+Open data
-Basic information
Entry | Database: PDB / ID: 7zg8 | ||||||||||||||||||
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Title | Crystal structure of A. baumannii penicillin-binding protein 2 | ||||||||||||||||||
Components | Peptidoglycan D,D-transpeptidase MrdA | ||||||||||||||||||
Keywords | HYDROLASE / Peptidoglycan D / D-transpeptidase | ||||||||||||||||||
Function / homology | Function and homology information 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 / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||||||||||||||
Authors | Micelli, C. / Crow, A. / Roper, D.I. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: A conserved zinc-binding site in Acinetobacter baumannii PBP2 required for elongasome-directed bacterial cell shape. Authors: Micelli, C. / Dai, Y. / Raustad, N. / Isberg, R.R. / Dowson, C.G. / Lloyd, A.J. / Geisinger, E. / Crow, A. / Roper, D.I. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zg8.cif.gz | 226.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zg8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7zg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zg8_validation.pdf.gz | 446.4 KB | Display | wwPDB validaton report |
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Full document | 7zg8_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 7zg8_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 7zg8_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/7zg8 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/7zg8 | HTTPS FTP |
-Related structure data
Related structure data | 5lp4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 62 - 615 / Label seq-ID: 32 - 585
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 70770.969 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, Aba9201_18945, ABKPCSM17A_03355, ABR2091_1008, APC21_12345, AUO97_12320, AYR68_04860, B7L45_13860, BAA1790NC_2670, BS065_13515, C5H40_15225, CBE85_06915, CBL15_ ...Gene: pbpA, ftsI_2, mrdA, A7M90_11050, Aba9201_18945, ABKPCSM17A_03355, ABR2091_1008, APC21_12345, AUO97_12320, AYR68_04860, B7L45_13860, BAA1790NC_2670, BS065_13515, C5H40_15225, CBE85_06915, CBL15_12940, CPI82_12065, CTZ19_13825, D8O08_019760, DLI71_06110, DLI72_10975, DVA69_07035, E2532_18440, E2533_01825, E2534_02130, E2535_02530, E2536_16000, E2538_02065, E2539_12745, E2540_02675, E2541_02210, EA706_11320, EA720_005325, EA722_01945, EGM95_15605, EKS29_18090, EP550_13800, EP560_04330, EQH48_13445, F4T85_05015, F4T91_06035, FDN00_07050, FE003_14290, FJU36_11640, FJU42_01870, FR761_06255, G3N53_08595, GSE42_05635, H0529_10125, HBK86_03170, IAG11_14580, IMO23_05010, ITE13_01515, SAMEA104305281_03511, SAMEA104305318_00781, SAMEA104305385_03293, SI89_19130 Production host: Escherichia coli (E. coli) References: UniProt: G1C6X4, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M Na2HPO4 adjusted to pH 4.2 with citric acid, 16% (v/v) ethanol, and 5% (w/v) PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→44.34 Å / Num. obs: 46823 / % possible obs: 98.7 % / Redundancy: 9.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.065 / Rrim(I) all: 0.213 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 2 / Num. unique obs: 4576 / CC1/2: 0.754 / Rpim(I) all: 0.36 / Rrim(I) all: 1.167 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LP4 Resolution: 2.65→44.334 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.179 / SU B: 17.42 / SU ML: 0.316 / Average fsc free: 0.7923 / Average fsc work: 0.8029 / Cross valid method: FREE R-VALUE / ESU R: 0.48 / ESU R Free: 0.294 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.653 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→44.334 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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