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- PDB-2wtp: Crystal Structure of Cu-form Czce from C. metallidurans CH34 -

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Basic information

Entry
Database: PDB / ID: 2wtp
TitleCrystal Structure of Cu-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
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
COPPER (II) ION / DI(HYDROXYETHYL)ETHER / 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: 1.5 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,77021
Polymers27,6982
Non-polymers1,07219
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-100.4 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.000, 29.530, 71.170
Angle α, β, γ (deg.)90.00, 113.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2043-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 7 types, 219 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.5→19.14 Å / Num. obs: 32477 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 14.18 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.5 / % possible all: 97.9

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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: 1.5→19.141 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 16.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 1645 5.1 %
Rwork0.1599 --
obs0.1613 32477 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.04 Å2 / ksol: 0.441 e/Å3
Displacement parametersBiso mean: 20.982 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 47 200 1622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0261488
X-RAY DIFFRACTIONf_angle_d2.4482017
X-RAY DIFFRACTIONf_dihedral_angle_d18.919565
X-RAY DIFFRACTIONf_chiral_restr0.151227
X-RAY DIFFRACTIONf_plane_restr0.012260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.54420.18871200.17872560X-RAY DIFFRACTION99
1.5442-1.5940.18891510.16892532X-RAY DIFFRACTION100
1.594-1.6510.20771380.16752564X-RAY DIFFRACTION100
1.651-1.7170.22571370.15882534X-RAY DIFFRACTION100
1.717-1.79510.20341230.15282550X-RAY DIFFRACTION100
1.7951-1.88970.17121410.14352569X-RAY DIFFRACTION100
1.8897-2.00790.16071350.13762564X-RAY DIFFRACTION100
2.0079-2.16280.21431390.14492581X-RAY DIFFRACTION100
2.1628-2.38010.17411480.14622571X-RAY DIFFRACTION100
2.3801-2.72360.16541410.15732579X-RAY DIFFRACTION100
2.7236-3.42830.17441290.15052623X-RAY DIFFRACTION100
3.4283-19.14260.18551430.16332605X-RAY DIFFRACTION97
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)
10.28760.010.35230.33491.1923-1.15280.11720.06570.0852-0.4386-0.17070.0537-0.1295-0.00090.09910.23490.0352-0.02260.089-0.00540.132513.42223.69820.8671
20.34050.4268-0.1381-0.0087-0.190.26650.03320.0212-0.0643-0.0386-0.031-0.09580.0787-0.02510.0030.123-0.0016-0.00110.0752-0.00440.123728.547125.74334.3975
30.5110.40230.03040.66240.22960.465-0.01530.0157-0.1068-0.0150.0536-0.09060.02720.0419-0.02110.09370.00220.00690.0723-0.00190.123523.460721.861235.0269
40.3962-0.49020.07870.13340.23790.1645-0.04570.05090.01410.05280.0183-0.04910.12290.00960.00110.102-0.00720.00160.0915-0.00830.11520.633218.284328.9495
50.0917-0.2383-0.29031.26640.61150.3415-0.0734-0.0704-0.08070.3544-0.0075-0.10820.12560.06780.07180.15460.01020.00680.0725-0.00150.085811.799424.769543.8314
60.7126-0.02310.84490.2126-0.2832-0.26850.2261-0.2101-0.04460.178-0.182-0.0252-0.0370.4153-0.0620.2592-0.01730.01390.25840.02540.100530.571812.339864.3921
70.5596-0.8794-0.14380.20380.62490.4712-0.06650.01850.0289-0.01810.0730.00580.06920.0323-0.00780.1206-0.00210.00690.06910.01110.096727.722111.475845.7619
80.2807-0.03270.32310.4828-0.2840.5287-0.0798-0.0725-0.00460.14940.00960.0080.0180.05510.01530.11560.01690.01640.07850.01180.071125.528212.271752.0818
90.1898-0.0981-0.16170.25550.04980.3214-0.050.0286-0.00140.0940.0002-0.19060.15690.32390.06130.16070.0431-0.02170.210.00140.117434.436713.958853.4682
100.1374-0.0214-0.08670.3696-0.13950.6041-0.01720.07150.01560.11650.02020.0223-0.2584-0.026400.11940.0153-0.00210.0834-0.00640.106721.74419.345551.3219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:28)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 29:44)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 45:76)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 77:97)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 98:105)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 16:28)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 29:61)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 62:78)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 79:92)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 93:104)

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