[English] 日本語
Yorodumi
- PDB-2qvb: Crystal Structure of Haloalkane Dehalogenase Rv2579 from Mycobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qvb
TitleCrystal Structure of Haloalkane Dehalogenase Rv2579 from Mycobacterium tuberculosis
ComponentsHaloalkane dehalogenase 3
KeywordsHYDROLASE / Rv2579 / haloalkane dehalogenase / alpha-beta hydrolase protein / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


halogenated hydrocarbon catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / peptidoglycan-based cell wall / hydrolase activity / plasma membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Haloalkane dehalogenase 3 / Haloalkane dehalogenase 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsMazumdar, P.A. / Hulecki, J. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: X-ray crystal structure of Mycobacterium tuberculosis haloalkane dehalogenase Rv2579.
Authors: Mazumdar, P.A. / Hulecki, J.C. / Cherney, M.M. / Garen, C.R. / James, M.N.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haloalkane dehalogenase 3
B: Haloalkane dehalogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0606
Polymers66,8652
Non-polymers1954
Water12,052669
1
A: Haloalkane dehalogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5303
Polymers33,4331
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5303
Polymers33,4331
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.7, 65.7, 129.7
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Haloalkane dehalogenase 3


Mass: 33432.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dhaA / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q50642, UniProt: P9WMR9*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, magnesium acetate, 0.1M Tris, 5% ethylene glycol , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 134255 / % possible obs: 81.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.053 / Χ2: 1.038 / Net I/σ(I): 14.6
Reflection shellResolution: 1.19→1.23 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.278 / Num. unique all: 10126 / Χ2: 0.804 / % possible all: 62

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MJ5

1mj5


Resolution: 1.19→36.11 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.138 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16 6695 5 %RANDOM
Rwork0.12 ---
obs-127495 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.19→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 10 669 5347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224873
X-RAY DIFFRACTIONr_bond_other_d0.0020.023380
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.9476617
X-RAY DIFFRACTIONr_angle_other_deg1.19238144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.627236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1548
X-RAY DIFFRACTIONr_chiral_restr0.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.025487
X-RAY DIFFRACTIONr_gen_planes_other0.021067
X-RAY DIFFRACTIONr_nbd_refined0.2975
X-RAY DIFFRACTIONr_nbd_other0.23719
X-RAY DIFFRACTIONr_nbtor_refined0.22396
X-RAY DIFFRACTIONr_nbtor_other0.22520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2404
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.252
X-RAY DIFFRACTIONr_mcbond_it1.53036
X-RAY DIFFRACTIONr_mcbond_other1.51203
X-RAY DIFFRACTIONr_mcangle_it24772
X-RAY DIFFRACTIONr_scbond_it32123
X-RAY DIFFRACTIONr_scangle_it4.51845
X-RAY DIFFRACTIONr_rigid_bond_restr39463
X-RAY DIFFRACTIONr_sphericity_free3676
X-RAY DIFFRACTIONr_sphericity_bonded38117
LS refinement shellResolution: 1.19→1.222 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.2 337
Rwork0.15 7010
obs-7347

+
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