[English] 日本語
Yorodumi
- PDB-9l8x: The crystal structure of Halogenases XhnO11 complex with vanadate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9l8x
TitleThe crystal structure of Halogenases XhnO11 complex with vanadate
ComponentsVanadium-dependent haloperoxidase
KeywordsOXIDOREDUCTASE / haloperoxidases vanadate complex
Function / homology
Function and homology information


peroxidase activity
Similarity search - Function
: / : / Domain of unknown function (DUF6851) / VCPO second helical-bundle domain / Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
VANADATE ION / Vanadium-dependent haloperoxidase
Similarity search - Component
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4000540414 Å
AuthorsWu, L. / Fang, S.Q. / Nie, Q.Y. / Tang, G.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The crystal structure of Halogenases XhnO11 complex with vanadate
Authors: Nie, Q.Y. / Fang, S.Q. / Wu, L. / Tang, G.L.
History
DepositionDec 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Vanadium-dependent haloperoxidase
A: Vanadium-dependent haloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4575
Polymers116,1912
Non-polymers2653
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-26 kcal/mol
Surface area33820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.886, 94.033, 126.029
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Vanadium-dependent haloperoxidase


Mass: 58095.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces xinghaiensis (bacteria) / Gene: Sfr7A_13920, SFRA_005355 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A420V7T7
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPS/HEPES-Na pH 7.5, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 10% pEG8000, 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.4→47.02 Å / Num. obs: 41580 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 27.7395597488 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.053 / Net I/σ(I): 11.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4278 / CC1/2: 0.91 / Rpim(I) all: 0.227 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4000540414→47.0165 Å / SU ML: 0.299692708701 / Cross valid method: FREE R-VALUE / σ(F): 1.33580547025 / Phase error: 25.0989024333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246949382561 2106 5.07714561234 %
Rwork0.189627920348 39374 -
obs0.192531209555 41480 99.8964429352 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.1739039889 Å2
Refinement stepCycle: LAST / Resolution: 2.4000540414→47.0165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7130 0 11 370 7511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007604459560847318
X-RAY DIFFRACTIONf_angle_d0.9177449950459922
X-RAY DIFFRACTIONf_chiral_restr0.04862436708741034
X-RAY DIFFRACTIONf_plane_restr0.005917118228731312
X-RAY DIFFRACTIONf_dihedral_angle_d19.82600158994354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.45590.3163495765761350.2253233516732573X-RAY DIFFRACTION99.6320824135
2.4559-2.51730.3710969157631360.2336340842682587X-RAY DIFFRACTION99.9266055046
2.5173-2.58530.2658328853911590.2148484760112572X-RAY DIFFRACTION100
2.5853-2.66140.2835264295351280.2278453307332599X-RAY DIFFRACTION99.8169838946
2.6614-2.74730.3424935016841360.238246522332593X-RAY DIFFRACTION99.9267667521
2.7473-2.84550.2895029309911540.2167702816362590X-RAY DIFFRACTION99.9271667881
2.8455-2.95940.2801189635571410.2084084786412591X-RAY DIFFRACTION100
2.9594-3.09410.2751750990931480.2052526597322594X-RAY DIFFRACTION100
3.0941-3.25720.2531448480071580.1995444042062603X-RAY DIFFRACTION99.9637943519
3.2572-3.46120.2753776581541250.2149342488312619X-RAY DIFFRACTION99.9635701275
3.4612-3.72830.2673310963891380.2088681526022634X-RAY DIFFRACTION99.8918918919
3.7283-4.10330.2454681255471290.1745569821042659X-RAY DIFFRACTION99.8567335244
4.1033-4.69660.1774334051791500.1506992445732648X-RAY DIFFRACTION100
4.6966-5.91540.1901728666781330.1491665814542693X-RAY DIFFRACTION99.8586572438
5.9154-47.01650.1654786393511360.1479183546142819X-RAY DIFFRACTION99.7636731938

+
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