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- PDB-7t4z: Crystal structure of the molybdate-binding periplasmic protein Mo... -

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Basic information

Entry
Database: PDB / ID: 7t4z
TitleCrystal structure of the molybdate-binding periplasmic protein ModA from the bacteria Pseudomonsa aeruginosa in ligand-free form
ComponentsMolybdate-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / Molybdate-binding periplasmic protein
Function / homologyAMMONIUM ION
Function and homology information
Biological speciesPseudomonas aeruginosa PA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsNgu, D.H.Y. / Luo, Z. / Lim, B.Y.J. / Kobe, B.
Funding support Australia, 7items
OrganizationGrant numberCountry
Australian Research Council (ARC)LE170100200 Australia
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1122582 Australia
National Health and Medical Research Council (NHMRC, Australia)1180826 Australia
Australian Research Council (ARC)DP170102102 Australia
Australian Research Council (ARC)FL180100109 Australia
Australian Research Council (ARC)FT170100006 Australia
CitationJournal: Front Microbiol / Year: 2022
Title: The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis.
Authors: Maunders, E.A. / Ngu, D.H.Y. / Ganio, K. / Hossain, S.I. / Lim, B.Y.J. / Leeming, M.G. / Luo, Z. / Tan, A. / Deplazes, E. / Kobe, B. / McDevitt, C.A.
History
DepositionDec 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdate-binding periplasmic protein
B: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0616
Polymers48,7592
Non-polymers3024
Water5,008278
1
A: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4903
Polymers24,3791
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5723
Polymers24,3791
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.492, 128.908, 67.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

21B-419-

HOH

31B-493-

HOH

41B-533-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 24 through 124 or resid 126 through 172 or resid 174 through 251))
d_2ens_1(chain "B" and (resid 24 through 124 or resid 126 through 172 or resid 174 through 251))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPLYSA2 - 102
d_12ens_1GLYTYRA104 - 150
d_13ens_1PHELEUA152 - 229
d_21ens_1ASPLYSD1 - 101
d_22ens_1GLYTYRD103 - 149
d_23ens_1PHELEUD151 - 228

NCS oper: (Code: givenMatrix: (0.529418366487, 0.785485412688, -0.320513431356), (0.750580081135, -0.609770766846, -0.254576420164), (-0.395405785276, -0.105793564803, -0.912393548101)Vector: -13. ...NCS oper: (Code: given
Matrix: (0.529418366487, 0.785485412688, -0.320513431356), (0.750580081135, -0.609770766846, -0.254576420164), (-0.395405785276, -0.105793564803, -0.912393548101)
Vector: -13.4274801972, 22.8852273588, -9.80310275734)

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Components

#1: Protein Molybdate-binding periplasmic protein


Mass: 24379.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA1 (bacteria) / Strain: Laboratory strain PAO1 / Gene: modA / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M sodium citrate pH 3.5, 2.0 M ammonium sulfate, 25% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.78→46.68 Å / Num. obs: 44640 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 16.7
Reflection shellResolution: 1.78→1.82 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2473 / CC1/2: 0.896 / CC star: 0.972 / Rpim(I) all: 0.214 / Rrim(I) all: 0.562 / % possible all: 98.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATG

1atg


Resolution: 1.78→46.68 Å / SU ML: 0.2092 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 2207 4.95 %
Rwork0.1873 42413 -
obs0.1884 44620 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.62 Å2
Refinement stepCycle: LAST / Resolution: 1.78→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 17 278 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773511
X-RAY DIFFRACTIONf_angle_d0.96974770
X-RAY DIFFRACTIONf_chiral_restr0.0595535
X-RAY DIFFRACTIONf_plane_restr0.0081620
X-RAY DIFFRACTIONf_dihedral_angle_d12.48261245
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.45179149106 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.32241300.27952588X-RAY DIFFRACTION98.37
1.82-1.870.30131350.23522607X-RAY DIFFRACTION100
1.87-1.910.27031290.20032635X-RAY DIFFRACTION100
1.91-1.960.20851450.18012615X-RAY DIFFRACTION100
1.96-2.020.21181360.17842610X-RAY DIFFRACTION100
2.02-2.090.22441490.18252620X-RAY DIFFRACTION100
2.09-2.160.20881400.18582627X-RAY DIFFRACTION100
2.16-2.250.22081470.18382654X-RAY DIFFRACTION100
2.25-2.350.20911240.17372635X-RAY DIFFRACTION100
2.35-2.470.21931330.18652653X-RAY DIFFRACTION100
2.47-2.630.21871460.18372640X-RAY DIFFRACTION99.96
2.63-2.830.19881300.20142669X-RAY DIFFRACTION100
2.83-3.120.23321370.20582658X-RAY DIFFRACTION99.96
3.12-3.570.21141530.18162667X-RAY DIFFRACTION100
3.57-4.490.16831340.15842717X-RAY DIFFRACTION100
4.49-46.680.19481390.19462818X-RAY DIFFRACTION99.76

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