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- PDB-3udi: Crystal structure of Acinetobacter baumannii PBP1a in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3udi
TitleCrystal structure of Acinetobacter baumannii PBP1a in complex with penicillin G
ComponentsPenicillin-binding protein 1a
KeywordsPenicillin-binding protein/ANTIBIOTIC / Transglycosylase / transpeptidase / Penicillin-binding protein-ANTIBIOTIC complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Nucleic acid-binding proteins / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Nucleic acid-binding proteins / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
OPEN FORM - PENICILLIN G / Penicillin-binding protein 1A
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1a
B: Penicillin-binding protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,4474
Polymers163,7742
Non-polymers6732
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-21 kcal/mol
Surface area49330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.000, 242.680, 49.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Penicillin-binding protein 1a


Mass: 81886.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ponA / Production host: Escherichia coli (E. coli) / References: UniProt: G1C794
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G / Benzylpenicillin


Mass: 336.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEGMME 5000, 0.1M MES pH 6.5, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: May 21, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→121 Å / Num. obs: 41207 / % possible obs: 91.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 61.38 Å2
Reflection shellResolution: 2.6→2.67 Å / % possible all: 78.3

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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: 2.6→48.08 Å / Cor.coef. Fo:Fc: 0.9392 / Cor.coef. Fo:Fc free: 0.9001 / SU R Cruickshank DPI: 1.045 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 2060 5.01 %RANDOM
Rwork0.1874 ---
obs0.1905 41143 91.7 %-
Displacement parametersBiso mean: 75.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.8236 Å20 Å20 Å2
2--5.2635 Å20 Å2
3----10.0871 Å2
Refine analyzeLuzzati coordinate error obs: 0.412 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9457 0 46 223 9726
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019730HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1713206HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3337SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes243HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1409HARMONIC5
X-RAY DIFFRACTIONt_it9730HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion20.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1257SEMIHARMONIC5
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_contact11278SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2803 120 4.73 %
Rwork0.217 2416 -
all0.2198 2536 -
obs--91.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.332-0.5824-0.18433.1582-0.03230.0106-0.1054-0.0753-0.2830.39820.13850.31210.0182-0.0293-0.03310.05690.0544-0.0178-0.2951-0.02140.280826.71321.84350.7761
21.53770.91690.05082.15920.3020.8650.2368-0.1428-0.16970.2846-0.0560.0087-0.19710.0167-0.18080.1203-0.03340.0403-0.28760.0341-0.392538.820474.25488.8738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|27 - A|735 }A27 - 735
2X-RAY DIFFRACTION2{ B|27 - B|733 }B27 - 733

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