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- PDB-2ov3: Crystal structure of 138-173 ZnuA deletion mutant plus zinc bound -

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Basic information

Entry
Database: PDB / ID: 2ov3
TitleCrystal structure of 138-173 ZnuA deletion mutant plus zinc bound
ComponentsPeriplasmic binding protein component of an ABC type zinc uptake transporter
KeywordsTRANSPORT PROTEIN / ABC Transporter / solute binding domain / zinc transport
Function / homologymetal ion transport / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Periplasmic binding protein component of an ABC type zinc uptake transporter
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSmith, T.J. / Wei, B.
CitationJournal: Biochemistry / Year: 2007
Title: Possible Regulatory Role for the Histidine-Rich Loop in the Zinc Transport Protein, ZnuA
Authors: Wei, B. / Randich, A.M. / Bhattacharyya-Pakrasi, M. / Pakrasi, H.B. / Smith, T.J.
History
DepositionFeb 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Periplasmic binding protein component of an ABC type zinc uptake transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7432
Polymers28,6771
Non-polymers651
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.329, 76.982, 127.311
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Periplasmic binding protein component of an ABC type zinc uptake transporter


Mass: 28677.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: 6803 / Gene: zntC / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P73085
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM ADA, pH 6.5, 1.8-2.0 ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 2, 2006
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 11550 / Num. obs: 10719 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rsym value: 0.555 / Net I/σ(I): 16.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.297 / % possible all: 63.1

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OV1

2ov1


Resolution: 2.4→48.44 Å / σ(F): 265 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.275 530 4.3 %
Rwork0.227 --
obs0.227 10719 87 %
all-10719 -
Solvent computationBsol: 29.221 Å2
Displacement parametersBiso mean: 26.152 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2--7.063 Å20 Å2
3----4.733 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 1 101 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.249
X-RAY DIFFRACTIONc_mcbond_it1.4081.5
X-RAY DIFFRACTIONc_scbond_it2.0232
X-RAY DIFFRACTIONc_mcangle_it2.3922
X-RAY DIFFRACTIONc_scangle_it2.9752.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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