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- PDB-1pq4: Crystal structure of ZnuA -

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Basic information

Entry
Database: PDB / ID: 1pq4
TitleCrystal structure of ZnuA
Componentsperiplasmic binding protein component of an ABC type zinc uptake transporter
KeywordsMETAL BINDING PROTEIN / ZnuA / loop / metal-binding
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: 1.9 Å
AuthorsBanerjee, S. / Wei, B. / Bhattacharyya-Pakrasi, M. / Pakrasi, H.B. / Smith, T.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural Determinants of Metal Specificity in the Zinc Transport Protein ZnuA from Synechocystis 6803.
Authors: Banerjee, S. / Wei, B. / Bhattacharyya-Pakrasi, M. / Pakrasi, H.B. / Smith, T.J.
History
DepositionJun 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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: periplasmic binding protein component of an ABC type zinc uptake transporter
B: periplasmic binding protein component of an ABC type zinc uptake transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4224
Polymers64,2922
Non-polymers1312
Water4,324240
1
A: periplasmic binding protein component of an ABC type zinc uptake transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2112
Polymers32,1461
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: periplasmic binding protein component of an ABC type zinc uptake transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2112
Polymers32,1461
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.990, 78.300, 68.400
Angle α, β, γ (deg.)90.00, 118.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32145.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pET41a / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: potassium phosphate, ammonium sulfate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.5-2.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 1, 2003
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 47799 / Num. obs: 43019 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.9 Å / % possible all: 40
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 90 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 40 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.72 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1400440.66 / Data cutoff high rms absF: 1400440.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4124 9.6 %RANDOM
Rwork0.172 ---
all0.22 45789 --
obs0.172 42802 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.6337 Å2 / ksol: 0.398968 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å22.44 Å2
2--0.49 Å20 Å2
3----3.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 0 2 240 4197
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.417
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it3.161.5
X-RAY DIFFRACTIONc_mcangle_it4.222
X-RAY DIFFRACTIONc_scbond_it5.432
X-RAY DIFFRACTIONc_scangle_it7.622.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 258 5.8 %
Rwork0.224 4224 -
obs--57 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.82
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.52
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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