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- PDB-2xmv: Copper chaperone Atx1 from Synechocystis PCC6803 (Cu1, trimeric f... -

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Basic information

Entry
Database: PDB / ID: 2xmv
TitleCopper chaperone Atx1 from Synechocystis PCC6803 (Cu1, trimeric form, His61Tyr mutant)
ComponentsSSR2857 PROTEIN
KeywordsCHAPERONE / 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: 1.8 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 1.1Apr 25, 2012Group: Data collection / Database references ...Data collection / Database references / Refinement description / 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
C: SSR2857 PROTEIN
D: SSR2857 PROTEIN
E: SSR2857 PROTEIN
F: SSR2857 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,80214
Polymers40,2936
Non-polymers5088
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-143.7 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.690, 77.100, 90.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SSR2857 PROTEIN / ATX1


Mass: 6715.540 Da / Num. of mol.: 6 / Mutation: YES
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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 61 TO TYR ENGINEERED RESIDUE IN CHAIN B, HIS 61 TO TYR ...ENGINEERED RESIDUE IN CHAIN A, HIS 61 TO TYR ENGINEERED RESIDUE IN CHAIN B, HIS 61 TO TYR ENGINEERED RESIDUE IN CHAIN C, HIS 61 TO TYR ENGINEERED RESIDUE IN CHAIN D, HIS 61 TO TYR ENGINEERED RESIDUE IN CHAIN E, HIS 61 TO TYR ENGINEERED RESIDUE IN CHAIN F, HIS 61 TO TYR

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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: 2.06 Å3/Da / Density % sol: 40.42 % / Description: NONE
Crystal growpH: 7 / Details: 2.1 M D,L-MALIC ACID AT PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.38
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 31381 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 29.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 13.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMJ

2xmj


Resolution: 1.8→29.97 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.248 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25315 1566 5 %RANDOM
Rwork0.19063 ---
obs0.19372 29712 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.921 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 8 254 2951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222713
X-RAY DIFFRACTIONr_bond_other_d0.0010.021594
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9683720
X-RAY DIFFRACTIONr_angle_other_deg0.98734024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.222890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89415444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.193156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
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_it0.9891.51896
X-RAY DIFFRACTIONr_mcbond_other0.2911.5760
X-RAY DIFFRACTIONr_mcangle_it1.76823065
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8723817
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1724.5651
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 134 -
Rwork0.262 2154 -
obs--99.31 %

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