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- PDB-4bp0: Crystal structure of the closed form of Pseudomonas aeruginosa SPM-1 -

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Basic information

Entry
Database: PDB / ID: 4bp0
TitleCrystal structure of the closed form of Pseudomonas aeruginosa SPM-1
ComponentsMETALLO-B-LACTAMASE
KeywordsHYDROLASE / METALLO BETA LACTAMASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsMcDonough, M.A. / Brem, J. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2015
Title: Studying the active-site loop movement of the Sao Paolo metallo-beta-lactamase-1
Authors: Brem, J. / Struwe, W.B. / Rydzik, A.M. / Tarhonskaya, H. / Pfeffer, I. / Flashman, E. / van Berkel, S.S. / Spencer, J. / Claridge, T.D. / McDonough, M.A. / Benesch, J.L. / Schofield, C.J.
History
DepositionMay 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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: METALLO-B-LACTAMASE
B: METALLO-B-LACTAMASE
C: METALLO-B-LACTAMASE
D: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,34829
Polymers111,7094
Non-polymers1,63925
Water7,530418
1
A: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3788
Polymers27,9271
Non-polymers4517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2867
Polymers27,9271
Non-polymers3596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3137
Polymers27,9271
Non-polymers3866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3707
Polymers27,9271
Non-polymers4436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.650, 83.550, 282.410
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
METALLO-B-LACTAMASE / SPM-1 / METALLO-BETA-LACTAMASE BLASPM-1


Mass: 27927.178 Da / Num. of mol.: 4 / Fragment: RESIDUES 29-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: 48-1997A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q8G9Q0, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCHLORIDE ION (CL): CHLORIDE WAS MODELED AS PUTATIVE ION DUE TO LACK OF BETTER ALTERNATIVE BASED ON ...CHLORIDE ION (CL): CHLORIDE WAS MODELED AS PUTATIVE ION DUE TO LACK OF BETTER ALTERNATIVE BASED ON CRYSTALLISATION CONDITION CONTENTS.
Sequence detailsTHE TWO N-TERMINAL RESIDUES 'GP' FROM THE 3C PROTEASE CLEAVAGE SITE REMAIN PART OF THE PROTEIN ...THE TWO N-TERMINAL RESIDUES 'GP' FROM THE 3C PROTEASE CLEAVAGE SITE REMAIN PART OF THE PROTEIN AFTER CLEAVAGE OF THE HIS-TAG

