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- PDB-3iwp: Crystal structure of human copper homeostasis protein CutC -

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Basic information

Entry
Database: PDB / ID: 3iwp
TitleCrystal structure of human copper homeostasis protein CutC
ComponentsCopper homeostasis protein cutC homolog
KeywordsMETAL BINDING PROTEIN / Copper homeostasis protein / CutC / conserved sequence motif / metal-binding site / Copper / Polymorphism
Function / homology
Function and homology information


copper ion homeostasis / copper ion transport / Ion transport by P-type ATPases / protein tetramerization / copper ion binding / nucleolus / nucleoplasm / nucleus / cytoplasm / cytosol
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
Copper homeostasis protein cutC homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, Y. / Du, J. / Zhang, P. / Ding, J.
CitationJournal: To be Published
Title: Crystal structure of human copper homeostasis protein CutC reveals a potential copper-binding site
Authors: Li, Y. / Du, J. / Zhang, P. / Ding, J.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper homeostasis protein cutC homolog
B: Copper homeostasis protein cutC homolog
C: Copper homeostasis protein cutC homolog
D: Copper homeostasis protein cutC homolog
E: Copper homeostasis protein cutC homolog
F: Copper homeostasis protein cutC homolog
G: Copper homeostasis protein cutC homolog
H: Copper homeostasis protein cutC homolog
I: Copper homeostasis protein cutC homolog
J: Copper homeostasis protein cutC homolog
K: Copper homeostasis protein cutC homolog
L: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)371,50612
Polymers371,50612
Non-polymers00
Water15,997888
1
A: Copper homeostasis protein cutC homolog
B: Copper homeostasis protein cutC homolog
C: Copper homeostasis protein cutC homolog
D: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)123,8354
Polymers123,8354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Copper homeostasis protein cutC homolog
F: Copper homeostasis protein cutC homolog
G: Copper homeostasis protein cutC homolog
H: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)123,8354
Polymers123,8354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Copper homeostasis protein cutC homolog
J: Copper homeostasis protein cutC homolog
K: Copper homeostasis protein cutC homolog
L: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)123,8354
Polymers123,8354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Copper homeostasis protein cutC homolog
B: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)61,9182
Polymers61,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-34.7 kcal/mol
Surface area19270 Å2
MethodPISA
5
C: Copper homeostasis protein cutC homolog
D: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)61,9182
Polymers61,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-33.2 kcal/mol
Surface area19040 Å2
MethodPISA
6
E: Copper homeostasis protein cutC homolog
F: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)61,9182
Polymers61,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-32.9 kcal/mol
Surface area19080 Å2
MethodPISA
7
G: Copper homeostasis protein cutC homolog
H: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)61,9182
Polymers61,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-27.5 kcal/mol
Surface area19340 Å2
MethodPISA
8
I: Copper homeostasis protein cutC homolog
J: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)61,9182
Polymers61,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-26.1 kcal/mol
Surface area19470 Å2
MethodPISA
9
K: Copper homeostasis protein cutC homolog
L: Copper homeostasis protein cutC homolog


Theoretical massNumber of molelcules
Total (without water)61,9182
Polymers61,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-30.9 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.160, 78.406, 170.349
Angle α, β, γ (deg.)76.84, 87.88, 71.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Copper homeostasis protein cutC homolog


Mass: 30958.793 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUTC / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9NTM9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M citric acid, pH4.0, and 10% polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 129429 / Num. obs: 127488 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 23.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 4.1 / Num. unique all: 12925 / Rsym value: 0.299 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X7I

1x7i


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28254 6361 5 %RANDOM
Rwork0.23338 ---
all0.23584 122916 --
obs0.23584 121060 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.004 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20.72 Å20.26 Å2
2---0.8 Å20.34 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21852 0 0 888 22740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02222139
X-RAY DIFFRACTIONr_angle_refined_deg1.391.98729809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45452875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67823.17877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.877154050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.24715204
X-RAY DIFFRACTIONr_chiral_restr0.0930.23500
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216200
X-RAY DIFFRACTIONr_nbd_refined0.2450.211910
X-RAY DIFFRACTIONr_nbtor_refined0.3050.215164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.21311
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.217
X-RAY DIFFRACTIONr_mcbond_it1.6961.514294
X-RAY DIFFRACTIONr_mcangle_it3.137222945
X-RAY DIFFRACTIONr_scbond_it3.13837845
X-RAY DIFFRACTIONr_scangle_it5.6674.56864
X-RAY DIFFRACTIONr_rigid_bond_restr2.143322139
X-RAY DIFFRACTIONr_sphericity_free4.3433888
X-RAY DIFFRACTIONr_sphericity_bonded1.242321863
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 483 -
Rwork0.359 8884 -
obs--97.93 %

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