[English] 日本語
Yorodumi
- PDB-5vpq: Crystal structure of beta-lactamase from Burkholderia phymatum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vpq
TitleCrystal structure of beta-lactamase from Burkholderia phymatum
ComponentsBeta-lactamase
KeywordsHYDROLASE / SSGCID / beta-lactamase / Burkholderia phymatum / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of beta-lactamase from Burkholderia phymatum
Authors: Conrady, D.G. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4669
Polymers61,9662
Non-polymers5007
Water12,755708
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3266
Polymers30,9831
Non-polymers3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1403
Polymers30,9831
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.700, 165.610, 73.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21B-467-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 12 through 14 and (name N...
21(chain B and (resid 12 through 18 or resid 21...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 12 through 14 and (name N...A12 - 14
121(chain A and ((resid 12 through 14 and (name N...A5 - 293
131(chain A and ((resid 12 through 14 and (name N...A5 - 293
141(chain A and ((resid 12 through 14 and (name N...A5 - 293
151(chain A and ((resid 12 through 14 and (name N...A5 - 293
211(chain B and (resid 12 through 18 or resid 21...B12 - 18
221(chain B and (resid 12 through 18 or resid 21...B21 - 23
231(chain B and (resid 12 through 18 or resid 21...B25 - 31
241(chain B and (resid 12 through 18 or resid 21...B33 - 43
251(chain B and (resid 12 through 18 or resid 21...B45 - 49
261(chain B and (resid 12 through 18 or resid 21...B51 - 55
271(chain B and (resid 12 through 18 or resid 21...B57 - 60
281(chain B and (resid 12 through 18 or resid 21...B62
291(chain B and (resid 12 through 18 or resid 21...B64 - 67
2101(chain B and (resid 12 through 18 or resid 21...B69 - 70
2111(chain B and (resid 12 through 18 or resid 21...B72
2121(chain B and (resid 12 through 18 or resid 21...B74 - 75
2131(chain B and (resid 12 through 18 or resid 21...B78 - 79
2141(chain B and (resid 12 through 18 or resid 21...B82 - 92
2151(chain B and (resid 12 through 18 or resid 21...B94 - 98
2161(chain B and (resid 12 through 18 or resid 21...B100 - 118
2171(chain B and (resid 12 through 18 or resid 21...B120
2181(chain B and (resid 12 through 18 or resid 21...B122 - 129
2191(chain B and (resid 12 through 18 or resid 21...B132 - 138
2201(chain B and (resid 12 through 18 or resid 21...B139
2211(chain B and (resid 12 through 18 or resid 21...B12 - 281
2221(chain B and (resid 12 through 18 or resid 21...B12 - 281
2231(chain B and (resid 12 through 18 or resid 21...B12 - 281
2241(chain B and (resid 12 through 18 or resid 21...B12 - 281

-
Components

#1: Protein Beta-lactamase


Mass: 30983.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_2229 / Plasmid: BuphA.00104.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2JET9, beta-lactamase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: BuphA.00104.a.B1.PS37967 at 22.6mg/ml, mixed 1:1 with Rigaku Reagents MCSG1 A3: 0.2 M NaCl, 0.1M Sodium Phosphate pH 6.2, 10% PEG8000, cryo protected with 25% Ethylene Glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→41.104 Å / Num. obs: 114101 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.171 % / Biso Wilson estimate: 12.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.07 / Net I/σ(I): 27.32 / Num. measured all: 932366 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.447.5810.5553.2483620.880.596100
1.44-1.488.1540.4214.5181490.9350.449100
1.48-1.528.1580.335.8379340.960.352100
1.52-1.578.1930.2627.4177310.9730.28100
1.57-1.628.1990.2159.1674610.9820.23100
1.62-1.678.2230.17811.0872620.9880.191100
1.67-1.748.2240.14414.0669730.9910.153100
1.74-1.818.2480.11917.0867270.9940.127100
1.81-1.898.2510.09422.0164680.9960.1100
1.89-1.988.260.0728.2661980.9980.075100
1.98-2.098.2740.05535.458720.9980.059100
2.09-2.218.2770.04641.5755800.9990.049100
2.21-2.378.2760.04146.7152850.9990.043100
2.37-2.568.2910.03651.3348990.9990.039100
2.56-2.88.2930.03257.2345220.9990.034100
2.8-3.138.2990.02664.59408710.028100
3.13-3.618.2590.02273.21363910.023100
3.61-4.438.1990.01979.16311210.02100
4.43-6.268.0690.01978.22243910.021100
6.26-41.1047.4150.0276.14140110.02199

