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- PDB-3n7d: Crystal structure of CopK bound to Cu(I) and Cu(II) -

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Basic information

Entry
Database: PDB / ID: 3n7d
TitleCrystal structure of CopK bound to Cu(I) and Cu(II)
ComponentsCopper resistance protein K
KeywordsMETAL BINDING PROTEIN / copper (I) bound / copper (II) bound / copper resistance / methionine rich
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Copper resistance protein K / Copper resistance protein K / CopK superfamily / Copper resistance protein K / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / COPPER (I) ION / Copper resistance protein K
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.149 Å
AuthorsAsh, M.-R. / Maher, M.J.
CitationJournal: To be Published
Title: Two new crystal forms of copper resistance protein CopK
Authors: Ash, M.-R. / Maher, M.J.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper resistance protein K
B: Copper resistance protein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7805
Polymers16,5892
Non-polymers1913
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-5 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.725, 50.343, 52.053
Angle α, β, γ (deg.)90.000, 116.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-75-

CU

21B-75-

CU

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Components

#1: Protein Copper resistance protein K / CopK


Mass: 8294.567 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: copK / Plasmid: pCX07 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58AD3
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLINK RECORDS BETWEEN CU B 75 AND GLU B 29 HAVE BEEN OMITTED DUE TO AMBIGUITY IN THEIR ROLE IN METAL ...LINK RECORDS BETWEEN CU B 75 AND GLU B 29 HAVE BEEN OMITTED DUE TO AMBIGUITY IN THEIR ROLE IN METAL COORDINATION AT THIS SITE.

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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: 1.751525 Å3/Da / Density % sol: 29.775499 % / Mosaicity: 0.619 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M sodium acetate pH 3.8, 0.2M ammonium acetate, 32% (w/v) PEG 4000, 22mM NiCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.3776 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 2.149→50 Å / Num. all: 6136 / Num. obs: 6136 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.114 / Net I/σ(I): 15.2
Reflection shellResolution: 2.149→2.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 8.7 / Num. unique all: 622 / Χ2: 1.07 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DSO

3dso


Resolution: 2.149→24.852 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.34 / Isotropic thermal model: Isotropic with TLS / Cross valid method: Throught / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.276 604 9.85 %Random
Rwork0.219 ---
obs0.224 6130 96.7 %-
all-6130 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.142 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 121.54 Å2 / Biso mean: 49.489 Å2 / Biso min: 23.81 Å2
Baniso -1Baniso -2Baniso -3
1--8.098 Å20 Å2-4.734 Å2
2--5.322 Å2-0 Å2
3---2.776 Å2
Refinement stepCycle: LAST / Resolution: 2.149→24.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms858 0 3 7 868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005876
X-RAY DIFFRACTIONf_angle_d0.9891166
X-RAY DIFFRACTIONf_chiral_restr0.063128
X-RAY DIFFRACTIONf_plane_restr0.003151
X-RAY DIFFRACTIONf_dihedral_angle_d16.565331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.149-2.3650.3051460.2513751521154396
2.365-2.7070.3451640.2413711535153198
2.707-3.4090.3031450.22213861531153598
3.409-24.8540.2421490.20413941543152195
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)
12.84950.69760.43850.1379-0.0250.7515-0.07240.10760.25070.0769-0.0362-0.01270.00710.1367-00.2741-0.010.010.2052-0.04760.3203-14.8014-9.99263.5477
21.9347-0.03111.59680.15890.23721.63380.251-0.2375-0.00970.2593-0.08020.00940.10850.190800.3689-0.0468-0.03240.38310.00790.25124.9427-12.296515.1768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 5:63A5 - 63
2X-RAY DIFFRACTION2chain B and resseq 6:63B6 - 63

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