[English] 日本語
Yorodumi
- PDB-9miq: Wild-type Coproheme Decarboxylase from Streptomyces Coelicolor in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9miq
TitleWild-type Coproheme Decarboxylase from Streptomyces Coelicolor in complex with Monovinyl, Monopropionate Deuteroheme
ComponentsCoproheme decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / heme biosynthesis / oxidative decarboxylase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / hydrogen peroxide-dependent heme synthase / heme B biosynthetic process / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
harderoheme (III) / Coproheme decarboxylase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCarriuolo, A.J. / Lanzilotta, W.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Wild-type Coproheme Decarboxylase from Streptomyces Coelicolor in complex with Monovinyl, Monopropionate Deuteroheme
Authors: Carriuolo, A.J. / Lanzilotta, W.N.
History
DepositionDec 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coproheme decarboxylase
B: Coproheme decarboxylase
C: Coproheme decarboxylase
D: Coproheme decarboxylase
E: Coproheme decarboxylase
F: Coproheme decarboxylase
G: Coproheme decarboxylase
H: Coproheme decarboxylase
I: Coproheme decarboxylase
J: Coproheme decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,35320
Polymers281,72810
Non-polymers6,62510
Water66737
1
A: Coproheme decarboxylase
B: Coproheme decarboxylase
C: Coproheme decarboxylase
D: Coproheme decarboxylase
E: Coproheme decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,17710
Polymers140,8645
Non-polymers3,3135
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15620 Å2
ΔGint-15 kcal/mol
Surface area38620 Å2
MethodPISA
2
F: Coproheme decarboxylase
G: Coproheme decarboxylase
H: Coproheme decarboxylase
I: Coproheme decarboxylase
J: Coproheme decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,17710
Polymers140,8645
Non-polymers3,3135
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15640 Å2
ΔGint-11 kcal/mol
Surface area38950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.707, 184.707, 241.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
Coproheme decarboxylase / Coproheme III oxidative decarboxylase / Hydrogen peroxide-dependent heme synthase


Mass: 28172.793 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: chdC, SCO6042 / Production host: Escherichia coli (E. coli)
References: UniProt: O69830, hydrogen peroxide-dependent heme synthase
#2: Chemical
ChemComp-VOV / harderoheme (III)


Mass: 662.513 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C35H34FeN4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7
Details: Protein (500 uM) prepared with coproheme (15 mg/mL) in 100 mM HEPES/100 mM KCl pH7.5 buffer and 10 mM of KCN. Batch crystallization against a solution of 0.2 ammonium phosphate pH 7.0, 20% ...Details: Protein (500 uM) prepared with coproheme (15 mg/mL) in 100 mM HEPES/100 mM KCl pH7.5 buffer and 10 mM of KCN. Batch crystallization against a solution of 0.2 ammonium phosphate pH 7.0, 20% w/v polyethylene glycol 3,350, and 200mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 144172 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 0.993 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 14204 / CC1/2: 0.592

-
Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 2000 1.41 %
Rwork0.2086 --
obs0.2092 141841 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18280 0 460 37 18777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d18.6267454
X-RAY DIFFRACTIONf_chiral_restr0.0582660
X-RAY DIFFRACTIONf_plane_restr0.0133364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.42121390.36349687X-RAY DIFFRACTION96
2.56-2.630.37791390.31089726X-RAY DIFFRACTION97
2.63-2.710.39091410.29969830X-RAY DIFFRACTION98
2.8-2.90.33931410.29559874X-RAY DIFFRACTION98
2.9-3.010.37081430.28549952X-RAY DIFFRACTION99
3.01-3.150.31451420.27419991X-RAY DIFFRACTION99
3.15-3.310.33241430.262510014X-RAY DIFFRACTION99
3.31-3.520.3051440.249210056X-RAY DIFFRACTION100
3.52-3.790.25761440.209610077X-RAY DIFFRACTION99
3.79-4.180.25211440.187810050X-RAY DIFFRACTION99
4.18-4.780.19061440.160510030X-RAY DIFFRACTION98
4.78-6.020.19941450.157910194X-RAY DIFFRACTION99
6.02-420.1881510.157810514X-RAY DIFFRACTION98

+
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