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- PDB-2vb2: Crystal structure of Cu(I)CusF -

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Basic information

Entry
Database: PDB / ID: 2vb2
TitleCrystal structure of Cu(I)CusF
ComponentsCATION EFFLUX SYSTEM PROTEIN CUSF
KeywordsMETAL TRANSPORT / CATION PI / METAL-BINDING / COPPER TOLERANCE / COPPER TRANSPORT
Function / homology
Function and homology information


metallochaperone activity / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / copper chaperone activity / copper ion export / detoxification of copper ion / response to copper ion / response to zinc ion / intracellular copper ion homeostasis ...metallochaperone activity / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / copper chaperone activity / copper ion export / detoxification of copper ion / response to copper ion / response to zinc ion / intracellular copper ion homeostasis / transition metal ion binding / response to toxic substance / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding
Similarity search - Function
Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Cation efflux system protein CusF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXue, Y. / Davis, A.V. / Balakrishnan, G. / Stasser, J.P. / Staehlin, B.M. / Focia, P. / Spiro, T.G. / Penner-Hahn, J.E. / O'Halloran, T.V.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Cu(I) Recognition Via Cation-Pi and Methionine Interactions in Cusf.
Authors: Xue, Y. / Davis, A.V. / Balakrishnan, G. / Stasser, J.P. / Staehlin, B.M. / Focia, P. / Spiro, T.G. / Penner-Hahn, J.E. / O'Halloran, T.V.
History
DepositionSep 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: CATION EFFLUX SYSTEM PROTEIN CUSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0263
Polymers9,8661
Non-polymers1602
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.468, 41.264, 44.573
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 CATION EFFLUX SYSTEM PROTEIN CUSF / COPPER PROTEIN


Mass: 9866.225 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77214
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.9 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 7 / Details: 2.5M AMMONIUM SULFATE 5% ISOPROPANOL, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 8250 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEQ

1zeq


Resolution: 1.7→30.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.266 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-12 AND 88 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 370 4.7 %RANDOM
Rwork0.238 ---
obs0.239 7573 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--2.42 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms582 0 6 46 634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022599
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.96807
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg52.2126.36422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6515112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.508151
X-RAY DIFFRACTIONr_chiral_restr0.0750.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2220
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2408
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.216
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6621.5385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.092616
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8043235
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9664.5191
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 25
Rwork0.326 443
Refinement TLS params.Method: refined / Origin x: 8.7128 Å / Origin y: 2.9775 Å / Origin z: 8.9896 Å
111213212223313233
T-0.1136 Å20.0269 Å2-0.003 Å2--0.1078 Å20.0233 Å2---0.1065 Å2
L3.499 °20.8509 °21.5248 °2-4.6709 °23.8898 °2--7.7766 °2
S0.0703 Å °-0.0442 Å °-0.1039 Å °-0.0269 Å °0.0686 Å °-0.2871 Å °0.038 Å °-0.0019 Å °-0.1388 Å °

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