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- PDB-3fry: Crystal structure of the CopA C-terminal metal binding domain -

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Basic information

Entry
Database: PDB / ID: 3fry
TitleCrystal structure of the CopA C-terminal metal binding domain
ComponentsProbable copper-exporting P-type ATPase A
KeywordsHYDROLASE / TRANSPORT PROTEIN / METAL BINDING DOMAIN / DOMAIN SWAP / ATP-binding / Cell membrane / Copper transport / Ion transport / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Transmembrane / Transport
Function / homology
Function and homology information


P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / intracellular copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Probable copper-exporting P-type ATPase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAgarwal, S. / Sazinsky, M. / Arguello, J. / Rosenzweig, A.C.
CitationJournal: Proteins / Year: 2010
Title: Structure and interactions of the C-terminal metal binding domain of Archaeoglobus fulgidus CopA.
Authors: Agarwal, S. / Hong, D. / Desai, N.K. / Sazinsky, M.H. / Arguello, J.M. / Rosenzweig, A.C.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: Probable copper-exporting P-type ATPase A
B: Probable copper-exporting P-type ATPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8443
Polymers15,6522
Non-polymers1921
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-20 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.131, 35.989, 51.262
Angle α, β, γ (deg.)90.00, 104.89, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-75-

HOH

21A-100-

HOH

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Components

#1: Protein Probable copper-exporting P-type ATPase A


Mass: 7825.902 Da / Num. of mol.: 2 / Fragment: C-Terminal Domain
Source method: isolated from a genetically manipulated source
Details: Strep tagged protein / Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0473, copA, pacS / Plasmid: pPR-IBA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O29777, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 298 K / pH: 4.5
Details: 0.1M citrate, 30% PEG-6000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.37757
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37757 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 9568 / % possible obs: 97.3 % / Redundancy: 6.5 % / Rsym value: 0.076

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OSD

1osd


Resolution: 2→27.32 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.238 --RANDOM
Rwork0.222 ---
obs0.222 9568 97.3 %-
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.486 Å20 Å2-0.498 Å2
2---1.306 Å20 Å2
3----3.18 Å2
Refinement stepCycle: LAST / Resolution: 2→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 13 44 1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4871.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.5322
X-RAY DIFFRACTIONc_scangle_it3.9812.5
LS refinement shellResolution: 2→2.07 Å / % reflection obs: 81.7 %
Xplor fileSerial no: 1 / Param file: cit.param

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