[English] 日本語
- PDB-6mzz: Fluoroacetate dehalogenase, room temperature structure, using fir... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6mzz
TitleFluoroacetate dehalogenase, room temperature structure, using first 1 degree of total 3 degree oscillation
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / Dehalogenase / defluorinase
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 CGA009 (phototrophic)
AuthorsFinke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: IUCrJ / Year: 2019
Title: Fixed-target serial oscillation crystallography at room temperature.
Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / Szebenyi, D.M.E. / Gruner, S.M. / Miller, R.J.D. / Finke, A.D.
DepositionNov 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)68,1873

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-22 kcal/mol
Surface area19940 Å2
Unit cell
Length a, b, c (Å)41.600, 79.100, 83.800
Angle α, β, γ (deg.)90.000, 103.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z


#1: Protein Fluoroacetate dehalogenase / Haloacetate dehalogenase

Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 16-20% PEG 3350, 100mM Tris-Cl pH 8.5, and 200mM CaCl2.

Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Type: CHESS BEAMLINE G3 / Wavelength: 1.216 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 1, 2018
RadiationMonochromator: W/B4C mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.216 Å / Relative weight: 1
ReflectionResolution: 1.8→39.55 Å / Num. obs: 48562 / % possible obs: 99.02 % / Redundancy: 5.7 % / Biso Wilson estimate: 34.41 Å2 / CC1/2: 0.954 / Rpim(I) all: 0.1648 / Rrim(I) all: 0.4132 / Net I/σ(I): 4.71
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 4680 / CC1/2: 0.0739 / Rpim(I) all: 3.646 / Rrim(I) all: 8.37
Serial crystallography measurementCollimation: Compound refractive lens
Serial crystallography sample deliveryDescription: Si fixed target / Method: fixed target
Serial crystallography data reductionCrystal hits: 1082 / Frames indexed: 1970 / Frames total: 32000


XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSX
Resolution: 1.8→39.55 Å / SU ML: 0.3456 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0932
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 2442 5.03 %Rnadom
Rwork0.1749 ---
obs0.1766 48558 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 1 217 4922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754914
X-RAY DIFFRACTIONf_angle_d0.95266698
X-RAY DIFFRACTIONf_chiral_restr0.0504684
X-RAY DIFFRACTIONf_plane_restr0.0063879
X-RAY DIFFRACTIONf_dihedral_angle_d16.07843964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.49681360.50152563X-RAY DIFFRACTION94.87
1.84-1.880.40211480.40672663X-RAY DIFFRACTION98.46
1.88-1.920.44241420.37022709X-RAY DIFFRACTION98.51
1.92-1.970.33921430.31062713X-RAY DIFFRACTION98.99
1.97-2.020.29741430.28252666X-RAY DIFFRACTION98.8
2.02-2.080.3211450.26372765X-RAY DIFFRACTION99.28
2.08-2.150.26411420.24862650X-RAY DIFFRACTION98.94
2.15-2.230.26691430.22722716X-RAY DIFFRACTION99.41
2.23-2.310.25951460.20392752X-RAY DIFFRACTION99.59
2.31-2.420.23891420.182719X-RAY DIFFRACTION99.31
2.42-2.550.20481440.17532696X-RAY DIFFRACTION99.4
2.55-2.710.22991440.17362725X-RAY DIFFRACTION99.69
2.71-2.920.19281440.16942730X-RAY DIFFRACTION99.65
2.92-3.210.22511440.16292775X-RAY DIFFRACTION99.86
3.21-3.670.17221430.14052718X-RAY DIFFRACTION99.86
3.67-4.630.15051460.11862787X-RAY DIFFRACTION99.76
4.63-40.840.16291470.14942769X-RAY DIFFRACTION98.95

About Yorodumi


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


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