[English] 日本語
Yorodumi
- PDB-5hal: Crystal Structure of a putative beta-lactamase from Burkholderia ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hal
TitleCrystal Structure of a putative beta-lactamase from Burkholderia vietnamiensis
ComponentsUncharacterized protein
KeywordsHYDROLASE / SSGCID / putative beta-lactamase / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyUncharacterized protein
Function and homology information
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SAD / molecular replacement / Resolution: 2.1507 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a putative beta-lactamase from Burkholderia vietnamiensis
Authors: SSGCID / Dranow, D.M. / Davies, D.R. / Lorimer, D. / Edwards, T.E.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9322
Polymers12,8701
Non-polymers621
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.840, 110.840, 110.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
DetailsMonomer confirmed by size exclusion chromatography

-
Components

#1: Protein Uncharacterized protein


Mass: 12870.111 Da / Num. of mol.: 1 / Fragment: BuviA.16002.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_3604 / Plasmid: BuviA.16002.a.B1BuviA.16002.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JJY8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 4.41 Å3/Da / Density % sol: 72.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: BuviA.16002.a.B1.PS02517 at 19 mg/ml was mixed 1:1 with MCSG1(h4): 0.1 M sodium citrate:HCl, pH = 5.6, 20% (v/v) 2-propanol, 20% (w/v) PEG-400, harvested with 15% ethylene glycol in two steps.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 22, 2015
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 544959 / Rmerge(I) obs: 0.084 / Χ2: 1.1 / D res high: 2.1 Å / Num. obs: 24773 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
9.395027910.035
6.649.3950310.036
5.426.6465910.04
4.75.4279010.039
4.24.787610.042
3.834.298710.048
3.553.83107010.053
3.323.55112510.062
3.133.32122910.081
2.973.13126610.093
2.832.97132910.116
2.712.83142710.138
2.62.71145310.172
2.512.6150710.228
2.422.51155010.292
2.352.42166910.336
2.282.35164810.397
2.212.28176110.451
2.152.21174210.568
2.12.15190310.641
ReflectionResolution: 2.15→50 Å / Num. obs: 12481 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 31.77 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.07 / Χ2: 0.929 / Net I/σ(I): 28.03 / Num. measured all: 135544
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.15-2.2110.50.9370.5285.1195919119100.55599.9
2.21-2.270.950.426.4396098898890.441100
2.27-2.330.9590.3896.8694308738720.40999.9
2.33-2.40.9720.3218.0292698498480.33799.9
2.4-2.480.980.3028.6387948118090.31799.8
2.48-2.570.9860.23410.985887837820.24599.9
2.57-2.670.9920.16814.283787677670.177100
2.67-2.780.9950.1317.8380987357350.137100
2.78-2.90.9970.1120.2877417017000.11599.9
2.9-3.040.9980.08425.5573026676660.08899.9
3.04-3.210.9990.06631.2672016516510.069100
3.21-3.40.9990.05438.3667786136130.057100
3.4-3.640.9990.04450.1763725795790.046100
3.64-3.930.9990.03957.7358065335320.04199.8
3.93-4.310.03265.754074964960.033100
4.3-4.8110.02775.948644534530.029100
4.81-5.550.9990.02869.8942794014010.03100
5.55-6.810.02966.8837813503500.03100
6.8-9.6210.02474.5728152692690.025100
9.62-5010.01987.4914411611590.0298.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: EP_AUTO

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1507→45.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 630 5.05 %
Rwork0.1629 11851 -
obs0.1641 12481 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.99 Å2 / Biso mean: 38.7782 Å2 / Biso min: 18.11 Å2
Refinement stepCycle: final / Resolution: 2.1507→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 4 85 891
Biso mean--61.13 43.86 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007840
X-RAY DIFFRACTIONf_angle_d0.8451148
X-RAY DIFFRACTIONf_chiral_restr0.057122
X-RAY DIFFRACTIONf_plane_restr0.005153
X-RAY DIFFRACTIONf_dihedral_angle_d14.993484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1507-2.36710.25071570.204629303087
2.3671-2.70960.22071570.192729403097
2.7096-3.41370.18841550.17129413096
3.4137-45.26020.16121610.141130403201
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)
18.454-0.116-3.07965.06113.64174.4236-0.31450.0164-0.14760.17540.3953-0.32740.74660.234-0.08620.28160.0648-0.00590.2571-0.0680.20843.717341.655521.5798
27.00731.3127-4.80285.2144-4.18099.3509-0.2571-0.4337-0.31880.5212-0.41770.35980.3666-0.30730.48050.3898-0.07830.10930.3254-0.13960.3626-4.179939.436120.2118
34.6372-1.5198-1.85872.33730.90134.4627-0.11-0.1672-0.15540.06650.1964-0.13640.26490.3773-0.10960.21370.0095-0.0060.2109-0.0650.1984-0.211648.449824.9931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 28 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 47 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 107 )A0

+
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://pdbjlvh1.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