[English] 日本語
Yorodumi
- PDB-5k3d: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k3d
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/Apo - No Halide
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / Homodimer / Dehalogenase
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity
Similarity search - Function
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
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMehrabi, P. / Kim, T.H. / Prosser, S.R. / Pai, E.F.
CitationJournal: Science / Year: 2017
Title: The role of dimer asymmetry and protomer dynamics in enzyme catalysis.
Authors: Kim, T.H. / Mehrabi, P. / Ren, Z. / Sljoka, A. / Ing, C. / Bezginov, A. / Ye, L. / Pomes, R. / Prosser, R.S. / Pai, E.F.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase


Theoretical massNumber of molelcules
Total (without water)66,8182
Polymers66,8182
Non-polymers00
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-17 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.772, 79.677, 85.291
Angle α, β, γ (deg.)90.00, 102.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fluoroacetate dehalogenase


Mass: 33408.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350 19-22%, 200mM Calcium acetate, 100mM Tris SO4 pH 8.5

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→33.9 Å / Num. obs: 96439 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 49.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R3U

3r3u


Resolution: 1.45→33.86 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.215 4758 4.93 %
Rwork0.183 --
obs0.185 96439 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.21 Å2
Refinement stepCycle: LAST / Resolution: 1.45→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 0 604 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014907
X-RAY DIFFRACTIONf_angle_d1.3756701
X-RAY DIFFRACTIONf_dihedral_angle_d13.551780
X-RAY DIFFRACTIONf_chiral_restr0.057678
X-RAY DIFFRACTIONf_plane_restr0.008884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.30321650.26682982X-RAY DIFFRACTION99
1.4665-1.48370.30961500.25323070X-RAY DIFFRACTION100
1.4837-1.50180.26931670.23373031X-RAY DIFFRACTION100
1.5018-1.52080.25571510.22663032X-RAY DIFFRACTION100
1.5208-1.54080.25141810.22373031X-RAY DIFFRACTION100
1.5408-1.5620.23551450.21333062X-RAY DIFFRACTION100
1.562-1.58430.26991470.21093049X-RAY DIFFRACTION100
1.5843-1.60790.23461750.21743080X-RAY DIFFRACTION100
1.6079-1.6330.23041810.20852994X-RAY DIFFRACTION100
1.633-1.65980.27061590.20423042X-RAY DIFFRACTION100
1.6598-1.68840.22241580.19773037X-RAY DIFFRACTION100
1.6884-1.71910.2551590.19873028X-RAY DIFFRACTION100
1.7191-1.75220.22661670.20023065X-RAY DIFFRACTION100
1.7522-1.7880.25571520.1963053X-RAY DIFFRACTION100
1.788-1.82680.26921200.19453110X-RAY DIFFRACTION100
1.8268-1.86930.22561520.19443045X-RAY DIFFRACTION100
1.8693-1.91610.24821630.19093061X-RAY DIFFRACTION100
1.9161-1.96790.23551630.19263042X-RAY DIFFRACTION100
1.9679-2.02580.22911460.19293075X-RAY DIFFRACTION100
2.0258-2.09120.22751720.19323057X-RAY DIFFRACTION100
2.0912-2.16590.21871540.18673033X-RAY DIFFRACTION100
2.1659-2.25260.22311830.18113037X-RAY DIFFRACTION100
2.2526-2.35510.20731700.18313056X-RAY DIFFRACTION100
2.3551-2.47920.2261520.18153067X-RAY DIFFRACTION100
2.4792-2.63450.21761460.18093075X-RAY DIFFRACTION100
2.6345-2.83780.19861380.18493079X-RAY DIFFRACTION100
2.8378-3.12320.23371460.18473094X-RAY DIFFRACTION100
3.1232-3.57470.19081700.17423075X-RAY DIFFRACTION100
3.5747-4.50210.17151510.1373107X-RAY DIFFRACTION100
4.5021-33.87110.13571750.14243112X-RAY DIFFRACTION100

+
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