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- PDB-4wbj: Crystal structure of Bradyrhizobium japonicum ScoI in the oxidize... -

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Basic information

Entry
Database: PDB / ID: 4wbj
TitleCrystal structure of Bradyrhizobium japonicum ScoI in the oxidized state
ComponentsBlr1131 protein
KeywordsCHAPERONE / copper / cytochrome oxidase / CuA
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Blr1131 protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsQuade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
CitationJournal: To Be Published
Title: Crystal structure of Bradyrhizobium japonicum ScoI in the oxidized state
Authors: Quade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Blr1131 protein
B: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5584
Polymers36,3222
Non-polymers2362
Water8,827490
1
A: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2792
Polymers18,1611
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2792
Polymers18,1611
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.776, 82.629, 45.853
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Blr1131 protein / ScoIox


Mass: 18160.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: blr1131 / Plasmid: pET11a-ScoIK34 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89VB6
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG, 25% PEG15000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→45.8 Å / Num. obs: 65098 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 15.447 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 0.977 / Net I/σ(I): 28.35 / Num. measured all: 460789
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.3-1.330.9860.1519.9429698523843810.16383.6
1.33-1.370.9880.14211.0731062505843430.15385.9
1.37-1.410.990.12812.1930665494643890.13888.7
1.41-1.450.990.11712.9428781485343450.12789.5
1.45-1.50.9940.10215.330046470043100.1191.7
1.5-1.550.9940.09317.1229471446441440.192.8
1.55-1.610.9960.08119.7529003435040720.08793.6
1.61-1.680.9960.07222.0627338418438900.07793
1.68-1.750.9970.06424.2926090402837110.06992.1
1.75-1.840.9980.05628.5826944385336590.06195
1.84-1.940.9980.0532.4625497367234850.05494.9
1.94-2.060.9990.04237.6823534345732610.04694.3
2.06-2.20.9990.03741.5920763324529820.0491.9
2.2-2.370.9990.03447.5221813304529400.03796.6
2.37-2.60.9990.03349.2419630279026770.03695.9
2.6-2.910.9990.03251.7217248252124000.03495.2
2.91-3.360.9990.02859.2214474223420680.0392.6
3.36-4.110.9990.02666.2113424189518490.02897.6
4.11-5.810.9990.02666.199658147513900.02994.2
5.810.9990.02667.4556508288020.02896.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.3 Å45.85 Å
Translation1.3 Å45.85 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4txo

4txo


Resolution: 1.3→45.8 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.148 / WRfactor Rwork: 0.1102 / FOM work R set: 0.9307 / SU B: 1.126 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0421 / SU Rfree: 0.0427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1418 3255 5 %RANDOM
Rwork0.1041 61844 --
obs0.106 65098 91.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.23 Å2 / Biso mean: 13.3 Å2 / Biso min: 3.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0.13 Å2
2--0.15 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.3→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 16 490 2961
Biso mean--20.87 27.23 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192622
X-RAY DIFFRACTIONr_bond_other_d0.0010.022502
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9923575
X-RAY DIFFRACTIONr_angle_other_deg1.02335830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95823.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0615460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7371516
X-RAY DIFFRACTIONr_chiral_restr0.1280.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212952
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02556
X-RAY DIFFRACTIONr_mcbond_it1.9130.9021292
X-RAY DIFFRACTIONr_mcbond_other1.9130.9021291
X-RAY DIFFRACTIONr_mcangle_it2.5081.3631620
X-RAY DIFFRACTIONr_rigid_bond_restr5.68735124
X-RAY DIFFRACTIONr_sphericity_free31.522584
X-RAY DIFFRACTIONr_sphericity_bonded12.03955457
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 217 -
Rwork0.105 4131 -
all-4348 -
obs--83.14 %

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