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- PDB-4wbr: Structure of Bradyrhizobium japonicum ScoI with copper bound -

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Basic information

Entry
Database: PDB / ID: 4wbr
TitleStructure of Bradyrhizobium japonicum ScoI with copper bound
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
COPPER (II) ION / Blr1131 protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsQuade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
CitationJournal: To Be Published
Title: Structure of Bradyrhizobium japonicum ScoI with copper bound
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4972
Polymers17,4341
Non-polymers641
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.860, 44.760, 40.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-376-

HOH

21D-414-

HOH

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Components

#1: Protein Blr1131 protein


Mass: 17433.846 Da / Num. of mol.: 1
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89VB6
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Na-citrate, 20% PEG 6000

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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: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→46 Å / Num. obs: 30788 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 19.097 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.103 / Χ2: 0.958 / Net I/σ(I): 17.04 / Num. measured all: 378601
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
1.4-1.430.7760.7632.3312200246713800.80955.9
1.43-1.470.8630.6563.1718023237416040.68667.6
1.47-1.520.9010.5713.8823618232019640.59684.7
1.52-1.560.9470.4884.9228191225320910.50792.8
1.56-1.610.9680.4056.0127813222421020.42194.5
1.61-1.670.9720.3467.0826247213120520.3696.3
1.67-1.730.9750.2988.0624256204319650.31196.2
1.73-1.810.9820.25610.2325975199919460.26697.3
1.81-1.890.9920.19612.924094189818540.20497.7
1.89-1.980.9930.15616.1422665183418010.16298.2
1.98-2.080.9950.12818.520153172916870.13497.6
2.08-2.210.9960.11123.4721272166516400.11698.5
2.21-2.360.9970.09726.1319087155715280.10298.1
2.36-2.550.9970.09827.9417275144314270.10298.9
2.55-2.80.9980.08531.7415994135713230.08897.5
2.8-3.130.9990.0737.3215270121812130.07399.6
3.13-3.610.9990.05342.5112910110010950.05599.5
3.61-4.420.9990.04646.2105289459340.04898.8
4.42-6.250.9990.04347.9784797347320.04599.7
6.250.9990.03546.6245514564500.03798.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.4 Å46.43 Å
Translation1.4 Å46.43 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: 1.4→42 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1672 / WRfactor Rwork: 0.1197 / FOM work R set: 0.8892 / SU B: 2.144 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0571 / SU Rfree: 0.0582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1494 4.9 %RANDOM
Rwork0.126 29294 --
obs0.1283 30788 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.95 Å2 / Biso mean: 18.926 Å2 / Biso min: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.4→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 1 235 1461
Biso mean--18.5 35.07 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191305
X-RAY DIFFRACTIONr_bond_other_d0.0010.021254
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9891780
X-RAY DIFFRACTIONr_angle_other_deg0.98932922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43624.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45915234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.667157
X-RAY DIFFRACTIONr_chiral_restr0.1460.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211469
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02276
X-RAY DIFFRACTIONr_mcbond_it3.7291.404645
X-RAY DIFFRACTIONr_mcbond_other3.7211.4644
X-RAY DIFFRACTIONr_mcangle_it3.7792.114809
X-RAY DIFFRACTIONr_rigid_bond_restr5.40532557
X-RAY DIFFRACTIONr_sphericity_free49.923561
X-RAY DIFFRACTIONr_sphericity_bonded14.63252697
LS refinement shellResolution: 1.398→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 62 -
Rwork0.256 1315 -
all-1377 -
obs--55.91 %

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