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- PDB-9r7j: Repair of Iron Centre (RIC) protein from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 9r7j
TitleRepair of Iron Centre (RIC) protein from Staphylococcus aureus
ComponentsIron-sulfur cluster repair protein ScdA
KeywordsMETAL BINDING PROTEIN / hemerythrin / assembly / Fe-S cluster / ytfe
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: 2.73 Å
AuthorsRomao, C.V. / Matias, P.M. / Saraiva, L.M.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaUIIDB/04612/2020, UIDP/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0087/2020 Portugal
Citation
Journal: To Be Published
Title: Repair of Iron Centre (RIC) protein from Staphylococcus aureus
Authors: Romao, C.V. / Matias, P.M. / Saraiva, L.M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,83620
Polymers102,0644
Non-polymers77216
Water77543
1
A: Iron-sulfur cluster repair protein ScdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7095
Polymers25,5161
Non-polymers1934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron-sulfur cluster repair protein ScdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7095
Polymers25,5161
Non-polymers1934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Iron-sulfur cluster repair protein ScdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7746
Polymers25,5161
Non-polymers2595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Iron-sulfur cluster repair protein ScdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6444
Polymers25,5161
Non-polymers1283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.219, 111.105, 122.634
Angle α, β, γ (deg.)90.000, 93.933, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Iron-sulfur cluster repair protein ScdA


Mass: 25515.936 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Hemerythrin domain of the Repair of Iron Centre protein from Staphylococcus aureus
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: CA-MRSA USA300 LAC / Gene: scdA, SAUSA300_0253 / Variant: JE2 / Plasmid: pET-24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: Q2FK11
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.33 Å3/Da / Density % sol: 76.96 % / Description: hexagonal shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Na-HEPES pH7.5, 0.6M NaH2PO4, 0.6M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.73→55.56 Å / Num. obs: 38819 / % possible obs: 92.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 61.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.059 / Net I/av σ(I): 8.9 / Net I/σ(I): 8.9
Reflection shellResolution: 2.73→2.99 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.788 / Num. unique obs: 1942 / CC1/2: 0.494 / Rpim(I) all: 0.488 / Rrim(I) all: 0.93 / % possible all: 67.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDS20170615data reduction
STARANISO1.0.4data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→55.55 Å / SU ML: 0.3631 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.4654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2957 2007 5.17 %
Rwork0.2625 36782 -
obs0.2642 38789 68.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.85 Å2
Refinement stepCycle: LAST / Resolution: 2.73→55.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 16 43 5235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055300
X-RAY DIFFRACTIONf_angle_d1.32197197
X-RAY DIFFRACTIONf_chiral_restr0.2652816
X-RAY DIFFRACTIONf_plane_restr0.0204917
X-RAY DIFFRACTIONf_dihedral_angle_d26.74981985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.80.4767110.4073193X-RAY DIFFRACTION5.09
2.8-2.870.3828190.3871488X-RAY DIFFRACTION12.75
2.87-2.960.4099390.3776812X-RAY DIFFRACTION21.28
2.96-3.050.4233680.37481265X-RAY DIFFRACTION33.13
3.05-3.160.36671030.33761837X-RAY DIFFRACTION48.37
3.16-3.290.34341410.33812526X-RAY DIFFRACTION66.61
3.29-3.440.37451870.30133352X-RAY DIFFRACTION87.64
3.44-3.620.30372240.28313717X-RAY DIFFRACTION98.55
3.62-3.850.32612010.26413768X-RAY DIFFRACTION98.12
3.85-4.140.26871930.23513705X-RAY DIFFRACTION97.43
4.14-4.560.26142130.22413773X-RAY DIFFRACTION99.03
4.56-5.220.24121980.233734X-RAY DIFFRACTION97.3
5.22-6.580.3482040.29113815X-RAY DIFFRACTION98.75
6.58-55.550.27132060.24983797X-RAY DIFFRACTION96.95
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)
11.198717510310.6363610707530.1079763480851.89508314613-0.1851728328391.281021742870.0662638302808-0.00335471074618-0.24985345292-0.0312407594182-0.1824200483640.425308520970.245255221518-0.0829087776046-0.03339109971880.0184570022615-0.08622074725270.0337771334168-0.0792492038128-0.09358966568610.36984150953150.37422286820.3224533382315.44068555356
22.123782733980.6303185940720.4688282877062.53236557631.107063946282.210197002180.0817105280013-0.0188524770530.5279625106310.124001227373-0.14343354039-0.323322236805-0.227316742492-0.07306714197740.006420405841930.1428237588570.03657611742310.03476704307380.05701856781830.1242328015190.32663950644328.816041091-30.9674779526-5.27785291393
31.00510208118-0.512140721795-0.1139875231871.85630454692-0.07967470734510.6825932215090.1690193410820.05975780495390.201035081712-0.0235688663985-0.1196531849310.423239150195-0.126819317281-0.1240870132020.02668564954260.1141827619160.0650378161324-0.07595546542540.02430915312-0.08424149395620.53436682913254.6078727415-54.681181538-66.798133249
42.30711208939-1.0892583826-0.3003396222912.316954249621.324558342281.605996668160.070881973833-0.0950197411645-0.332437444704-0.126191397702-0.146328289558-0.1806377304270.125890522644-0.003162778836350.01008900337890.118427733860.0359593821558-0.0247743333786-0.01911156005520.06660655496220.31753657997233.1012236255-23.5057251627-56.1131918008
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 66:224)AA67 - 2241 - 158
22(chain B and resseq 67:224)BE67 - 2241 - 158
33(chain C and resseq 64:224)CI67 - 2241 - 158
44(chain D and resseq 66:224)DM66 - 2241 - 159

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