[English] 日本語
Yorodumi
- PDB-7pq1: Ligand-free crystal structure of a staphylococcal orthologue of C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pq1
TitleLigand-free crystal structure of a staphylococcal orthologue of CYP134A1
ComponentsCytochrome P450 protein
KeywordsOXIDOREDUCTASE / CypX / Pulcherrimin / Cyclic / Diketopiperazine / P450 / Heme / Iron / Staphylococcus / Aureus
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsSnee, M. / Levy, C. / Leys, D. / Katariya, M. / Munro, A.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with Cyclo-L-leucyl-L-leucine
Authors: Snee, M. / Katariya, M.
History
DepositionSep 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6833
Polymers45,9751
Non-polymers7092
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-24 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.414, 109.222, 105.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Cytochrome P450 protein / cypX


Mass: 45974.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cypX_1, NCTC5664_01270, cypX / Plasmid: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: A0A380DQV1, pulcherriminic acid synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.82 % / Description: Oblong
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: Bicine pH 9.3, 25 % v/v PEG Smear Medium

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.46→55.52 Å / Num. obs: 17398 / % possible obs: 99.22 % / Redundancy: 13.1 % / Biso Wilson estimate: 40.37 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.042 / Rrim(I) all: 0.152 / Net I/σ(I): 8.7
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 13 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 822 / CC1/2: 0.935 / Rpim(I) all: 0.213 / % possible all: 97.62

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NC5

3nc5


Resolution: 2.46→55.52 Å / SU ML: 0.3443 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 872 5.03 %
Rwork0.2139 16452 -
obs0.216 17324 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.18 Å2
Refinement stepCycle: LAST / Resolution: 2.46→55.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 49 86 3301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323315
X-RAY DIFFRACTIONf_angle_d0.63484499
X-RAY DIFFRACTIONf_chiral_restr0.0426501
X-RAY DIFFRACTIONf_plane_restr0.0035575
X-RAY DIFFRACTIONf_dihedral_angle_d7.1567441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.610.37471320.31572692X-RAY DIFFRACTION97.95
2.61-2.810.30451650.26232652X-RAY DIFFRACTION98.29
2.81-3.090.29081300.25022727X-RAY DIFFRACTION98.76
3.09-3.540.25351460.2212729X-RAY DIFFRACTION99.07
3.54-4.460.25481490.19822761X-RAY DIFFRACTION99.11
4.46-55.520.20031500.17722891X-RAY DIFFRACTION99.54
Refinement TLS params.Method: refined / Origin x: -17.5859952495 Å / Origin y: -23.5416349698 Å / Origin z: -5.6518911604 Å
111213212223313233
T0.17942562212 Å2-0.022439837262 Å20.019784069493 Å2-0.544919779169 Å20.0359493536164 Å2--0.273706914358 Å2
L0.704105428353 °2-0.118559430562 °20.457735462793 °2-0.772145799544 °20.519161029809 °2--4.0866614241 °2
S-0.0547169940527 Å °0.0603076556903 Å °0.0795799502994 Å °-0.0728971524473 Å °0.0198335266347 Å °-0.0169214362462 Å °-0.351966561769 Å °0.0749505304243 Å °0.0219966543868 Å °
Refinement TLS groupSelection details: all

+
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