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- PDB-2y3d: Zn-bound form of Cupriavidus metallidurans CH34 CnrXs -

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Basic information

Entry
Database: PDB / ID: 2y3d
TitleZn-bound form of Cupriavidus metallidurans CH34 CnrXs
ComponentsNICKEL AND COBALT RESISTANCE PROTEIN CNRR
KeywordsMETAL BINDING PROTEIN
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 / Nickel and cobalt resistance protein CnrR
Function and homology information
Biological speciesCUPRIAVIDUS METALLIDURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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_asym_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_asym_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
B: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,99710
Polymers26,6242
Non-polymers3738
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-144.4 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.721, 155.721, 155.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11B-2013-

HOH

21B-2030-

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.: 2 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.36 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES PH7.5 10% PEG 6000 1M LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2010
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.3→44.95 Å / Num. obs: 14718 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 34.78 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

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

Resolution: 2.3→44.953 Å / SU ML: 0.36 / σ(F): 1.38 / Phase error: 25.3 / Stereochemistry target values: ML
Details: RESIDUES A31-A34 ARE DISORDERED RESIDUES B31-B37 ARE DISORDERED. RESIDUES 1-30 ARE NOT PRESENT IN THE CONSTRUCTION
RfactorNum. reflection% reflection
Rfree0.2593 732 5 %
Rwork0.207 --
obs0.2096 14640 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.12 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 8 125 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161793
X-RAY DIFFRACTIONf_angle_d1.1692422
X-RAY DIFFRACTIONf_dihedral_angle_d17.993697
X-RAY DIFFRACTIONf_chiral_restr0.079264
X-RAY DIFFRACTIONf_plane_restr0.006331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3005-2.47810.35311430.25192713X-RAY DIFFRACTION100
2.4781-2.72740.32721440.24122724X-RAY DIFFRACTION100
2.7274-3.1220.28131450.23292748X-RAY DIFFRACTION100
3.122-3.93310.25081470.20362788X-RAY DIFFRACTION100
3.9331-44.96130.21381530.182935X-RAY DIFFRACTION100
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)
14.2652-0.2106-1.04335.04912.7751.74440.48921.436-0.7967-1.0454-0.54780.21910.6273-0.02690.01050.59220.14120.03640.4386-0.11670.239330.59560.647938.0544
21.55120.1479-1.13371.0327-0.66751.1543-0.4622-0.5815-0.4742-0.434-0.37460.41461.14650.49180.51050.74570.3032-0.05330.48220.05560.460433.683559.526150.2315
30.9896-0.34740.51350.5209-0.32090.42710.2006-0.246-0.1616-0.1743-0.10710.11330.14030.0856-0.03050.242-0.00080.03490.27120.02250.184829.302267.63353.856
41.36641.00970.93881.49810.540.6344-0.1452-0.05940.2902-0.1214-0.07640.1752-0.2047-0.06650.19840.22490.0386-0.02540.26910.00090.161616.312570.413924.7836
51.3731-0.59251.22410.5839-0.63293.3445-0.15150.24940.1730.1151-0.0003-0.1339-0.14450.9880.06260.3020.07170.00080.3749-0.01990.236936.68368.645442.8149
62.13752.235-0.25043.96331.18965.8802-0.79550.0696-1.09960.27740.2996-1.25590.9463-0.19730.1430.42230.18270.11620.4137-0.09790.610239.790260.156735.927
72.15231.07950.56851.2833-0.30451.06780.1184-0.64460.061-0.0144-0.43130.0330.28270.17220.2650.20390.05310.04960.36780.04130.22617.481650.690511.3597
83.0375-0.8164-0.94411.6816-1.482.61430.4954-0.8005-0.3511-0.3666-0.08980.20810.72230.4373-0.29810.3591-0.0106-0.04120.36930.05090.235722.047149.32820.9007
90.78050.8361.30450.91561.56163.0820.36180.2693-0.6269-0.21530.6423-0.72170.16761.0634-0.77860.1678-0.02920.05610.7415-0.21560.420431.911661.895711.9151
100.97220.27840.31370.27790.25970.60990.05050.69790.1493-0.0036-0.05370.05880.06360.4014-0.01950.2209-0.0084-0.0130.3703-0.08580.265939.799871.658329.4094
110.0811-0.07160.2120.12820.10791.3420.01960.51140.0324-0.05160.18740.01580.04190.4334-0.16850.186-0.03250.00180.3944-0.02930.209719.045862.589110.9682
12-0.0057-0.059-0.02951.03190.440.1849-0.08420.09070.14190.19180.11280.23190.20140.1044-0.06810.20250.0091-0.00550.2275-0.00890.124710.620658.066517.1237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 35:40)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 41:51)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 52:65)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 66:112)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 113:132)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 133:145)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 39:53)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 54:64)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 65:78)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 79:103)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 104:131)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 132:148)

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