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- PDB-7rcj: Crystal structure of ZnuA from Citrobacter koseri -

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Basic information

Entry
Database: PDB / ID: 7rcj
TitleCrystal structure of ZnuA from Citrobacter koseri
ComponentsHigh-affinity zinc uptake system protein ZnuA
KeywordsMETAL BINDING PROTEIN / zinc / transport / solute binding protein
Function / homologyHigh-affinity zinc uptake system protein ZnuA / zinc ion transport / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / cell adhesion / metal ion binding / 6-tungstotellurate(VI) / High-affinity zinc uptake system protein ZnuA
Function and homology information
Biological speciesCitrobacter koseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsYukl, E.T. / Yekwa, E.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM122819-01A1 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Conformational flexibility in the zinc solute-binding protein ZnuA.
Authors: Yekwa, E.L. / Serrano, F.A. / Yukl, E.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: High-affinity zinc uptake system protein ZnuA
D: High-affinity zinc uptake system protein ZnuA
E: High-affinity zinc uptake system protein ZnuA
F: High-affinity zinc uptake system protein ZnuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,83515
Polymers206,5996
Non-polymers5,2369
Water00
1
A: High-affinity zinc uptake system protein ZnuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4992
Polymers34,4331
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: High-affinity zinc uptake system protein ZnuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1133
Polymers34,4331
Non-polymers1,6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: High-affinity zinc uptake system protein ZnuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4992
Polymers34,4331
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: High-affinity zinc uptake system protein ZnuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1133
Polymers34,4331
Non-polymers1,6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: High-affinity zinc uptake system protein ZnuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4992
Polymers34,4331
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: High-affinity zinc uptake system protein ZnuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1133
Polymers34,4331
Non-polymers1,6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.246, 81.667, 126.555
Angle α, β, γ (deg.)90.000, 112.990, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-402-

TEW

21D-402-

TEW

31F-402-

TEW

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA27 - 31332 - 315
21GLYGLYBB27 - 31332 - 315
12GLYGLYAA27 - 31332 - 315
22GLYGLYCC27 - 31332 - 315
13LYSLYSAA27 - 31232 - 314
23LYSLYSDD27 - 31232 - 314
14LYSLYSAA27 - 31232 - 314
24LYSLYSEE27 - 31232 - 314
15GLYGLYAA27 - 31332 - 315
25GLYGLYFF27 - 31332 - 315
16GLYGLYBB27 - 31332 - 315
26GLYGLYCC27 - 31332 - 315
17GLYGLYBB27 - 31332 - 315
27GLYGLYDD27 - 31332 - 315
18GLYGLYBB27 - 31332 - 315
28GLYGLYEE27 - 31332 - 315
19GLYGLYBB27 - 31332 - 315
29GLYGLYFF27 - 31332 - 315
110LYSLYSCC27 - 31232 - 314
210LYSLYSDD27 - 31232 - 314
111LYSLYSCC27 - 31232 - 314
211LYSLYSEE27 - 31232 - 314
112GLYGLYCC27 - 31332 - 315
212GLYGLYFF27 - 31332 - 315
113ASPASPDD27 - 31432 - 316
213ASPASPEE27 - 31432 - 316
114LYSLYSDD27 - 31232 - 314
214LYSLYSFF27 - 31232 - 314
115LYSLYSEE27 - 31232 - 314
215LYSLYSFF27 - 31232 - 314

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 34433.094 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (bacteria)
Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_01106 / Production host: Escherichia coli (E. coli) / References: UniProt: A8AFI6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O24TeW6
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein at 18 mg/mL and containing one molar equivalent of ZnCl2 was combined with an equal volume of reservoir solution containing 0.1 M sodium citrate pH 6.0, 0.05 M ammonium acetate, 1 mM ...Details: Protein at 18 mg/mL and containing one molar equivalent of ZnCl2 was combined with an equal volume of reservoir solution containing 0.1 M sodium citrate pH 6.0, 0.05 M ammonium acetate, 1 mM tellurium polyoxo tungstate, and 26% w/v PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2021
RadiationMonochromator: Single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 3.15→47.47 Å / Num. obs: 39993 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.131 / Rrim(I) all: 0.257 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.15-3.283.71.6921667244890.3391.0021.9720.899.8
11.36-47.423.40.03230138850.9980.020.03828.497.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XY4

2xy4


Resolution: 3.15→47.47 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 23.58 / SU ML: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 2006 5 %RANDOM
Rwork0.2173 ---
obs0.2191 37978 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 434.74 Å2 / Biso min: 46 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å22.98 Å2
2--1.25 Å20 Å2
3----1.48 Å2
Refinement stepCycle: final / Resolution: 3.15→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 99 0 12243
Biso mean--290.01 --
Num. residues----1581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912510
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212078
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.99517184
X-RAY DIFFRACTIONr_angle_other_deg1.1043.00127804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.751569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02424.798519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.236152097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9591554
X-RAY DIFFRACTIONr_chiral_restr0.0850.21899
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114001
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022685
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A168930.03
12B168930.03
21A167510.04
22C167510.04
31A168020.04
32D168020.04
41A168530.03
42E168530.03
51A168150.04
52F168150.04
61B168460.04
62C168460.04
71B168660.04
72D168660.04
81B168760.04
82E168760.04
91B168350.04
92F168350.04
101C167920.04
102D167920.04
111C167270.05
112E167270.05
121C168710.03
122F168710.03
131D168640.04
132E168640.04
141D168590.04
142F168590.04
151E168080.04
152F168080.04
LS refinement shellResolution: 3.15→3.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 144 -
Rwork0.365 2771 -
all-2915 -
obs--99.42 %

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