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- PDB-4wwf: High-resolution structure of two Ni-bound forms of the M123C muta... -

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Basic information

Entry
Database: PDB / ID: 4wwf
TitleHigh-resolution structure of two Ni-bound forms of the M123C mutant of C. metallidurans CnrXs
ComponentsNickel and cobalt resistance protein CnrR
KeywordsMETAL BINDING PROTEIN / nickel sensor
Function / homologyHeavy-metal resistance protein / Heavy-metal resistance / periplasmic space / NICKEL (II) ION / Nickel and cobalt resistance protein CnrR
Function and homology information
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsVolbeda, A. / Coves, J. / Maillard, A.P. / Kinnemann, S. / Grosse, C. / Schleuder, G. / Petit-Hurtlein, I. / de Rosny, E. / Nies, D.H.
CitationJournal: Metallomics / Year: 2015
Title: Response of CnrX from Cupriavidus metallidurans CH34 to nickel binding.
Authors: Maillard, A.P. / Kunnemann, S. / Groe, C. / Volbeda, A. / Schleuder, G. / Petit-Hartlein, I. / de Rosny, E. / Nies, D.H. / Coves, J.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nickel and cobalt resistance protein CnrR
B: Nickel and cobalt resistance protein CnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7085
Polymers26,5682
Non-polymers1403
Water6,972387
1
A: Nickel and cobalt resistance protein CnrR
hetero molecules

A: Nickel and cobalt resistance protein CnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6854
Polymers26,5682
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2600 Å2
ΔGint-43 kcal/mol
Surface area11980 Å2
MethodPISA
2
B: Nickel and cobalt resistance protein CnrR
hetero molecules

B: Nickel and cobalt resistance protein CnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7316
Polymers26,5682
Non-polymers1634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area3150 Å2
ΔGint-69 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.910, 47.520, 193.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-496-

HOH

21B-367-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Nickel and cobalt resistance protein CnrR


Mass: 13283.821 Da / Num. of mol.: 2 / Fragment: Metal-sensor domain of CnrX, UNP residues 31-148 / Mutation: M123C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: cnrR, cnrX, Rmet_6206, RMe0087 / Plasmid: pET30b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37975
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98027 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98027 Å / Relative weight: 1
ReflectionResolution: 1.1→25 Å / Num. obs: 156029 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 11.987 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Χ2: 1.087 / Net I/σ(I): 16.03 / Num. measured all: 937411
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.1-1.160.7820.5863.518083723534224870.68995.6
1.16-1.240.8870.4155.178914524504236820.48396.6
1.24-1.340.9380.4057.6410055423029224420.45597.5
1.34-1.470.9720.34711.2912317421428210540.37898.3
1.47-1.640.9890.23217.1714840018578184400.24899.3
1.64-1.90.9960.12223.2914369717202171520.1399.7
1.9-2.320.9980.06132.4511480613890138800.06599.9
2.32-3.270.9990.04639.948997810856108470.04999.9
3.27-160.9990.03848.1746657601260020.04199.8
16-2010.04934.519419190.061100
20-230.9990.03236.693511110.04100
2310.0429.223418130.05872.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→24.79 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1417 / WRfactor Rwork: 0.1113 / FOM work R set: 0.9307 / SU B: 0.91 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0279 / SU Rfree: 0.0295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1448 4038 5 %RANDOM
Rwork0.115 77363 --
obs0.1164 77363 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 127.99 Å2 / Biso mean: 13.88 Å2 / Biso min: 3.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.1→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 4 429 2153
Biso mean--13.78 22.85 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192202
X-RAY DIFFRACTIONr_bond_other_d0.0010.022188
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9683012
X-RAY DIFFRACTIONr_angle_other_deg0.8713.0015039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2255305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58322.721136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86115428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6551540
X-RAY DIFFRACTIONr_chiral_restr0.1050.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_mcbond_it2.1160.9871014
X-RAY DIFFRACTIONr_mcbond_other2.1070.9831013
X-RAY DIFFRACTIONr_mcangle_it2.5111.8591295
X-RAY DIFFRACTIONr_rigid_bond_restr4.38634390
X-RAY DIFFRACTIONr_sphericity_free29.542591
X-RAY DIFFRACTIONr_sphericity_bonded13.90454638
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 317 -
Rwork0.197 5514 -
all-5831 -
obs--96.25 %

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