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- PDB-2y39: Ni-bound form of Cupriavidus metallidurans CH34 CnrXs -

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Basic information

Entry
Database: PDB / ID: 2y39
TitleNi-bound form of Cupriavidus metallidurans CH34 CnrXs
ComponentsNICKEL AND COBALT RESISTANCE PROTEIN CNRR
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


Heavy-metal resistance protein / Heavy-metal resistance / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Nickel and cobalt resistance protein CnrR
Similarity search - Component
Biological speciesCUPRIAVIDUS METALLIDURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.41 Å
AuthorsTrepreau, J. / Girard, E. / Maillard, A.P. / de Rosny, E. / Petit-Haertlein, I. / Kahn, R. / Coves, J.
Citation
#1: Journal: 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
DepositionDec 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4303
Polymers13,3121
Non-polymers1182
Water3,171176
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)26,8596
Polymers26,6242
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2900 Å2
ΔGint-16.3 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.198, 32.198, 195.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2067-

HOH

21A-2100-

HOH

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Components

#1: Protein NICKEL AND COBALT RESISTANCE PROTEIN CNRR / NICKEL AND COBALT RESISTANCE PROTEIN CNRX


Mass: 13311.874 Da / Num. of mol.: 1 / Fragment: METAL-SENSOR DOMAIN, RESIDUES 31-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS (bacteria) / Strain: CH34 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37975
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.91 Å3/Da / Density % sol: 28 % / Description: NONE
Crystal growpH: 7.5
Details: 0,1M HEPES PH7,5 0.6 M SODIUM PHOSPHATE, 1M POTASSIUM PHOSPHATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 10, 2010
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.41→32.2 Å / Num. obs: 21101 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 10.38 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.2
Reflection shellResolution: 1.41→1.48 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.2 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.41→30.589 Å / SU ML: 0.14 / σ(F): 1.41 / Phase error: 16.51 / Stereochemistry target values: ML / Details: RESIDUES 31-38 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1978 1002 5 %
Rwork0.1795 --
obs0.1804 20038 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.296 Å2 / ksol: 0.424 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.149 Å20 Å20 Å2
2--1.149 Å20 Å2
3----2.298 Å2
Refinement stepCycle: LAST / Resolution: 1.41→30.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 5 176 1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007910
X-RAY DIFFRACTIONf_angle_d1.0641232
X-RAY DIFFRACTIONf_dihedral_angle_d10.907360
X-RAY DIFFRACTIONf_chiral_restr0.073135
X-RAY DIFFRACTIONf_plane_restr0.006169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.48440.23711360.18092563X-RAY DIFFRACTION93
1.4844-1.57730.18561380.17582625X-RAY DIFFRACTION94
1.5773-1.69910.18241400.1652669X-RAY DIFFRACTION94
1.6991-1.87010.21061400.17412666X-RAY DIFFRACTION95
1.8701-2.14060.17411440.17052737X-RAY DIFFRACTION96
2.1406-2.69670.19221480.16582810X-RAY DIFFRACTION96
2.6967-30.59630.20351560.19172966X-RAY DIFFRACTION95
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)
10.20660.07340.0950.26540.10940.21840.0476-0.0560.03260.0489-0.06610.0812-0.0063-0.16810.00310.0625-0.01560.00940.0444-0.0010.049312.32678.233328.8973
21.3624-0.845-0.97980.62520.65771.1903-0.04640.32260.07820.0308-0.1124-0.01110.0736-0.28390.05710.203-0.1661-0.00790.21650.02620.081814.0281-0.349945.2854
30.2507-0.1147-0.19820.1729-0.01080.2264-0.0265-0.0656-0.0305-0.04250.0375-0.01590.18560.0344-0.03360.1007-0.0483-0.01290.10740.00270.066321.2148-0.660564.4854
40.0097-0.02320.0380.0439-0.10730.9950.1052-0.01210.0026-0.02830.0483-0.04150.30470.2826-0.10820.10870.0135-0.02420.0814-0.00360.071123.73931.46246.3853
50.18870.0883-0.03020.0404-0.0070.16050.0254-0.00210.01670.02870.01430.0549-0.05910.0261-0.04230.0764-0.00670.00340.03530.00360.0721.339112.979626.4531
60.2764-0.16490.04270.26630.11680.19580.1252-0.1134-0.0177-0.0413-0.14920.0356-0.202-0.01960.00730.2136-0.0624-0.00870.13720.00930.097624.020316.92440.2339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 39:67)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 68:80)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 81:99)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 100:118)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 119:143)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 144:148)

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