RESIDUES 340-730
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM TETANI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q899Y1
#2: Protein/peptide ISOAMYL-PHOSPHONYL-GLY-PRO-ALA


Mass: 391.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.78 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% PEG 3350, 0.1 M NACL, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.05→45.7 Å / Num. obs: 48639 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3U
Resolution: 2.05→45.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.714 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26793 2453 5.1 %RANDOM
Rwork0.21765 ---
obs0.22013 46113 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.109 Å2
Baniso -1Baniso -2Baniso -3
1-15.93 Å20 Å20 Å2
2---37.79 Å20 Å2
3---21.86 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6279 0 4 280 6563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.026468
X-RAY DIFFRACTIONr_bond_other_d0.0020.024256
X-RAY DIFFRACTIONr_angle_refined_deg0.8641.9428743
X-RAY DIFFRACTIONr_angle_other_deg0.833310354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4365782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23524.846324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.138151039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2451518
X-RAY DIFFRACTIONr_chiral_restr0.0520.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027301
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021384
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr310724
X-RAY DIFFRACTIONr_sphericity_free28.603594
X-RAY DIFFRACTIONr_sphericity_bonded17.7210738
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 177 -
Rwork0.339 3331 -
obs--96.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.00710.0384-0.00750.2202-0.02370.0322-0.0094-0.0017-0.0002-0.03570.00950.00470.01610.031-0.00020.02320.003-0.00070.04150.00350.02619.370728.4401-49.0197
20.0670.0525-0.01060.1675-0.03970.01120.0080.00890.0028-0.01160.00120.00850.0059-0.0029-0.00920.02630.00230.00230.0336-0.00140.027228.260915.534-44.4907
30.23260.1414-0.27720.4138-0.3350.41490.0037-0.0020.0004-0.0024-0.0094-0.0151-0.00330.00320.00570.02390.0001-0.00040.03520.00060.028336.330811.3149-41.054
40.0004-0.0007-0.00040.00120.00060.0004-0.0012-0.00110.00170.00520.0018-0.0020.00230-0.00070.0260.00010.00080.03480.00130.02928.43266.1122-25.0092
50.00170.0249-0.00160.4063-0.02950.00550.0016-0.0027-0.0001-0.0047-0.0002-0.00080.01020.0001-0.00140.02940.0001-0.00410.03810.00160.025814.375512.406-28.9429
60.0672-0.0269-0.02360.0110.00990.00920.00410.00530.0079-0.00150.0005-0.00520.00090.0018-0.00460.0248-0.00180.00240.03360.00140.028827.710725.4915-36.7507
70.4654-0.1279-0.53520.03620.14240.637-0.022-0.0451-0.00060.01120.02280.00280.01050.0273-0.00080.04090.00950.00850.04520.00430.040544.135926.2543-37.1107
80.0407-0.0124-0.03730.00860.00840.03660.0052-0.0010.0044-0.0041-0.0024-0.0049-0.0004-0.0005-0.00280.0242-0.0002-0.00140.03540.00050.026826.569618.5416-25.1477
90.0049-0.028-0.01140.16620.06790.0279-0.00110.0013-0.0037-0.0015-0.00130.00890.0010.00170.00240.02560.001-0.00040.03510.00090.027731.096217.3953-18.8023
100.05470.07150.06950.32090.07130.092-0.00310.01050.00490.0054-0.01090.0075-0.00340.01440.0140.0209-0.00290.00220.03620.00330.026245.797521.5034-17.0311
110.00610.0242-0.0030.1323-0.00120.0185-0.0020.00330.0036-0.001-0.00320.00590.00280.0020.00520.0211-0.0013-0.00140.03480.00070.026834.974521.3957-12.7944
120.08140.0250.09090.0221-0.00010.1570.00580.0026-0.00610.00550.0003-0.00370.00650.0004-0.00610.0247-0.0010.00060.0350.00150.02620.47213.6035-10.5015
130.3489-0.03420.36420.0204-0.06040.41660.0119-0.0037-0.00180.0025-0.00120.00440.00520.0013-0.01070.02660.00020.00090.031-0.00130.024127.535520.3425-2.8801
140.078-0.01070.0170.0159-0.07510.3785-0.00770.0077-0.0043-0.0023-0.0025-0.00230.00930.02390.01020.0174-0.0008-0.0010.03340.00150.026246.134216.9784-13.0285
150.24050.18730.02640.44690.02970.1481-0.0060.01290.0016-0.02940.00470.0014-0.01340.00170.00130.02380.0025-0.00050.0333-0.00050.025839.3645-2.7127-40.0467
160.0059-0.00010.04780.23290.14310.536-0.0083-0.0023-0.00010.0019-0.00230.0102-0.01670.00370.01060.018-0.00140.00340.03520.00120.030631.8584-13.8411-30.1738
170.0283-0.0214-0.03710.2449-0.1840.25220.00390.0011-0.0010.0056-0.00810.0103-0.01730.00090.00420.0205-0.00150.00060.0357-0.00030.026927.169-3.8937-37.1501
