[English] 日本語
Yorodumi
- PDB-6jsd: Crystal structure of the domain-swapped dimer H434A variant of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jsd
TitleCrystal structure of the domain-swapped dimer H434A variant of the C-terminal domain of HtaA from Corynebacterium glutamicum
ComponentsHypothetical membrane protein
KeywordsHEME-BINDING PROTEIN / heme / heme transport
Function / homologyHtaa / Htaa / metal ion binding / ISOPROPYL ALCOHOL / Hypothetical membrane protein
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.042 Å
AuthorsMuraki, N. / Aono, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K15081 Japan
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Structural basis for the heme transfer reaction in heme uptake machinery from Corynebacteria.
Authors: Muraki, N. / Kitatsuji, C. / Okamoto, Y. / Uchida, T. / Ishimori, K. / Aono, S.
History
DepositionApr 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical membrane protein
B: Hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3833
Polymers36,3232
Non-polymers601
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer (gel filtration)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-35 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.900, 40.230, 87.020
Angle α, β, γ (deg.)90.00, 113.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hypothetical membrane protein


Mass: 18161.576 Da / Num. of mol.: 2 / Mutation: H434A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl0388 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NTB9
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, Tris-HCl pH8, 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 23, 2017
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 21370 / % possible obs: 98.71 % / Redundancy: 3.7 % / Biso Wilson estimate: 41.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0529 / Rpim(I) all: 0.0321 / Rrim(I) all: 0.062 / Net I/σ(I): 15.06
Reflection shellResolution: 2.04→2.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.816 / Num. unique obs: 2022 / CC1/2: 0.602 / Rpim(I) all: 0.498 / Rrim(I) all: 0.959 / % possible all: 93.86

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JSA

6jsa


Resolution: 2.042→39.608 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1067 5 %Random selection
Rwork0.2035 ---
obs0.2056 21341 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.042→39.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 4 11 2361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072400
X-RAY DIFFRACTIONf_angle_d0.7523262
X-RAY DIFFRACTIONf_dihedral_angle_d10.9551365
X-RAY DIFFRACTIONf_chiral_restr0.055366
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0415-2.13440.36741250.32332366X-RAY DIFFRACTION94
2.1344-2.2470.32691350.28242552X-RAY DIFFRACTION100
2.247-2.38770.31721320.27982509X-RAY DIFFRACTION99
2.3877-2.5720.3241350.25562555X-RAY DIFFRACTION100
2.572-2.83080.30811330.23542557X-RAY DIFFRACTION100
2.8308-3.24030.26161340.21972550X-RAY DIFFRACTION100
3.2403-4.08180.22821370.17612585X-RAY DIFFRACTION99
4.0818-39.61560.19381360.16782600X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.18291.7142-0.51234.5568-0.2131.2781-0.1136-0.4278-0.1422-0.33980.0906-0.0065-0.0749-0.251-0.02380.3874-0.0105-0.03650.45430.13550.3603-33.0858-16.775523.7113
22.41281.0864-1.28531.5351-0.72575.3425-0.0750.28620.0904-0.1981-0.0847-0.17680.19930.53470.14680.29280.01850.02810.33780.08750.3483-14.912812.21576.9022
32.9410.3238-0.16671.2077-1.38844.3862-0.0037-0.0803-0.2377-0.40620.0034-0.02520.53980.455-0.04340.38840.0371-0.00050.32830.04230.3881-11.16156.79053.2912
43.14410.7419-0.91493.4303-0.43612.7738-0.289-0.2337-0.7459-0.01260.38010.2090.95670.3724-0.03340.61920.13550.09030.42050.03930.5398-13.26892.84324.3628
51.59371.5894-1.14626.1938-4.17914.1007-0.05160.03860.07770.0726-0.00090.14180.03620.12490.00750.4336-0.02320.01390.42440.03420.4302-19.19195.51137.0647
65.1329-1.00710.14792.6474-0.08673.6043-0.0582-0.3537-0.0877-0.10710.19440.2037-0.0961-0.4986-0.15630.35710.0141-0.00320.35940.10110.2849-30.7549-22.729725.5035
75.4270.49963.18463.0923-1.39314.0984-0.8085-0.34480.63980.20940.51020.4597-0.8163-0.42850.25860.4780.1346-0.04630.53270.0240.3577-34.0759-16.535431.8095
82.78512.7013-0.43868.2877-2.18391.3352-0.0613-0.4566-0.1006-0.28240.0844-0.0379-0.1204-0.1957-0.02480.4338-0.0161-0.05260.50980.13140.5299-35.662-8.78520.718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 364 through 389)
2X-RAY DIFFRACTION2chain 'A' and (resid 390 through 452)
3X-RAY DIFFRACTION3chain 'A' and (resid 453 through 500 )
4X-RAY DIFFRACTION4chain 'A' and (resid 501 through 528)
5X-RAY DIFFRACTION5chain 'B' and (resid 364 through 389)
6X-RAY DIFFRACTION6chain 'B' and (resid 390 through 452 )
7X-RAY DIFFRACTION7chain 'B' and (resid 453 through 500 )
8X-RAY DIFFRACTION8chain 'B' and (resid 501 through 528 )

+
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