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- PDB-8zja: Acinetobacter baumannii ModA with tungstate H2O2 -

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Basic information

Entry
Database: PDB / ID: 8zja
TitleAcinetobacter baumannii ModA with tungstate H2O2
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: 1.44 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
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-2 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.112, 39.727, 79.352
Angle α, β, γ (deg.)90.000, 109.349, 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-601-

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.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 48.79 %
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 PILATUS 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: 1.44→33.64 Å / Num. obs: 299495 / % possible obs: 98.52 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.91 / Net I/σ(I): 9.6
Reflection shellResolution: 1.44→1.49 Å / Num. unique obs: 23859 / CC1/2: 0.998

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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: 1.44→33.64 Å / SU ML: 0.1608 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.3328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 1969 4.34 %
Rwork0.1767 43444 -
obs0.1771 45413 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.06 Å2
Refinement stepCycle: LAST / Resolution: 1.44→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 5 307 2041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01041772
X-RAY DIFFRACTIONf_angle_d1.14442408
X-RAY DIFFRACTIONf_chiral_restr0.0932281
X-RAY DIFFRACTIONf_plane_restr0.008306
X-RAY DIFFRACTIONf_dihedral_angle_d5.6554241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.480.41741350.3732974X-RAY DIFFRACTION95.99
1.48-1.520.30751400.27543079X-RAY DIFFRACTION99.08
1.52-1.560.23221380.25863073X-RAY DIFFRACTION98.65
1.56-1.610.23861380.23743090X-RAY DIFFRACTION98.66
1.61-1.670.22941410.21083093X-RAY DIFFRACTION98.18
1.67-1.740.19631410.20153105X-RAY DIFFRACTION98.72
1.74-1.810.18841410.18773105X-RAY DIFFRACTION99.24
1.81-1.910.19581410.18073111X-RAY DIFFRACTION99.27
1.91-2.030.19661390.17323109X-RAY DIFFRACTION99.3
2.03-2.190.15851430.16053134X-RAY DIFFRACTION99.27
2.19-2.410.15941430.163159X-RAY DIFFRACTION99.31
2.41-2.750.18121400.16723114X-RAY DIFFRACTION98.61
2.75-3.470.19111430.17513144X-RAY DIFFRACTION98.5
3.47-33.640.16031460.15233154X-RAY DIFFRACTION96.63
Refinement TLS params.Method: refined / Origin x: -2.51817353951 Å / Origin y: -0.175930160904 Å / Origin z: 16.3591445347 Å
111213212223313233
T0.18406413888 Å20.0332952116955 Å2-0.00635126421746 Å2-0.153602841369 Å20.00622377815759 Å2--0.168378339775 Å2
L1.4299365109 °2-0.0504001254429 °2-0.0708769686035 °2-0.492343072435 °20.175232282099 °2--1.34609444524 °2
S-0.019929840941 Å °-0.0964659442015 Å °-0.0488261875691 Å °0.0462162765045 Å °-0.00715075195818 Å °0.00503356054502 Å °0.0664851952188 Å °-0.0522613335946 Å °0.010535186056 Å °
Refinement TLS groupSelection details: all

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