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- PDB-8zj8: Acinetobacter baumannii ModA with molybdate H2O2 -

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Basic information

Entry
Database: PDB / ID: 8zj8
TitleAcinetobacter baumannii ModA with molybdate H2O2
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: 1.44 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
B: Molybdate ABC transporter substrate-binding protein
C: Molybdate ABC transporter substrate-binding protein
D: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2788
Polymers106,6384
Non-polymers6404
Water17,997999
1
A: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8202
Polymers26,6601
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8202
Polymers26,6601
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8202
Polymers26,6601
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8202
Polymers26,6601
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.312, 73.773, 79.146
Angle α, β, γ (deg.)94.717, 107.431, 100.584
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Molybdate ABC transporter substrate-binding protein


Mass: 26659.617 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 48.82 %
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 S 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→33.52 Å / Num. obs: 167285 / % possible obs: 92.08 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.5
Reflection shellResolution: 1.44→1.49 Å / Rmerge(I) obs: 0.935 / Num. unique obs: 15781 / CC1/2: 0.743

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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→33.52 Å / SU ML: 0.2201 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 45.9002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3054 1836 1.11 %
Rwork0.276 163441 -
obs0.2763 165277 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.95 Å2
Refinement stepCycle: LAST / Resolution: 1.44→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 20 1000 8002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727167
X-RAY DIFFRACTIONf_angle_d1.04319737
X-RAY DIFFRACTIONf_chiral_restr0.09261126
X-RAY DIFFRACTIONf_plane_restr0.00631241
X-RAY DIFFRACTIONf_dihedral_angle_d5.4545974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.480.48261380.45811906X-RAY DIFFRACTION86.9
1.48-1.520.36241420.41712488X-RAY DIFFRACTION91.83
1.52-1.570.45871420.381512524X-RAY DIFFRACTION91.92
1.57-1.630.38711400.364312386X-RAY DIFFRACTION90.55
1.63-1.690.31711420.333212596X-RAY DIFFRACTION92.6
1.69-1.770.29431410.299712704X-RAY DIFFRACTION93.1
1.77-1.860.34461440.304512827X-RAY DIFFRACTION94.01
1.86-1.980.29981400.290612739X-RAY DIFFRACTION92.95
1.98-2.130.35511410.269512727X-RAY DIFFRACTION93.06
2.13-2.350.2771440.257412827X-RAY DIFFRACTION94
2.35-2.690.31681420.270112786X-RAY DIFFRACTION93.63
2.69-3.390.27311460.257912714X-RAY DIFFRACTION93.15
3.39-33.520.26181340.223112217X-RAY DIFFRACTION89.4
Refinement TLS params.Method: refined / Origin x: -8.46134178483 Å / Origin y: -18.748546306 Å / Origin z: -0.057443859619 Å
111213212223313233
T0.102693836329 Å20.0789960034453 Å20.0198323989477 Å2-0.205360012267 Å2-0.00218218974964 Å2--0.0944625560456 Å2
L0.421624146894 °2-0.156272152592 °20.0804303020327 °2-0.263469894673 °2-0.00929000231085 °2--0.619359972946 °2
S-0.0467463238538 Å °0.0404942193105 Å °-0.0114389015273 Å °0.0519365725805 Å °0.0483127847106 Å °0.00170858700614 Å °-0.0627686005405 Å °-0.0107827756823 Å °-0.00446667520018 Å °
Refinement TLS groupSelection details: all

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