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- PDB-2bdq: Crystal Structure of the Putative Copper Homeostasis Protein CutC... -

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Basic information

Entry
Database: PDB / ID: 2bdq
TitleCrystal Structure of the Putative Copper Homeostasis Protein CutC from Streptococcus agalactiae, Northeast Strucural Genomics Target SaR15.
Componentscopper homeostasis protein CutC
KeywordsMETAL TRANSPORT / alpha beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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 speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Abashidze, M. / Jayaraman, S. / Ho, C.K. / Cooper, B. / 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 Streptococcus agalactiae, Northeast Strucural Genomics Target SaR15.
Authors: Forouhar, F. / Abashidze, M. / Jayaraman, S. / Ho, C.K. / Cooper, B. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE Residue 212 is a modified residue and a cloning artifact.

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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


Theoretical massNumber of molelcules
Total (without water)50,4422
Polymers50,4422
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-12 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.458, 71.542, 128.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein copper homeostasis protein CutC


Mass: 25220.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: 2603V-R / Gene: SAG1569 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DYB9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 44.14 %
Description: The reflections reported in data collection include friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM Tris, 18% PEG3350, 200 mM NaSCN, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2005 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 38496 / Num. obs: 36017 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.109 / Net I/σ(I): 19.71
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 9.61 / Num. unique all: 2013 / Rsym value: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 395954.69 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs have been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3549 9.9 %RANDOM
Rwork0.221 ---
all0.223 38496 --
obs0.221 36017 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.4141 Å2 / ksol: 0.332444 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å20 Å2
2--0.87 Å20 Å2
3----3.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 0 216 3476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 549 9.9 %
Rwork0.226 5019 -
obs-5019 87 %

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