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- PDB-1twd: Crystal Structure of the Putative Copper Homeostasis Protein (Cut... -

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Basic information

Entry
Database: PDB / ID: 1twd
TitleCrystal Structure of the Putative Copper Homeostasis Protein (CutC) from Shigella flexneri, Northeast Structural Genomics Target SfR33
ComponentsCopper homeostasis protein cutC
KeywordsMETAL BINDING PROTEIN / TIM-like protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyCopper homeostasis (CutC) domain / Copper homeostasis protein CutC / Copper homeostasis (CutC) domain superfamily / CutC family / TIM Barrel / Alpha-Beta Barrel / cytoplasm / Alpha Beta / PF03932 family protein CutC
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsForouhar, F. / Lee, I. / Vorobiev, S.M. / Ma, L.-C. / Shastry, R. / Conover, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Forouhar, F. / Lee, I. / Vorobiev, S.M. / Ma, L.-C. / Shastry, R. / Conover, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative Copper Homeostasis Protein (CutC) from Shigella flexneri, Northeast Structural Genomics Target SfR33
Authors: Forouhar, F. / Lee, I. / Vorobiev, S.M. / Ma, L.-C. / Shastry, R. / Conover, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper homeostasis protein cutC
B: Copper homeostasis protein cutC


Theoretical massNumber of molelcules
Total (without water)56,5722
Polymers56,5722
Non-polymers00
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-24 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.625, 97.515, 131.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Copper homeostasis protein cutC


Mass: 28285.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 301 / Gene: CUTC, CUTCM, B1874, SF1915, S2005 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P67825
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.23 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM Tris, pH 7.5, 14% PEG3350, 140mM MgCl2, and 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.7→29.8 Å / Num. all: 98127 / Num. obs: 94398 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.74 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 21.87
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.64 / Num. unique all: 98127 / Rsym value: 0.283 / % possible all: 90.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
CNSrefinement
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.8 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.215 9193 -random
Rwork0.189 ---
all0.189 94782 --
obs0.189 94782 93.1 %-
Displacement parametersBiso mean: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---2.65 Å20 Å2
3---2.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 0 428 3967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.227 1324 -
Rwork0.19 --
obs-12615 82.2 %

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