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- PDB-2xmw: PacS, N-terminal domain, from Synechocystis PCC6803 -

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Basic information

Entry
Database: PDB / ID: 2xmw
TitlePacS, N-terminal domain, from Synechocystis PCC6803
ComponentsCATION-TRANSPORTING ATPASE PACS
KeywordsHYDROLASE / CU(I)-BINDING / TRAFFICKING
Function / homology
Function and homology information


P-type divalent copper transporter activity / copper ion import / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
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 / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain ...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 / P-type ATPase actuator domain / 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
COPPER (I) ION / Probable copper-transporting ATPase PacS
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / 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.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_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: CATION-TRANSPORTING ATPASE PACS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7172
Polymers7,6541
Non-polymers641
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.580, 45.580, 51.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein CATION-TRANSPORTING ATPASE PACS / PACS-N


Mass: 7653.774 Da / Num. of mol.: 1 / Fragment: N-TERMINAL, COPPER-BINDING DOMAIN, RESIDUES 1-71
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: P73241
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.03 Å3/Da / Density % sol: 39.43 % / Description: NONE
Crystal growpH: 4.6
Details: 40 % (W/V) PEG 300 AND 100 MM CITRATE -PHOSPHATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.37
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 1.8→39.47 Å / Num. obs: 6085 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 23.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 39
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 23.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 10.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX.HYSSphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→51.85 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.233 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25922 586 9.7 %RANDOM
Rwork0.24332 ---
obs0.24496 5475 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å20 Å2
2--0.65 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→51.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms480 0 1 12 493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021493
X-RAY DIFFRACTIONr_bond_other_d0.0030.02298
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.944675
X-RAY DIFFRACTIONr_angle_other_deg0.8963740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.87125.55618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.171572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.435151
X-RAY DIFFRACTIONr_chiral_restr0.0990.284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0288
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_it1.131.5339
X-RAY DIFFRACTIONr_mcbond_other0.251.5136
X-RAY DIFFRACTIONr_mcangle_it2.0062538
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8913154
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6464.5135
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
Rfree0.288 46 -
Rwork0.237 386 -
obs--99.08 %

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