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- PDB-8zj9: Acinetobacter baumannii ModA with tungstate DTT -

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Basic information

Entry
Database: PDB / ID: 8zj9
TitleAcinetobacter baumannii ModA with tungstate DTT
ComponentsMolybdate ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / Metal Binding / ModA / 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 / TUNGSTATE(VI)ION / Molybdate ABC transporter substrate-binding protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWen, Y. / Jiao, M.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
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)26,9072
Polymers26,6601
Non-polymers2481
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-2 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.591, 40.010, 79.261
Angle α, β, γ (deg.)90.000, 109.494, 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-535-

HOH

21A-675-

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-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 48.74 %
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: 1.35→31.39 Å / Num. obs: 328310 / % possible obs: 92.33 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.59 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 1.35→1.44 Å / Num. unique obs: 16352 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZJ6

8zj6


Resolution: 1.35→31.39 Å / SU ML: 0.1077 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8266
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1952 1842 3.57 %
Rwork0.1671 49805 -
obs0.168 51647 92.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 1.35→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 5 333 2076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781781
X-RAY DIFFRACTIONf_angle_d0.96352420
X-RAY DIFFRACTIONf_chiral_restr0.1016282
X-RAY DIFFRACTIONf_plane_restr0.0049308
X-RAY DIFFRACTIONf_dihedral_angle_d5.6079242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.2998890.27972431X-RAY DIFFRACTION58.62
1.38-1.430.24161180.22563049X-RAY DIFFRACTION74.12
1.43-1.470.22791400.19383808X-RAY DIFFRACTION92.31
1.47-1.520.18371430.16473992X-RAY DIFFRACTION96.34
1.52-1.580.1841490.16893976X-RAY DIFFRACTION96.47
1.59-1.660.22771480.17313985X-RAY DIFFRACTION96.95
1.66-1.740.19511480.17144054X-RAY DIFFRACTION97.09
1.74-1.850.18221480.16384036X-RAY DIFFRACTION97.64
1.85-20.16421510.15224047X-RAY DIFFRACTION97.65
2-2.20.18651500.16074074X-RAY DIFFRACTION97.73
2.2-2.520.18591520.17484102X-RAY DIFFRACTION98.11
2.52-3.170.19161520.1764112X-RAY DIFFRACTION98.02
3.17-31.390.20361540.1544139X-RAY DIFFRACTION96.36

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