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

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Basic information

Entry
Database: PDB / ID: 2xmk
TitleVisualising the Metal-binding Versatility of Copper Trafficking Sites: Atx1 side-to-side (anaerobic)
ComponentsSSR2857 PROTEIN
KeywordsCHAPERONE / COPPER HOMEOSTASIS / P-TYPE ATPASES / 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 / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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 / pdbx_struct_special_symmetry / 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 / _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

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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
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.991, 41.709, 55.791
Angle α, β, γ (deg.)90.00, 107.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1104-

CL

21A-1105-

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-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 241 / 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: 24 % (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: ID23-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→53.22 Å / Num. obs: 29653 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.4
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.1 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMJ

2xmj


Resolution: 1.35→53.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.251 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15274 1443 4.9 %RANDOM
Rwork0.1294 ---
obs0.13055 28177 97.21 %-
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: 8.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.34 Å2
2---0.16 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.35→53.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 7 241 1135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022936
X-RAY DIFFRACTIONr_bond_other_d0.0010.02561
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9541294
X-RAY DIFFRACTIONr_angle_other_deg1.00631427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.16427.93129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92315161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.929152
X-RAY DIFFRACTIONr_chiral_restr0.0970.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
X-RAY DIFFRACTIONr_nbd_refined0.2320.2179
X-RAY DIFFRACTIONr_nbd_other0.1780.2611
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2469
X-RAY DIFFRACTIONr_nbtor_other0.0880.2507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3730.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0730.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6941.5655
X-RAY DIFFRACTIONr_mcbond_other0.621.5261
X-RAY DIFFRACTIONr_mcangle_it2.72121071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5383281
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4764.5214
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.44631497
X-RAY DIFFRACTIONr_sphericity_free7.0263248
X-RAY DIFFRACTIONr_sphericity_bonded3.44131486
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 99 -
Rwork0.145 1984 -
obs--93.87 %

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