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- PDB-2wto: Crystal Structure of Apo-form Czce from C. metallidurans CH34 -

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Basic information

Entry
Database: PDB / ID: 2wto
TitleCrystal Structure of Apo-form Czce from C. metallidurans CH34
ComponentsORF131 PROTEIN
KeywordsMETAL BINDING PROTEIN / HEAVY METAL / COPPER BINDING
Function / homology
Function and homology information


methyltransferase activity / methylation / hydrolase activity / metal ion binding
Similarity search - Function
Heavy-metal resistance protein CzcE / Heavy-metal resistance protein CzcE / CzcE superfamily / Heavy-metal resistance protein CzcE / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CzcE, involved in Cd(II), Zn(II), Co(II) resistance / ORF131 protein
Similarity search - Component
Biological speciesRALSTONIA METALLIDURANS CH34 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsHaertlein, I. / Girard, E. / Sarret, G. / Hazemann, J. / Gourhant, P. / Kahn, R. / Coves, J.
Citation
Journal: Biochemistry / Year: 2010
Title: Evidence for Conformational Changes Upon Copper Binding to Cupriavidus Metallidurans Czce.
Authors: Petit-Haertlein, I. / Girard, E. / Sarret, G. / Hazemann, J. / Gourhant, P. / Kahn, R. / Coves, J.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Czce from Cupriavidus Metallidurans Ch34 is a Copper-Binding Protein.
Authors: Zoropogui, A. / Gambarelli, S. / Coves, J.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Overproduction, Purification and Preliminary X-Ray Diffraction Analysis of Czce from Cupriavidus Metallidurans Ch34.
Authors: Pompidor, G. / Zoropogui, A. / Kahn, R. / Coves, J.
History
DepositionSep 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Derived calculations / Version format compliance
Revision 1.2May 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_asym_id / _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_asym_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF131 PROTEIN
B: ORF131 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,07713
Polymers27,6982
Non-polymers37911
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-94.7 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.430, 29.610, 70.960
Angle α, β, γ (deg.)90.00, 113.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2083-

HOH

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Components

#1: Protein ORF131 PROTEIN / CZCE


Mass: 13848.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA METALLIDURANS CH34 (bacteria)
Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58AL9, UniProt: Q1LAJ1*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.16 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 8.5 / Details: PEG4K, MGCL2, TRIS PH 8.5, GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Details: KB FOCUSING MIRRORS
RadiationMonochromator: SI111 CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→48.2 Å / Num. obs: 17623 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 13.31 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.8
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 3.6 / % possible all: 97.3

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Processing

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

Resolution: 1.85→48.249 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 16.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 893 5.1 %
Rwork0.1635 --
obs0.1649 17541 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.663 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 17.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 11 233 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121460
X-RAY DIFFRACTIONf_angle_d1.3251992
X-RAY DIFFRACTIONf_dihedral_angle_d15.109543
X-RAY DIFFRACTIONf_chiral_restr0.095230
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.9660.19241490.17492760X-RAY DIFFRACTION100
1.966-2.11780.2091350.16172728X-RAY DIFFRACTION100
2.1178-2.33090.19961620.1592723X-RAY DIFFRACTION100
2.3309-2.66820.20081540.16732773X-RAY DIFFRACTION100
2.6682-3.36150.17841350.1592798X-RAY DIFFRACTION100
3.3615-48.26560.18281580.1582866X-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)
13.7518-0.47731.73413.591-2.53990.3836-0.04420.42960.2326-0.94970.09750.2990.1001-0.0523-0.00870.2864-0.0295-0.07510.12240.02630.056814.247322.299315.963
20.1324-0.23470.11820.470.0670.3230.05710.0006-0.05260.0047-0.04170.08550.0091-0.0139-0.0050.0592-0.0076-0.01380.05360.00040.087721.563227.346931.9525
30.20830.5211-0.54020.014-1.02540.4967-0.1161-0.01820.0072-0.2182-0.0435-0.21740.2259-0.0520.13460.10990.00780.00990.0910.0050.218430.908113.10232.2226
40.28140.27760.40750.56230.25470.6456-0.0109-0.0015-0.01790.03050.0433-0.10980.01680.0634-0.01870.0455-0.0009-0.01060.05180.00310.074423.84522.838234.7631
50.5031-0.26410.38090.56780.16430.069-0.03940.21110.0149-0.0370.0119-0.01320.0586-0.0089-0.01130.0413-0.0043-0.02130.0559-0.00270.087619.616118.200929.5578
60.95910.1408-0.1271.0928-0.06850.7535-0.1259-0.0762-0.11340.42330.00090.02460.2105-0.07330.08830.10610.0025-0.0140.069-0.00110.061212.011224.495143.3904
70.0428-0.01230.09770.2357-0.0064-0.2613-0.0164-0.12470.01850.1684-0.0039-0.0075-0.160.26420.03080.1847-0.0077-0.00120.21770.02860.078532.121611.638564.5128
80.55170.0936-0.12230.4020.2650.9223-0.14860.0378-0.14860.04960.0760.21530.34630.22310.03880.16370.01050.00920.10740.01160.104525.65012.705449.0336
90.65750.4481-0.22280.1283-0.03220.33940.06810.01390.4202-0.1277-0.09010.2418-0.19350.0907-0.02110.0993-0.0164-0.00060.0560.00680.119833.16914.036841.7071
100.171-0.04210.01870.4514-0.0790.6251-0.06910.0017-0.0079-0.03990.07630.06390.10160.0273-0.00370.0722-0.0005-0.00580.06690.00370.073927.640311.133147.6034
110.3937-0.06520.13820.5661-0.28830.33560.0214-0.0580.01380.2251-0.0064-0.0033-0.08270.15420.01920.10930.0008-0.02040.13680.00260.077329.830916.670453.6986
12-0.401-0.1274-0.19620.6281-0.24811.1302-0.05810.01270.10340.14960.21790.3798-0.2674-0.2097-0.11610.07740.03130.01870.09810.03690.171416.875918.404351.4162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:22)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 23:41)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 42:47)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 48:75)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 76:97)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 98:105)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 14:28)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 29:38)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 39:47)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 48:73)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 74:96)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 97:104)

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