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- PDB-8zpc: Acinetobacter baumannii Penicillin-Binding Protein 2 -

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Basic information

Entry
Database: PDB / ID: 8zpc
TitleAcinetobacter baumannii Penicillin-Binding Protein 2
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsHYDROLASE / Penicllin-Binding Protein 2 / PBP2
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / zinc ion binding / plasma membrane
Similarity search - Function
Penicillin-binding protein 2 / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.313 Å
AuthorsJang, H.S. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Fully closed conformation of penicillin-binding protein revealed by structure of PBP2 from Acinetobacter baumannii.
Authors: Jang, H. / Kim, C.M. / Hong, E. / Park, H.H.
History
DepositionMay 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase MrdA
B: Peptidoglycan D,D-transpeptidase MrdA


Theoretical massNumber of molelcules
Total (without water)139,3212
Polymers139,3212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.436, 151.531, 177.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2


Mass: 69660.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: pbpA, ftsI_2, mrdA, A7M90_11050, ABR2091_1008, APD17_02520, AUO97_12320, B9W25_14295, CAS83_05900, CBE85_06915, CV954_014345, EA706_11320, EA722_01945, F4T85_05015, FJU42_01870, G3N53_08595, ...Gene: pbpA, ftsI_2, mrdA, A7M90_11050, ABR2091_1008, APD17_02520, AUO97_12320, B9W25_14295, CAS83_05900, CBE85_06915, CV954_014345, EA706_11320, EA722_01945, F4T85_05015, FJU42_01870, G3N53_08595, GSE42_05635, IAG11_14580, IMO23_05010, ITE13_01515, JHZ39_003244, P9867_04120, SAMEA104305318_00781, SAMEA4394745_02684
Production host: Escherichia coli (E. coli)
References: UniProt: G1C6X4, serine-type D-Ala-D-Ala carboxypeptidase
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: 2.92 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG 2000 MME, 100 mM Sodium acetate/ Acetic acid pH 5.5, 200 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.313→47.381 Å / Num. obs: 24479 / % possible obs: 99.14 % / Redundancy: 12.9 % / Biso Wilson estimate: 48.52 Å2 / CC1/2: 0.984 / Net I/σ(I): 9.6
Reflection shellResolution: 3.313→3.432 Å / Num. unique obs: 2241 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.313→47.381 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2484 1212 4.95 %
Rwork0.1952 --
obs0.1979 24467 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.313→47.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8038 0 0 0 8038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118227
X-RAY DIFFRACTIONf_angle_d1.29511148
X-RAY DIFFRACTIONf_dihedral_angle_d7.5014890
X-RAY DIFFRACTIONf_chiral_restr0.0691211
X-RAY DIFFRACTIONf_plane_restr0.0091445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3132-3.44580.31581240.23432407X-RAY DIFFRACTION94
3.4458-3.60260.25921430.20262548X-RAY DIFFRACTION100
3.6026-3.79250.30571450.19892567X-RAY DIFFRACTION100
3.7925-4.030.21391230.18772579X-RAY DIFFRACTION100
4.03-4.34090.23221140.17072616X-RAY DIFFRACTION100
4.3409-4.77740.22111360.17182569X-RAY DIFFRACTION100
4.7774-5.46780.22361420.18382615X-RAY DIFFRACTION100
5.4678-6.88550.26721500.21722621X-RAY DIFFRACTION100
6.8855-47.3810.24141350.20812733X-RAY DIFFRACTION100

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