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6Y

4c6y


Resolution: 1.4→41.104 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.55
RfactorNum. reflection% reflection
Rfree0.1611 2084 1.83 %
Rwork0.1385 --
obs0.1389 114093 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.57 Å2 / Biso mean: 19.6872 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.4→41.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 30 719 4805
Biso mean--45.87 35.53 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084507
X-RAY DIFFRACTIONf_angle_d1.076190
X-RAY DIFFRACTIONf_chiral_restr0.085708
X-RAY DIFFRACTIONf_plane_restr0.007836
X-RAY DIFFRACTIONf_dihedral_angle_d18.8521714
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1918X-RAY DIFFRACTION4.586TORSIONAL
12B1918X-RAY DIFFRACTION4.586TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.43260.2221250.193674007525
1.4326-1.46840.19141420.17173977539
1.4684-1.50810.18161330.159674377570
1.5081-1.55250.15931540.147273647518
1.5525-1.60260.16781360.145274167552
1.6026-1.65990.1681600.14373867546
1.6599-1.72630.1691310.138874357566
1.7263-1.80490.17741510.139774277578
1.8049-1.90010.1571370.140974287565
1.9001-2.01910.15761640.136974197583
2.0191-2.1750.15531120.130475147626
2.175-2.39380.14631490.131874627611
2.3938-2.74020.17451290.140275487677
2.7402-3.45210.16421350.136975727707
3.4521-41.1220.14361260.129878047930
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.9026.7658-3.70277.4278-3.5261.8089-0.07380.0187-0.2489-0.0212-0.0726-0.41960.03890.10220.18580.09520.0153-0.02540.13910.00630.133-0.7735-23.59927.4187
21.0085-0.10970.12181.4977-0.27740.24990.01210.09550.0744-0.0872-0.0238-0.0204-0.02630.06050.01390.0881-0.00410.01410.090.00170.0584-15.6937-19.7622-3.426
33.85580.4815-1.4353.089-0.17254.42550.05470.30620.4747-0.0655-0.0110.1697-0.2477-0.2638-0.07430.10020.0188-0.01870.19590.04960.1903-39.2015-12.1142-7.4365
41.3553-0.37330.09281.2119-0.47430.5265-0.00070.06060.0473-0.1230.05220.04510.0281-0.0219-0.03740.1189-0.0114-0.00930.1288-0.0070.1063-26.682-22.8849-7.6287
51.59640.08690.39145.2232-1.06941.2341-0.08660.12130.1591-0.0723-0.0433-0.2265-0.14710.11420.12390.1219-0.00930.00210.12910.01740.1112-13.1792-18.0667-6.0286
66.9280.8218-3.30246.2837-0.15574.1586-0.00810.28180.243-0.30170.0682-0.1011-0.16720.0416-0.0390.1134-0.0155-0.02450.07270.01520.1037-19.1995-5.3022-7.4816
71.33910.7297-0.33242.851-0.52120.7482-0.0221-0.06470.09130.0919-0.0010.0159-0.0782-0.0130.02640.09130.0058-0.00970.0857-0.00530.0728-18.9662-18.90197.233
86.03625.3546-3.25317.2697-3.41723.5830.2267-0.57740.08980.2896-0.3149-0.1545-0.15810.28010.05520.08990.0018-0.01710.1095-0.02360.0748-10.1644-18.528712.6087
93.4725-1.66431.30121.7793-1.74152.01040.1584-0.0188-0.2034-0.2591-0.01210.22110.2492-0.2168-0.13590.1106-0.0091-0.01890.1081-0.00250.1047-45.2523-30.96124.2385
100.5539-0.19840.12380.9657-0.26160.97960.0367-0.0667-0.04230.0069-0.0065-0.05640.05250.1263-0.04640.06450.01420.00180.09880.00070.0741-25.6326-30.041528.3076
113.6437-1.82871.71366.209-1.05293.88410.1913-0.42640.24360.4392-0.0984-0.2326-0.29710.3079-0.04710.1992-0.0688-0.00170.2936-0.07550.1411-14.3092-15.039541.3177
121.18370.14280.12380.85640.04561.06720.0151-0.14010.13850.05180.0029-0.0065-0.07420.0428-0.01770.087-0.01230.00870.1157-0.01160.0936-21.1539-20.242327.9814
133.6532-2.16032.07065.0151-4.375.76620.114-0.1136-0.1948-0.0851-0.05540.04470.25570.0197-0.05940.0786-0.0018-0.00030.0749-0.00490.0809-27.1951-33.43226.4431
144.4606-1.6088-0.885.73381.89180.7648-0.0446-0.2431-0.06310.22790.0748-0.26460.14260.1719-0.020.14160.0197-0.02210.14990.03670.0859-20.1877-35.969338.9326
151.1872-0.70730.10982.6737-0.50411.38780.0146-0.12310.07150.1760.01310.1155-0.0406-0.0212-0.03010.0717-0.00070.0170.0896-0.0060.0827-36.4027-25.516935.0135
163.2892-1.16210.43786.68921.38594.23750.0231-0.2546-0.10150.1908-0.02810.42360.1331-0.17880.01410.0591-0.00130.02290.13520.01380.1053-44.8945-31.255434.0232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 27 )A5 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 73 )A28 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 107 )A74 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 168 )A108 - 168
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 183 )A169 - 183
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 202 )A184 - 202
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 265 )A203 - 265
8X-RAY DIFFRACTION8chain 'A' and (resid 266 through 281 )A266 - 281
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 39 )B12 - 39
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 74 )B40 - 74
11X-RAY DIFFRACTION11chain 'B' and (resid 75 through 107 )B75 - 107
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 168 )B108 - 168
13X-RAY DIFFRACTION13chain 'B' and (resid 169 through 183 )B169 - 183
14X-RAY DIFFRACTION14chain 'B' and (resid 184 through 202 )B184 - 202
15X-RAY DIFFRACTION15chain 'B' and (resid 203 through 265 )B203 - 265
16X-RAY DIFFRACTION16chain 'B' and (resid 266 through 281 )B266 - 281

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more