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- PDB-2xmj: Visualising the Metal-binding Versatility of Copper Trafficking S... -

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Basic information

Entry
Database: PDB / ID: 2xmj
TitleVisualising the Metal-binding Versatility of Copper Trafficking Sites: Atx1 side-to-side (aerobic)
ComponentsSSR2857 PROTEIN
KeywordsCHAPERONE / COPPER HOMEOSTASIS / P-TYPE ATPASE / METAL TRANSPORT
Function / homology
Function and homology information


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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Ssr2857 protein
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.08 Å
AuthorsBadarau, A. / Firbank, S.J. / McCarthy, A.A. / Banfield, M.J. / Dennison, C.
CitationJournal: Biochemistry / Year: 2010
Title: Visualizing the Metal-Binding Versatility of Copper Trafficking Sites .
Authors: Badarau, A. / Firbank, S.J. / Mccarthy, A.A. / Banfield, M.J. / Dennison, C.
History
DepositionJul 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Data collection / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: SSR2857 PROTEIN
B: SSR2857 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7299
Polymers13,3812
Non-polymers3487
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-24.4 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.460, 41.654, 55.832
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1067-

CL

21A-1069-

NA

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Components

#1: Protein SSR2857 PROTEIN / ATX1


Mass: 6690.513 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 2 COPPER IONS PER MONOMER / Source: (gene. exp.) SYNECHOCYSTIS SP. PCC 6803 (bacteria) / Plasmid: PET29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73213
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6.5
Details: 25 % (W/V) PEG 8000, 200 MM SODIUM ACETATE, 100 MM SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.08→13.81 Å / Num. obs: 56359 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 1.08→1.14 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.4 / % possible all: 92.8

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Processing

Software
NameClassification
SHELXrefinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: NONE

Resolution: 1.08→10 Å / Num. parameters: 11309 / Num. restraintsaints: 14392 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1488 3124 5.8 %RANDOM
all0.117 53765 --
obs--90.3 %-
Refine analyzeNum. disordered residues: 44 / Occupancy sum hydrogen: 641.63 / Occupancy sum non hydrogen: 1134.5
Refinement stepCycle: LAST / Resolution: 1.08→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 7 251 1156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0304
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.089

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