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- PDB-4u9r: Structure of the N-terminal Extension from Cupriavidus metallidur... -

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Basic information

Entry
Database: PDB / ID: 4u9r
TitleStructure of the N-terminal Extension from Cupriavidus metallidurans CzcP
ComponentsCzcP cation efflux P1-ATPase
KeywordsHYDROLASE / ferredoxin-like domain
Function / homology
Function and homology information


metal ion transport / ATPase-coupled monoatomic cation transmembrane transporter activity / membrane => GO:0016020 / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IB / Heavy metal-associated domain superfamily / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / 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 ...P-type ATPase, subfamily IB / Heavy metal-associated domain superfamily / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / 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 / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 3,3',3''-phosphanetriyltripropanoic acid / CzcP cation efflux P1-ATPase
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.17 Å
AuthorsSmith, A.T. / Rosenzweig, A.C.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: A new metal binding domain involved in cadmium, cobalt and zinc transport.
Authors: Smith, A.T. / Barupala, D. / Stemmler, T.L. / Rosenzweig, A.C.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CzcP cation efflux P1-ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0204
Polymers22,5451
Non-polymers4753
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.160, 58.160, 72.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Detailsbiological unit is the same as asym.

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Components

#1: Protein CzcP cation efflux P1-ATPase


Mass: 22545.195 Da / Num. of mol.: 1 / Fragment: ferredoxin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: czcP, Rmet_5970 / Plasmid: pBAD Strep TEV LIC 8R / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q1LAJ7
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#4: 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 4000, 1 mM CdSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.17→36.01 Å / Num. obs: 12757 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 46.473 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.016 / Net I/σ(I): 26.8 / Num. measured all: 144365
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.17-2.2311.20.7194102819200.22399.7
9.71-36.0110.70.02480.215981500.00797.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
xia2data scaling
RefinementResolution: 2.17→36.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.093 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 1233 9.9 %RANDOM
Rwork0.2275 11270 --
obs0.2313 12503 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 139.57 Å2 / Biso mean: 64.851 Å2 / Biso min: 25.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å2-0 Å2-0 Å2
2--1.52 Å2-0 Å2
3----3.04 Å2
Refinement stepCycle: final / Resolution: 2.17→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 18 12 1145
Biso mean--79.4 44.46 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191154
X-RAY DIFFRACTIONr_bond_other_d0.0010.021135
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9751551
X-RAY DIFFRACTIONr_angle_other_deg0.7953.0022601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5745146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23122.70848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77415195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3691513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_mcbond_it4.3686.231588
X-RAY DIFFRACTIONr_mcbond_other4.3356.221586
X-RAY DIFFRACTIONr_mcangle_it6.9239.307732
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 91 -
Rwork0.251 786 -
all-877 -
obs--95.12 %

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