180.0750.01580.03770.04860.01890.02180.00210.0012-0.00190.0067-0.004-0.00030.00220.00150.00190.02670.00050.00010.03440.00050.026530.7342-5.0978-12.9558
190.2401-0.013-0.26070.28040.38010.7670.00340.01940.01820.02850.014-0.00450.0448-0.0247-0.01750.0242-0.00560.00110.02820.00380.025539.2669-6.5812-23.4011
200.0276-0.0138-0.02720.0464-0.01010.04110.00160.00160.00190.0056-0.0007-0.0025-0.0041-0.0046-0.00090.023-0.0028-0.00040.0348-0.00040.02730.7555-4.9578-26.1856
210.5972-0.14490.06340.4545-0.67631.05160.2346-0.0894-0.14680.0411-0.11210.0595-0.15110.0678-0.12250.1997-0.0578-0.06250.075-0.00570.0674-20.4659-11.9446-2.264
220.00070.00050.00110.00060.00150.00350.0035-0.0014-0.00450.00230.0031-0.00370.00370.0047-0.00660.0337-0.0006-0.00250.02810.00390.0334-11.5054-9.4605-2.8512
230.02180.0310.00410.0515-0.0030.01260.0023-0.00090.0020.0007-0.0026-0.0009-0.00060.00190.00030.02220.00130.00190.0343-0.00020.0279-7.50216.8408-15.9807
240.398-0.18310.17050.5164-0.09730.07410.00330.00530.0136-0.027-0.01250.0039-0.00070.0040.00920.0128-0.00070.00640.03990.0020.0329-22.95784.5353-22.7577
250.07680-0.00630.0385-0.02780.07070.0088-0.0045-0.0014-0.0047-0.0013-0.02140.00360.0042-0.00750.0242-0.0013-0.00320.0344-0.00090.0288-9.2827-8.5446-14.5577
260.0174-0.00110.03450.0004-0.00260.0690.0047-0.0006-0.0088-0.00160.0053-0.00190.0019-0.0037-0.00990.02820.00050.00020.0348-0.00070.03020.7619-3.0315-19.2408
270.0160.01020.03460.00680.02290.0770.00020-0.00520.00040.0014-0.0007-0.0012-0.002-0.00160.0244-0.00050.0010.03570.00040.0311-17.3641-1.3348-30.1815
280.55690.04760.59310.35670.3350.86160.0235-0.0317-0.00410.013-0.02050.01580.0396-0.0399-0.0030.0261-0.00190.0020.036800.0222-11.2177-6.2296-36.6929
290.0281-0.0443-0.0340.09490.05060.04210.0011-0.00190.0023-0.00360.0033-0.008-0.0023-0.0022-0.00440.025-0.0009-0.00080.03530.00010.02595.1933-0.9567-32.2521
300.12990.1444-0.03940.2410.01930.0748-0.0042-0.009-0.0045-0.002-0.00010.0185-0.00010.00280.00430.02040.0010.00140.03450.00090.0281-3.9616-11.7243-38.006
310.1136-0.03970.02350.1892-0.03120.0511-0.00290.0040.0024-0.00380.00220.0019-0.0085-0.00120.00070.021-0.0008-0.00050.03440.00080.02590.45431.6831-38.582
320.11430.04570.01740.01840.0070.0027-0.00680.0065-0.0052-0.00270.0059-0.0009-0.00220.00230.00090.02630.0013-0.00020.035-0.00030.0289-13.91632.8814-41.898
330.3775-0.06180.09040.24890.0450.03690.00150.02050.0102-0.0128-0.00520.01-0.00460.00270.00370.0269-0.0010.0030.03580.00190.01430.4845-1.3885-48.4715
340.05460.03210.08410.3780.22010.97830.003-0.0191-0.0042-0.00750.0119-0.024-0.02920.048-0.01480.0077-0.00540.00160.02780.00050.028813.12660.2803-33.7197
350.1328-0.0258-0.01570.16320.07230.1004-0.0019-0.0046-0.00320.01310.0096-0.02380.01490.0148-0.00770.0262-0.00140.00260.03440.00210.02553.588616.6055-12.0176
360.0649-0.0375-0.08080.125-0.00420.127-0.0010.00230.00340.01330.00020.01170.00650.00320.00080.01890.00010.0010.03410.0010.0304-6.002230.8094-17.8074
370.04040.05120.01760.1847-0.09490.16690.0012-0.00280.0024-0.0070.00040.01190.0169-0.0052-0.00160.02320.0010.00290.0348-0.00150.0262-10.188321.9075-15.7725
380.00550.00810.00850.02050.00590.0199-0.00320.00410.0025-0.00240.00140.0004-0.00260.00580.00190.02510.001-0.00030.0339-0.00140.0271-3.669722.2712-30.2946
390.0046-0.01820.00430.0911-0.02460.00730.00670.0053-0.00610.01340.00220.0463-0.0048-0.0046-0.00890.0470.00410.0060.05170.00860.0492-15.720227.1561-43.2201
400.0011-0.00370.00140.0836-0.02730.00920.004-0.0008-0.00410.0018-0.00250.01110.00180.0004-0.00150.02260.00220.00170.03410.00010.0278-7.601120.3959-19.8003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A340 - 351
2X-RAY DIFFRACTION2A352 - 373
3X-RAY DIFFRACTION3A374 - 381
4X-RAY DIFFRACTION4A382 - 401
5X-RAY DIFFRACTION5A402 - 408
6X-RAY DIFFRACTION6A409 - 449
7X-RAY DIFFRACTION7A450 - 454
8X-RAY DIFFRACTION8A455 - 489
9X-RAY DIFFRACTION9A490 - 511
10X-RAY DIFFRACTION10A512 - 530
11X-RAY DIFFRACTION11A531 - 567
12X-RAY DIFFRACTION12A568 - 580
13X-RAY DIFFRACTION13A581 - 592
14X-RAY DIFFRACTION14A593 - 616
15X-RAY DIFFRACTION15A617 - 630
16X-RAY DIFFRACTION16A631 - 642
17X-RAY DIFFRACTION17A643 - 661
18X-RAY DIFFRACTION18A662 - 683
19X-RAY DIFFRACTION19A684 - 690
20X-RAY DIFFRACTION20A691 - 730
21X-RAY DIFFRACTION21B342 - 348
22X-RAY DIFFRACTION22B349 - 353
23X-RAY DIFFRACTION23B354 - 401
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