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- PDB-2osv: Crystal Structure of ZnuA from E. coli -

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Basic information

Entry
Database: PDB / ID: 2osv
TitleCrystal Structure of ZnuA from E. coli
ComponentsHigh-affinity zinc uptake system protein znuA
KeywordsMETAL TRANSPORT / protein-zinc complex
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 / sad / Resolution: 1.75 Å
AuthorsLi, H. / Jogl, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Zinc-binding Transport Protein ZnuA from Escherichia coli Reveals an Unexpected Variation in Metal Coordination.
Authors: Li, H. / Jogl, G.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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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)62,4854
Polymers62,3542
Non-polymers1312
Water10,737596
1
A: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2432
Polymers31,1771
Non-polymers651
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)31,2432
Polymers31,1771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.980, 87.985, 86.728
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 / Fragment: active form (N-terminal signal peptide cleaved) / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 Star / References: UniProt: P39172
#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.: 596 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100mM sodium acetate, 25% PEG 3350, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 56935 / % possible obs: 99.92 % / Observed criterion σ(F): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.3
Reflection shellResolution: 1.75→1.795 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.9 / Num. unique all: 4156 / % possible all: 99.8

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Phasing

PhasingMethod: sad
Phasing MADD res high: 1.7 Å / D res low: 30 Å / FOM : 0.3 / Reflection: 60659
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se17.0920.3730.5780.0930.413
2Se20.1040.6040.4180.0560.414
3Se25.6620.6530.360.0850.431
4Se19.6950.2940.0560.1880.397
5Se21.8550.7290.9490.1440.416
6Se21.5170.6230.3780.1990.385
7Se17.2310.2680.5580.0020.376
8Se18.8290.3640.620.2290.444
9Se14.8280.2790.6750.0970.247
10Se26.9140.3280.6390.1240.432
11Se22.2470.2020.0620.0410.298
12Se17.6390.7040.3250.060.227
13Se32.8720.40.2930.0010.18
Phasing MAD shell
Resolution (Å)FOM Reflection
6.13-300.433010
3.86-6.130.455145
3.02-3.860.436486
2.56-3.020.47601
2.26-2.560.348541
2.05-2.260.279421
1.88-2.050.29954
1.75-1.880.1410501

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVE2.11phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.54 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2868 5 %RANDOM
Rwork0.175 ---
all0.177 ---
obs-56935 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.59 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 2 596 4636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224202
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9735714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31224.884172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86515721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4231518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023166
X-RAY DIFFRACTIONr_nbd_refined0.2040.22177
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22949
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2480
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.233
X-RAY DIFFRACTIONr_mcbond_it0.7641.52741
X-RAY DIFFRACTIONr_mcangle_it1.15724325
X-RAY DIFFRACTIONr_scbond_it2.20331621
X-RAY DIFFRACTIONr_scangle_it3.64.51389
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 203 -
Rwork0.197 3953 -
obs-4156 99.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.94350.0319-0.39241.09850.42751.3255-0.01720.016-0.02330.0466-0.00120.0919-0.0266-0.03560.0184-0.03450.0020.0132-0.03890.0076-0.034748.231938.900115.0354
20.7278-0.5102-1.37261.66322.26044.26030.061-0.06230.1205-0.04340.0587-0.0105-0.13610.184-0.1197-0.0259-0.02780.0071-0.0219-0.007-0.030962.756747.67357.852
30.60420.2191-0.14531.84980.78521.353-0.08970.0128-0.0403-0.02150.055-0.01410.17170.07670.0347-0.01740.00020.02-0.0283-0.0007-0.042760.518526.4025-0.9339
40.83280.05740.50071.290.40161.482-0.0120.04450.0246-0.0950.00650.0475-0.0089-0.07890.0056-0.0469-0.00860.0028-0.02950.0079-0.026848.78877.176523.9416
51.38351.11762.43711.67922.55035.53560.06950.0706-0.20040.04160.0688-0.1170.15530.1618-0.1383-0.04370.03530.0052-0.04330.00220.009764.6765-3.344631.2175
61.037-0.34350.39131.46080.44521.5346-0.1183-0.04750.09620.12580.0501-0.1167-0.12210.02630.0682-0.0349-0.0018-0.0228-0.04250.0055-0.011761.824817.547541.0936
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA45 - 1351 - 91
21AA157 - 184113 - 140
32AA185 - 220141 - 176
43AA221 - 327177 - 283
54BB45 - 1361 - 92
75BB185 - 220141 - 176
86BB221 - 327177 - 283

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