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- PDB-1x8c: Crystal structure of the SeMet-derivative copper homeostasis prot... -

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Basic information

Entry
Database: PDB / ID: 1x8c
TitleCrystal structure of the SeMet-derivative copper homeostasis protein (cutCm) with calcium binding from Shigella flexneri 2a str. 301
ComponentsCopper homeostasis protein cutC
KeywordsMETAL BINDING PROTEIN / CutC family / Tim-like protein / Copper homeostasis
Function / homology
Function and homology information


copper ion binding / cytoplasm
Similarity search - Function
Copper homeostasis (CutC) domain / Copper homeostasis protein CutC / Copper homeostasis (CutC) domain superfamily / CutC family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PF03932 family protein CutC
Similarity search - Component
Biological speciesShigella flexneri 2a str. 301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWang, D.C. / Zhu, D.Y.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of the copper homeostasis protein (CutCm) from Shigella flexneri at 1.7 A resolution: the first structure of a new sequence family of TIM barrels
Authors: Zhu, D.Y. / Zhu, Y.Q. / Huang, R.H. / Xiang, Y. / Yang, N. / Lu, H.X. / Li, G.P. / Jin, Q. / Wang, D.C.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,8003
Polymers56,7602
Non-polymers401
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-34 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.579, 97.579, 131.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-669-

HOH

21B-675-

HOH

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Components

#1: Protein Copper homeostasis protein cutC / cutCm


Mass: 28379.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria)
Species: Shigella flexneri / Strain: 2a str. 301 / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P67825
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.2 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG8000, 0.1M HEPES-Na Ph 7.0, 0.1M Calcium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
31
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97938, 0.97850, 0.97000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
20.97851
30.971
ReflectionResolution: 2.1→59.26 Å / Num. all: 28370 / Num. obs: 28343 / % possible obs: 1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3989 / Rsym value: 0.164 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
CCP4(SCALA)data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→59.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4656473.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1377 4.9 %RANDOM
Rwork0.196 ---
obs0.196 28343 99.4 %-
all-28370 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9827 Å2 / ksol: 0.383496 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å20 Å2
2---2.44 Å20 Å2
3---4.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→59.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 1 382 3947
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 246 5.4 %
Rwork0.206 4297 -
obs-4297 97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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