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- PDB-3epv: X-ray Structure of the Metal-sensor CnrX in both the Apo- and Cop... -

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Basic information

Entry
Database: PDB / ID: 3epv
TitleX-ray Structure of the Metal-sensor CnrX in both the Apo- and Copper-bound Forms
ComponentsNickel and cobalt resistance protein cnrR
KeywordsMETAL BINDING PROTEIN / all alpha helix / Cobalt / Nickel
Function / homologyHeavy-metal resistance protein / Heavy-metal resistance / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / periplasmic space / Up-down Bundle / Mainly Alpha / COPPER (II) ION / Nickel and cobalt resistance protein CnrR
Function and homology information
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.742 Å
AuthorsPompidor, G. / Maillard, A.P. / Girard, E. / Gambarelli, S. / Kahn, R. / Coves, J.
CitationJournal: Febs Lett. / Year: 2008
Title: X-ray structure of the metal-sensor CnrX in both the apo- and copper-bound forms.
Authors: Pompidor, G. / Maillard, A.P. / Girard, E. / Gambarelli, S. / Kahn, R. / Coves, J.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
C: Nickel and cobalt resistance protein cnrR
D: Nickel and cobalt resistance protein cnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8307
Polymers49,6394
Non-polymers1913
Water7,945441
1
A: Nickel and cobalt resistance protein cnrR
B: Nickel and cobalt resistance protein cnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9474
Polymers24,8202
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-33 kcal/mol
Surface area12150 Å2
MethodPISA
2
C: Nickel and cobalt resistance protein cnrR
D: Nickel and cobalt resistance protein cnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8833
Polymers24,8202
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-34 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.940, 77.890, 93.200
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nickel and cobalt resistance protein cnrR / CnrX


Mass: 12409.807 Da / Num. of mol.: 4 / Fragment: metal-sensor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / Gene: cnrR, cnrX, RMe0087, Rmet_6206 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P37975
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 2000 MME, 10% Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97961 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2008
RadiationMonochromator: Si 111 / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 14.2 / Number: 286504 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / D res high: 1.74 Å / D res low: 46.6 Å / Num. obs: 45563 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.5146.687.210.0240.0245.9
3.95.5199.210.0240.0246.2
3.183.999.610.0260.0266.3
2.753.1899.510.0290.0296.3
2.462.7599.510.0360.0366.4
2.252.4698.710.0470.0476.4
2.082.2598.710.0620.0626.4
1.952.0898.410.1040.1046.4
1.841.9597.910.1810.1816.4
1.741.8493.810.2630.2636
ReflectionResolution: 1.742→46.6 Å / Num. obs: 45563 / % possible obs: 97.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 14.152
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.74-1.8460.26333797063540.26393.8
1.84-1.956.40.1814.33997362850.18197.9
1.95-2.086.40.1047.43774159120.10498.4
2.08-2.256.40.06212.23568355910.06298.7
2.25-2.466.40.04715.93292751440.04798.7
2.46-2.756.40.03619.82946846160.03699.5
2.75-3.186.30.02922.62619641390.02999.5
3.18-3.96.30.02623.72191134830.02699.6
3.9-5.516.20.02425.11676127100.02499.2
5.51-46.65.90.02425.4787413290.02487.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALA3.2.29data scaling
SHARPphasing
SOLOMONphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.742→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.848 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25894 2294 5 %RANDOM
Rwork0.19566 ---
obs0.1989 43242 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.45 Å2 / Biso mean: 19.949 Å2 / Biso min: 4.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.05 Å2
2--2.24 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 1.742→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 3 441 3904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0213626
X-RAY DIFFRACTIONr_bond_other_d0.0020.022572
X-RAY DIFFRACTIONr_angle_refined_deg2.3931.9684894
X-RAY DIFFRACTIONr_angle_other_deg1.26236204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1735457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06822.921202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99715658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9141555
X-RAY DIFFRACTIONr_chiral_restr0.1570.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
X-RAY DIFFRACTIONr_nbd_refined0.2480.2980
X-RAY DIFFRACTIONr_nbd_other0.2210.22799
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21692
X-RAY DIFFRACTIONr_nbtor_other0.0970.21960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0371.52751
X-RAY DIFFRACTIONr_mcbond_other0.5381.5871
X-RAY DIFFRACTIONr_mcangle_it2.17323542
X-RAY DIFFRACTIONr_scbond_it4.21331504
X-RAY DIFFRACTIONr_scangle_it5.94.51338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.742→1.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 161 -
Rwork0.225 2911 -
all-3072 -
obs--88.45 %

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