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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: 2.32 Å3/Da / Density % sol: 47.01 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: PROTEIN WAS CRYTALLISED FROM 10% W/V POLYETHYLENE GLYCOL 8000, 0.1M HEPES, PH7.5, VAPOR DIFFUSION SITTING DROP, ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0081
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 11, 2012
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0081 Å / Relative weight: 1
ReflectionResolution: 2.24→71.91 Å / Num. obs: 53352 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 40.96 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FHX
Resolution: 2.24→71.9428 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 3779 3.8 %
Rwork0.1516 --
obs0.1533 53254 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.51 Å2
Refinement stepCycle: LAST / Resolution: 2.24→71.9428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7707 0 65 418 8190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147967
X-RAY DIFFRACTIONf_angle_d1.17410766
X-RAY DIFFRACTIONf_dihedral_angle_d14.4992968
X-RAY DIFFRACTIONf_chiral_restr0.0651176
X-RAY DIFFRACTIONf_plane_restr0.0051358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.26840.29081460.25423662X-RAY DIFFRACTION100
2.2684-2.29820.2991390.24043553X-RAY DIFFRACTION100
2.2982-2.32970.26881370.22693532X-RAY DIFFRACTION100
2.3297-2.3630.24621360.21833568X-RAY DIFFRACTION100
2.363-2.39830.25541410.21453622X-RAY DIFFRACTION100
2.3983-2.43570.26571370.20223543X-RAY DIFFRACTION100
2.4357-2.47570.26741370.2013525X-RAY DIFFRACTION100
2.4757-2.51840.22611390.19563642X-RAY DIFFRACTION100
2.5184-2.56420.23541390.18263516X-RAY DIFFRACTION100
2.5642-2.61350.21811380.17243532X-RAY DIFFRACTION99
2.6135-2.66680.20971460.17293598X-RAY DIFFRACTION100
2.6668-2.72480.23981400.16833543X-RAY DIFFRACTION99
2.7248-2.78820.19871340.16253524X-RAY DIFFRACTION99
2.7882-2.85790.23371440.16413635X-RAY DIFFRACTION99
2.8579-2.93520.20351370.15773480X-RAY DIFFRACTION100
2.9352-3.02160.22511450.16263597X-RAY DIFFRACTION99
3.0216-3.11910.26881410.16053512X-RAY DIFFRACTION100
3.1191-3.23060.24521430.1593594X-RAY DIFFRACTION100
3.2306-3.35990.19611350.15083521X-RAY DIFFRACTION99
3.3599-3.51280.19751410.14833610X-RAY DIFFRACTION99
3.5128-3.6980.16861390.13713473X-RAY DIFFRACTION99
3.698-3.92970.2021410.13853582X-RAY DIFFRACTION100
3.9297-4.23310.16181400.12673580X-RAY DIFFRACTION100
4.2331-4.6590.14321430.1053551X-RAY DIFFRACTION100
4.659-5.3330.14711370.11593553X-RAY DIFFRACTION99
5.333-6.71830.16931410.14443549X-RAY DIFFRACTION99
6.7183-71.94280.18781430.15183520X-RAY DIFFRACTION98
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)
11.38991.58760.15683.37232.93094.8378-0.2780.336-0.3954-0.51370.21550.35270.4594-0.1852-0.0130.248-0.0578-0.03430.3653-0.03630.34334.5912-0.099542.6985
23.16850.48020.66413.93040.66775.69510.03660.1743-0.2106-0.15250.04830.22460.3181-0.0944-0.07950.1099-0.0352-0.00430.2104-0.01090.257737.99773.328851.3454
33.3547-0.07770.20947.90870.75535.1617-0.01430.077-0.2081-0.143-0.06030.33140.4403-0.54460.10710.2015-0.0776-0.03490.38870.00540.386328.71383.349851.7407
42.70590.74690.4023.68090.57094.433-0.0627-0.05370.11770.11510.06660.3176-0.0591-0.34120.05570.11060.01920.00980.22150.01910.267637.582613.012160.2853
58.56656.99414.77732.37948.31736.3629-0.7841.04970.9621-1.5980.23860.3128-1.5280.42110.58450.6073-0.0262-0.11620.42810.21080.623233.767324.833445.1097
65.264-0.9435-0.96444.2781-0.87755.0212-0.0417-0.61260.40120.38040.0441-0.286-0.14090.0729-0.09860.2009-0.0551-0.01720.1823-0.04770.22241.525114.468264.8197
73.1504-0.2762-0.75541.62530.40543.1079-0.0863-0.2648-0.33230.1177-0.0067-0.24020.30010.28130.09440.16050.0017-0.06240.23930.01470.297549.00783.461959.7382
86.2253-0.6326-0.31515.2188-0.14684.75090.0116-0.06660.1698-0.04690.1136-0.6255-0.25230.4957-0.11840.1647-0.0766-0.00780.3043-0.01770.323257.30613.46650.5488
92.3812.1704-1.16222.324-2.39829.76470.17350.6154-0.8327-0.3133-0.2028-0.06230.8957-0.0268-0.08960.2782-0.0378-0.03320.2906-0.07270.387150.43070.771948.3772
103.07674.0438-1.43822.1915-3.56488.9520.11670.29340.4987-0.5905-0.2704-0.3528-0.47980.55010.14660.23810.0460.09160.48190.02810.628461.901812.787145.1649
