[English] 日本語
Yorodumi
- PDB-3hx9: Structure of heme-degrader, MhuD (Rv3592), from Mycobacterium tub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hx9
TitleStructure of heme-degrader, MhuD (Rv3592), from Mycobacterium tuberculosis with two hemes bound in its active site
ComponentsProtein Rv3592
KeywordsOXIDOREDUCTASE / di-heme / beta barrel / dimer
Function / homology
Function and homology information


heme oxygenase (mycobilin-producing) / heme oxygenase (decyclizing) activity / heme catabolic process / cell wall / peptidoglycan-based cell wall / heme binding / metal ion binding / plasma membrane
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase (mycobilin-producing) / Heme oxygenase (mycobilin-producing)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChim, N. / Nguyen, T.Q. / Iniguez, A. / Goulding, C.W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Unusual Diheme Conformation of the Heme-Degrading Protein from Mycobacterium tuberculosis
Authors: Chim, N. / Iniguez, A. / Nguyen, T.Q. / Goulding, C.W.
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein Rv3592
B: Protein Rv3592
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0378
Polymers26,5002
Non-polymers2,5376
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-172 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.971, 64.622, 71.082
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Protein Rv3592


Mass: 13249.933 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3698, Rv3592, TB11.2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O06156, UniProt: P9WKH3*PLUS
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Bis-Tris pH 5.0, 0.2 M NaCl, 20% PEG-3350, 10 mM triethylamine HCl , VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97, 1.76
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2008
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.761
ReflectionResolution: 1.75→50 Å / Num. obs: 19968 / % possible obs: 98.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 28.1
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 10.7 / Num. unique all: 1974 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0089refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.34 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23119 1018 5.1 %RANDOM
Rwork0.18623 ---
obs0.18856 18936 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20.01 Å2
2--0.11 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 174 123 1793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211722
X-RAY DIFFRACTIONr_angle_refined_deg2.012.0472366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26523.80371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31315208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.771158
X-RAY DIFFRACTIONr_chiral_restr0.1610.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211384
X-RAY DIFFRACTIONr_mcbond_it1.3821.5985
X-RAY DIFFRACTIONr_mcangle_it2.43521558
X-RAY DIFFRACTIONr_scbond_it3.6493737
X-RAY DIFFRACTIONr_scangle_it5.5864.5808
LS refinement shellResolution: 1.749→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 69 -
Rwork0.196 1415 -
obs-18936 98.28 %

+
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://pdbjlvh1.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