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- PDB-3ue3: Crystal structure of Acinetobacter baumanni PBP3 -

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Basic information

Entry
Database: PDB / ID: 3ue3
TitleCrystal structure of Acinetobacter baumanni PBP3
ComponentsSeptum formation, penicillin binding protein 3, peptidoglycan synthetase
KeywordsTRANSFERASE / transpeptidase
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
Beta-Lactamase - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Peptidoglycan D,D-transpeptidase FtsI / 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 ...Beta-Lactamase - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Peptidoglycan D,D-transpeptidase FtsI / 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 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsHan, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Distinctive attributes of beta-lactam target proteins in Acinetobacter baumannii relevant to development of new antibiotics
Authors: Han, S. / Caspers, N. / Zaniewski, R.P. / Lacey, B.M. / Tomaras, A.P. / Feng, X. / Geoghegan, K.F. / Shanmugasundaram, V.
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septum formation, penicillin binding protein 3, peptidoglycan synthetase


Theoretical massNumber of molelcules
Total (without water)61,1671
Polymers61,1671
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.657, 89.707, 211.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Septum formation, penicillin binding protein 3, peptidoglycan synthetase


Mass: 61166.844 Da / Num. of mol.: 1 / Fragment: UNP residues 64-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter (bacteria) / Gene: ftsI, HMPREF0023_2561 / Production host: Escherichia coli (E. coli)
References: UniProt: C0VN42, peptidoglycan glycosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 4000, 0.1M Tris pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→105 Å / Num. obs: 33995 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 33.34 Å2
Reflection shellResolution: 2.3→2.39 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.9.6refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→38.32 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.8241 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1721 5.07 %RANDOM
Rwork0.217 ---
obs0.2187 33931 97.79 %-
Displacement parametersBiso mean: 34.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.5345 Å20 Å20 Å2
2--16.042 Å20 Å2
3----14.5075 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 0 165 3470
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013363HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.34552HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1173SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it3363HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion21.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3799SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2676 141 5.16 %
Rwork0.2114 2594 -
all0.2144 2735 -
obs--97.79 %
Refinement TLS params.Method: refined / Origin x: -10.7217 Å / Origin y: 15.5768 Å / Origin z: -42.8714 Å
111213212223313233
T-0.1734 Å2-0.0092 Å20.053 Å2--0.0047 Å2-0.007 Å2---0.0843 Å2
L0.6988 °20.1423 °20.0026 °2-1.6356 °2-0.4937 °2--0.7284 °2
S0.0983 Å °-0.1635 Å °0.0075 Å °0.0815 Å °-0.0593 Å °0.0215 Å °0.0094 Å °0.0097 Å °-0.039 Å °
Refinement TLS groupSelection details: { A|* }

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