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- PDB-2xmu: Copper chaperone Atx1 from Synechocystis PCC6803 (Cu2 form) -

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Basic information

Entry
Database: PDB / ID: 2xmu
TitleCopper chaperone Atx1 from Synechocystis PCC6803 (Cu2 form)
ComponentsSSR2857 PROTEIN
KeywordsCHAPERONE / COPPER HOMEOSTASIS / P-TYPE ATPASES / METAL TRANSPORT / METALLOCHAPERONE / CU(I)-BINDING / CU(I)-CLUSTER / TRAFFICKING
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 (I) ION / Ssr2857 protein
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Data collection / Version format compliance
Revision 1.2Dec 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 / 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.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_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)13,6356
Polymers13,3812
Non-polymers2544
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-59.3 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.243, 29.388, 38.702
Angle α, β, γ (deg.)91.69, 101.26, 118.62
Int Tables number1
Space group name H-MP1

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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
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-CU1 / COPPER (I) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.93 % / Description: NONE
Crystal growpH: 7.5
Details: 28 % (W/V) PEG 8000, 200 MM SODIUM ACETATE, 100 HEPES PH 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID2911.38
SYNCHROTRONESRF ID23-121.38
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDJul 10, 2008MIRRORS
MARRESEARCH2CCDMIRRORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.75→25.57 Å / Num. obs: 10938 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 9.7 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMJ

2xmj


Resolution: 1.75→37.58 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.695 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.31157 521 4.8 %RANDOM
Rwork0.26707 ---
obs0.26915 10368 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0.72 Å20.28 Å2
2---0.3 Å2-0.36 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 4 15 925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022898
X-RAY DIFFRACTIONr_bond_other_d0.0010.02539
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9561230
X-RAY DIFFRACTIONr_angle_other_deg0.9631352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.96827.93129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99815149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.862152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02135
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9011.5631
X-RAY DIFFRACTIONr_mcbond_other0.2061.5253
X-RAY DIFFRACTIONr_mcangle_it1.54221020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7843267
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1684.5209
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 38 -
Rwork0.35 741 -
obs--97.74 %

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