[English] 日本語
Yorodumi
- PDB-9j47: ScdA cysteine-free mutant from Staphylococcus aureus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j47
TitleScdA cysteine-free mutant from Staphylococcus aureus
ComponentsIron-sulfur cluster repair protein ScdA
KeywordsOXYGEN BINDING / hemerythrin
Function / homology
Function and homology information


response to nitrosative stress / protein repair / response to oxidative stress / metal ion binding / cytoplasm
Similarity search - Function
Iron-sulfur cluster repair protein ScdA / ScdA-like, N-terminal domain superfamily / Repair of iron centres family / Domain of Unknown function (DUF542) / Hemerythrin-like / Hemerythrin HHE cation binding domain
Similarity search - Domain/homology
: / OXYGEN ATOM / Iron-sulfur cluster repair protein ScdA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsLiao, W.Y. / Hu, N.J. / Chiang, Y.W.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of cysteine-free ScdA from Staphylococcus aureus
Authors: Liao, W.Y. / Hu, N.J. / Chiang, Y.W.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron-sulfur cluster repair protein ScdA
B: Iron-sulfur cluster repair protein ScdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0958
Polymers50,8392
Non-polymers2556
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-72 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.538, 92.492, 110.889
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 Iron-sulfur cluster repair protein ScdA


Mass: 25419.742 Da / Num. of mol.: 2 / Mutation: C30A, C31A, C191A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: scdA, SAUSA300_0253 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FK11
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop
Details: 0.24 M calcium chloride 0.1 M MES 5.6 20 % w/v PEG 6000 0.1 M b-Nicotinamide adenine dinucleotide hydrate

-
Data collection

DiffractionMean temperature: 297.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.38→28.07 Å / Num. obs: 29149 / % possible obs: 99.33 % / Redundancy: 6.1 % / Biso Wilson estimate: 52.31 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.037 / Rrim(I) all: 0.092 / Net I/σ(I): 11.7
Reflection shellResolution: 2.38→2.77 Å / Num. unique obs: 293628 / CC1/2: 0.858 / Rpim(I) all: 0.324 / Rrim(I) all: 0.799

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→28.07 Å / SU ML: 0.2986 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2522 2000 6.86 %
Rwork0.218 27149 -
obs0.2203 29149 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.46 Å2
Refinement stepCycle: LAST / Resolution: 2.38→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 6 0 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882644
X-RAY DIFFRACTIONf_angle_d0.9613590
X-RAY DIFFRACTIONf_chiral_restr0.0509408
X-RAY DIFFRACTIONf_plane_restr0.0069456
X-RAY DIFFRACTIONf_dihedral_angle_d18.0044988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.33431330.30991805X-RAY DIFFRACTION94.21
2.44-2.510.34851430.281925X-RAY DIFFRACTION99.76
2.51-2.580.31861410.29051923X-RAY DIFFRACTION99.95
2.58-2.660.28621390.26431900X-RAY DIFFRACTION99.76
2.66-2.760.26771420.25781918X-RAY DIFFRACTION99.85
2.76-2.870.29891420.25331936X-RAY DIFFRACTION99.95
2.87-30.31931430.27151920X-RAY DIFFRACTION99.71
3-3.160.37521410.29051930X-RAY DIFFRACTION99.86
3.16-3.350.31441440.27831948X-RAY DIFFRACTION99.9
3.35-3.610.29961430.23441942X-RAY DIFFRACTION99.76
3.61-3.980.241440.20971950X-RAY DIFFRACTION99.81
3.98-4.550.1891440.1721967X-RAY DIFFRACTION99.81
4.55-5.720.21181470.18151997X-RAY DIFFRACTION99.81
5.72-28.070.20251540.182088X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: 17.3364594992 Å / Origin y: -0.644366180649 Å / Origin z: -17.8921500834 Å
111213212223313233
T0.537214702498 Å2-0.016656178104 Å2-0.014100794967 Å2-0.599704032685 Å20.0228152291036 Å2--0.44327236942 Å2
L-0.0277773450144 °2-0.080079834273 °2-0.321631035815 °2-1.11403918649 °21.61310346884 °2--1.82875178984 °2
S-0.00326269098814 Å °0.0442220395065 Å °-0.0221988831244 Å °0.0490776145542 Å °0.0896528772181 Å °-0.0312822140464 Å °0.128074676254 Å °0.0315842371868 Å °-0.0949920129465 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