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- PDB-2ps3: Structure and metal binding properties of ZnuA, a periplasmic zin... -

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Basic information

Entry
Database: PDB / ID: 2ps3
TitleStructure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli
ComponentsHigh-affinity zinc uptake system protein znuA
KeywordsMETAL TRANSPORT / The protein consists of two domains with a typical (beta/alfa)4 fold
Function / homology
Function and homology information


zinc ion import across plasma membrane / zinc ion transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / cell adhesion / zinc ion binding / membrane
Similarity search - Function
High-affinity zinc uptake system protein ZnuA / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
High-affinity zinc uptake system protein ZnuA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsYatsunyk, L.A. / Kim, L.R. / Vorontsov, I.I. / Rosenzweig, A.C.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2008
Title: Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli.
Authors: Yatsunyk, L.A. / Easton, J.A. / Kim, L.R. / Sugarbaker, S.A. / Bennett, B. / Breece, R.M. / Vorontsov, I.I. / Tierney, D.L. / Crowder, M.W. / Rosenzweig, A.C.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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: High-affinity zinc uptake system protein znuA
B: High-affinity zinc uptake system protein znuA


Theoretical massNumber of molelcules
Total (without water)62,3542
Polymers62,3542
Non-polymers00
Water88349
1
A: High-affinity zinc uptake system protein znuA


Theoretical massNumber of molelcules
Total (without water)31,1771
Polymers31,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: High-affinity zinc uptake system protein znuA


Theoretical massNumber of molelcules
Total (without water)31,1771
Polymers31,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.875, 89.842, 91.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein High-affinity zinc uptake system protein znuA


Mass: 31177.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P39172
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5 mg/mL protein in 20 mM MOPS, pH 7.0, 5 mM EDTA, 20 mM NaCl, 5 % glycerol was mixed 1:1 with a cryoprotectant solution containing 35.5 % (w/v) PEG 4000, 0.2 M ammonium acetate, 9 % ...Details: 5 mg/mL protein in 20 mM MOPS, pH 7.0, 5 mM EDTA, 20 mM NaCl, 5 % glycerol was mixed 1:1 with a cryoprotectant solution containing 35.5 % (w/v) PEG 4000, 0.2 M ammonium acetate, 9 % glycerol, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 5ID-B10.97934
SYNCHROTRONAPS 19-ID20.97934
SYNCHROTRONAPS 23-ID-D30.97934
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 6, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.45→35.1 Å / Num. obs: 20560 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.3 Å2 / Rsym value: 0.084
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.4 % / Num. unique all: 1855 / Rsym value: 0.3 / % possible all: 90.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å35.1 Å
Translation2.5 Å35.1 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PS0

2ps0


Resolution: 2.47→35.1 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.284 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.711 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1068 5.2 %RANDOM
Rwork0.24 ---
obs0.243 20515 97.97 %-
all-20560 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.271 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å20 Å2
2---5.13 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.47→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 49 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224150
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9745629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99924.885174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68415706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9291518
X-RAY DIFFRACTIONr_chiral_restr0.090.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023120
X-RAY DIFFRACTIONr_nbd_refined0.2310.21863
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.25
X-RAY DIFFRACTIONr_mcbond_it0.6721.52704
X-RAY DIFFRACTIONr_mcangle_it1.1924242
X-RAY DIFFRACTIONr_scbond_it1.36631614
X-RAY DIFFRACTIONr_scangle_it2.1524.51387
LS refinement shellResolution: 2.472→2.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 60 -
Rwork0.332 1121 -
obs-1181 78.11 %

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