110.2815-1.23510.5257.0902-3.52531.9266-0.3717-1.3308-0.50331.13870.11530.31240.6271-0.0149-0.0050.76010.26550.11540.66710.05860.376537.9631-2.455999.5583
125.65872.59522.71697.24264.36398.7529-0.0502-0.8003-0.23371.04690.13930.22420.5214-0.1733-0.09140.4540.19860.08140.38580.11130.316637.73242.750391.1347
136.29335.41383.81377.21355.9839.76760.2096-0.491-0.49161.00220.123-0.130.7035-0.0778-0.28560.52570.19690.03290.41890.06290.366444.9324-3.023190.7346
143.48671.60050.19334.3885-0.66414.1107-0.2725-0.2423-0.01920.38630.191-0.2472-0.13530.06250.06280.27870.1042-0.02060.2763-0.02550.213844.360210.269182.5151
158.77922.1252-0.18312.0856-8.46886.9407-0.1852-2.0771.19092.0362-0.0304-0.1011-1.56360.64910.24181.12710.1637-0.23530.8446-0.24240.6954.879516.37297.9705
163.87670.90320.22333.69350.22263.476-0.132-0.19840.1150.320.18040.4951-0.21-0.4406-0.02770.33430.13860.01220.34580.06460.294832.930411.118181.5248
174.90240.7648-0.93135.4207-0.67544.4889-0.22-0.5280.12120.72380.33630.7644-0.4958-0.4917-0.10890.6170.320.1150.57840.01910.405328.258117.953992.9026
186.02735.7276-0.05549.88621.66255.39930.2738-0.77270.72510.8937-0.06570.6766-0.5482-0.1701-0.14280.78480.39190.16310.8987-0.01950.539524.644424.505797.8708
194.1229-0.1483-1.93382.4193-0.35795.9502-0.019-0.0525-0.05270.0605-0.07060.22770.295-0.64070.0710.3712-0.0788-0.02220.2815-0.01540.231239.4932-1.241217.6123
202.3231-1.7827-7.62969.22513.23975.86020.0447-1.1525-0.16791.3824-0.0939-0.28730.75751.12080.14470.79270.0708-0.10570.51130.06580.490954.1051-12.262626.2487
213.27620.21241.33615.1825-0.03295.5480.01580.00560.40210.0381-0.1254-0.2661-0.7590.05950.13720.3899-0.04530.06690.25720.02160.265348.28019.747213.3643
228.56062.45322.19128.36851.25648.5694-0.0745-0.5251.01850.6833-0.1194-0.1453-1.0614-0.05380.2110.7586-0.05750.02020.3252-0.07950.439349.601317.123723.7646
234.42710.7626-0.94052.60010.1114.6788-0.1068-0.1199-0.26110.2944-0.14650.16970.5805-0.3710.26640.47-0.08590.00110.28680.0090.281761.176138.345117.4125
242.29371.5673-6.01937.2696-6.6242.18340.2483-2.09-0.191.7105-0.4334-0.68790.47891.4277-0.03290.97980.0653-0.1690.98960.21320.723977.594532.392427.9487
253.21830.24260.39463.96840.22496.9796-0.09070.02020.2152-0.0036-0.0987-0.1291-0.57270.08270.2130.3598-0.05050.01830.22740.04530.242466.156949.177412.9065
268.53752.05210.51127.84781.01084.79160.0756-0.0671.03780.6018-0.21190.1541-1.62110.13630.15510.8078-0.0957-0.03130.298-0.00520.361667.345759.451521.9667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 31 THROUGH 46 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 47 THROUGH 79 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 80 THROUGH 96 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 97 THROUGH 141 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 142 THROUGH 162 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 163 THROUGH 177 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 178 THROUGH 216 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 217 THROUGH 245 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 246 THROUGH 290 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 291 THROUGH 310 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 31 THROUGH 46 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 47 THROUGH 79 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 80 THROUGH 96 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 97 THROUGH 141 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 142 THROUGH 162 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 163 THROUGH 216 )
17X-RAY DIFFRACTION17CHAIN B AND (RESID 217 THROUGH 290 )
18X-RAY DIFFRACTION18CHAIN B AND (RESID 291 THROUGH 309 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 31 THROUGH 141 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 142 THROUGH 162 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 163 THROUGH 243 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 244 THROUGH 308 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 31 THROUGH 141 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 142 THROUGH 161 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 162 THROUGH 232 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 233 THROUGH 308 )

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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