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- PDB-2c9r: apo-H91F CopC -

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Basic information

Entry
Database: PDB / ID: 2c9r
Titleapo-H91F CopC
ComponentsCOPPER RESISTANCE PROTEIN C
KeywordsELECTRON TRANSPORT / COPPER TRANSPORT / COPPER PROTEINS / COPPER DISSOCIATION CONSTANTS / METAL-BINDING
Function / homology
Function and homology information


copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane
Similarity search - Function
: / Copper transport protein C/D / CopC domain / CopC domain / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Copper resistance protein C
Similarity search - Component
Biological speciesPSEUDOMONAS SYRINGAE PV. TOMATO (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, L. / Koay, M. / Maher, M.J. / Xiao, Z. / Wedd, A.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Intermolecular Transfer of Copper Ions from the Copc Protein of Pseudomonas Syringae. Crystal Structures of Fully Loaded Cu(I)Cu(II) Forms.
Authors: Zhang, L. / Koay, M. / Maher, M.J. / Xiao, Z. / Wedd, A.G.
History
DepositionDec 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2006Provider: 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 / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COPPER RESISTANCE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5792
Polymers10,5561
Non-polymers231
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.315, 72.315, 47.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein COPPER RESISTANCE PROTEIN C / COPC


Mass: 10556.105 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SYRINGAE PV. TOMATO (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P12376
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFACILITATES COPPER RESISTANCE BY SEQUESTRATION OF COPPER IN THE PERIPLASM ALONG WITH THE COPPER- ...FACILITATES COPPER RESISTANCE BY SEQUESTRATION OF COPPER IN THE PERIPLASM ALONG WITH THE COPPER-BINDING PROTEIN COPA. ENGINEERED RESIDUE IN CHAIN A, HIS 115 TO PHE

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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: 2.66 Å3/Da / Density % sol: 53.37 %
Crystal growpH: 6.6
Details: 2.4 M SODIUM ACETATE, PH 7.0, 0.1 M BIS-TRIS PROPANE, PH 6.6, EDTA, 10 MM.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5412
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 8189 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.7 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9Q

2c9q


Resolution: 2→26.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.153 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS (RESIDUES 45-49) WERE OMMITTED FROM THE COORDINATES
RfactorNum. reflection% reflectionSelection details
Rfree0.213 378 4.6 %RANDOM
Rwork0.175 ---
obs0.177 7806 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---0.66 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 0 1 63 766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022797
X-RAY DIFFRACTIONr_bond_other_d0.0010.02728
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9771102
X-RAY DIFFRACTIONr_angle_other_deg0.72831717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1775115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.85723.68419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51215127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.85152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02146
X-RAY DIFFRACTIONr_nbd_refined0.210.2123
X-RAY DIFFRACTIONr_nbd_other0.1790.2642
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2403
X-RAY DIFFRACTIONr_nbtor_other0.0840.2535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6581.5545
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1892901
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0333258
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4014.5201
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 32
Rwork0.208 549
Refinement TLS params.Method: refined / Origin x: 0.1096 Å / Origin y: 19.5941 Å / Origin z: 1.2407 Å
111213212223313233
T-0.2771 Å20.0154 Å20.0195 Å2--0.2773 Å2-0.0438 Å2---0.2672 Å2
L4.7389 °21.5104 °23.5008 °2-2.6085 °21.537 °2--3.961 °2
S-0.0759 Å °0.0079 Å °0.1966 Å °-0.047 Å °0.0201 Å °-0.0089 Å °-0.1133 Å °0.0482 Å °0.0558 Å °

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