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- PDB-8zj6: Acinetobacter baumannii ModA with molybdate DTT -

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Basic information

Entry
Database: PDB / ID: 8zj6
TitleAcinetobacter baumannii ModA with molybdate DTT
ComponentsMolybdate ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / molybdate bind protein / ModA / DTT / acinetobacter baumannii
Function / homologyMolybdate ABC transporter, substrate-binding protein / molybdate ion binding / : / Bacterial extracellular solute-binding protein / molybdate ion transport / outer membrane-bounded periplasmic space / metal ion binding / MOLYBDATE ION / Molybdate ABC transporter substrate-binding protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsWen, Y. / Jiao, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv
Title: Acinetobacter baumannii ModA
Authors: Wen, Y. / Jiao, M.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8202
Polymers26,6601
Non-polymers1601
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-2 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.628, 39.949, 79.301
Angle α, β, γ (deg.)90.000, 109.436, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

21A-654-

HOH

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Components

#1: Protein Molybdate ABC transporter substrate-binding protein


Mass: 26659.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: modA, ATCC19606_17990 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6F8TFE1
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate pH 4.6, 30% polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.39→33.56 Å / Num. obs: 50299 / % possible obs: 97.98 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.31 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.7
Reflection shellResolution: 1.39→1.44 Å / Rmerge(I) obs: 0.738 / Num. unique obs: 19214 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Y

2h5y


Resolution: 1.39→33.56 Å / SU ML: 0.1789 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.0874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1935 1957 3.9 %
Rwork0.162 48166 -
obs0.1632 50123 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.43 Å2
Refinement stepCycle: LAST / Resolution: 1.39→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 5 300 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551788
X-RAY DIFFRACTIONf_angle_d0.86992432
X-RAY DIFFRACTIONf_chiral_restr0.0865282
X-RAY DIFFRACTIONf_plane_restr0.0058311
X-RAY DIFFRACTIONf_dihedral_angle_d5.4935244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.48721240.49132977X-RAY DIFFRACTION85.73
1.42-1.460.34781350.30043384X-RAY DIFFRACTION96.73
1.46-1.510.24831380.22083422X-RAY DIFFRACTION98.94
1.51-1.550.23421410.20393470X-RAY DIFFRACTION99.2
1.55-1.610.25091400.20653451X-RAY DIFFRACTION99.09
1.61-1.670.23071420.16633493X-RAY DIFFRACTION99.37
1.67-1.750.21321390.15223490X-RAY DIFFRACTION99.51
1.75-1.840.1751420.13593468X-RAY DIFFRACTION99.59
1.84-1.960.16411420.13553471X-RAY DIFFRACTION99.42
1.96-2.110.21351430.14473499X-RAY DIFFRACTION99.4
2.11-2.320.18581420.1453499X-RAY DIFFRACTION99.45
2.32-2.660.17461440.16443520X-RAY DIFFRACTION99.19
2.66-3.350.1881430.16333520X-RAY DIFFRACTION99.3
3.35-33.560.17721420.15183502X-RAY DIFFRACTION96.53

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