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- PDB-2ps0: Structure and metal binding properties of ZnuA, a periplasmic zin... -

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Basic information

Entry
Database: PDB / ID: 2ps0
TitleStructure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli
ComponentsHigh-affinity zinc uptake system protein znuA
KeywordsMETAL TRANSPORT / protein consists of two domains with (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 / SAD / Resolution: 2 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 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: High-affinity zinc uptake system protein znuA
B: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6166
Polymers62,3542
Non-polymers2624
Water7,098394
1
A: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3083
Polymers31,1771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3083
Polymers31,1771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.438, 86.266, 88.147
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 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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 30 % (w/v) PEG 4000, 5 % isopropanol, 0.1 M succinate, pH 4.9 mixed 1:1 with 10 mg/mL ZnZnuA or 1:2 with 2.5 mg/mL ZnZnuA, 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-B11.2828162
SYNCHROTRONAPS 19-ID21.2828162
SYNCHROTRONAPS 23-ID-D31.2828162
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828162 Å / Relative weight: 1
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 9.8 / Number: 262168 / Rmerge(I) obs: 0.082 / Χ2: 1.02 / D res high: 2 Å / D res low: 45 Å / Num. obs: 38461 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.314599.210.0461.2976.6
3.424.3110010.0760.9857
2.993.4210010.0750.9887
2.712.9910010.0970.9847
2.522.7110010.1160.9817
2.372.5210010.1430.9767.1
2.252.3710010.1741.0046.9
2.152.2510010.20.9977
2.072.1510010.2540.996.8
22.0798.410.2890.9925.8
ReflectionResolution: 2→37.2 Å / Num. obs: 38461 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.082
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Num. unique all: 3729 / Rsym value: 0.289 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.193 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1925 5 %RANDOM
Rwork0.199 ---
obs0.201 38401 99.75 %-
all-38461 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.835 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2--0.32 Å20 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 2→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 4 394 4488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224174
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9735672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11425.227176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19315713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8461516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023148
X-RAY DIFFRACTIONr_nbd_refined0.1950.22029
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2335
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.218
X-RAY DIFFRACTIONr_mcbond_it0.6811.52730
X-RAY DIFFRACTIONr_mcangle_it1.18824279
X-RAY DIFFRACTIONr_scbond_it1.58231614
X-RAY DIFFRACTIONr_scangle_it2.6394.51390
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 139 -
Rwork0.216 2650 -
obs-2789 98.17 %

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