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- PDB-3udf: Crystal structure of Apo PBP1a from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 3udf
TitleCrystal structure of Apo PBP1a from Acinetobacter baumannii
ComponentsPenicillin-binding protein 1a
KeywordsPenicillin-binding protein / transglycosylase / transpeptidase
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
Penicillin-binding protein 1A
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)164,5556
Polymers163,7742
Non-polymers7814
Water16,646924
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-18 kcal/mol
Surface area50430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.870, 243.000, 49.400
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 / Fragment: UNP residues 50-764
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEGMME, 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: 1.7→243 Å / Num. obs: 153704 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 26.49 Å2
Reflection shellResolution: 1.7→1.79 Å / % possible all: 76.3

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Processing

Software
NameVersionClassification
autoPROCdata collection
SHARPphasing
BUSTER2.9.6refinement
autoPROCdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→24.89 Å / Cor.coef. Fo:Fc: 0.9588 / Cor.coef. Fo:Fc free: 0.9505 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 7659 5 %RANDOM
Rwork0.1766 ---
obs0.1777 153066 96.72 %-
Displacement parametersBiso mean: 34.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.8179 Å20 Å20 Å2
2--2.4562 Å20 Å2
3----1.6383 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9417 0 48 924 10389
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019694HARMONIC2
X-RAY DIFFRACTIONt_angle_deg113149HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3315SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes241HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1403HARMONIC5
X-RAY DIFFRACTIONt_it9694HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion16.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1247SEMIHARMONIC5
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_contact12064SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2624 343 4.89 %
Rwork0.2406 6676 -
all0.2417 7019 -
obs--96.72 %
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)
10.0011-0.3956-0.01641.40330.0260-0.0221-0.0436-0.0327-0.00860.0344-0.14420.01120.0041-0.0124-0.04630.0051-0.0247-0.03920.01850.030691.209100.140.5453
20.3436-0.02790.03420.4312-0.19630.37390.0086-0.03610.11060.01570.01130.0102-0.0043-0.0261-0.0199-0.04230.0067-0.0005-0.0459-0.0146-0.066478.507847.20459.681
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|737 }B27 - 737

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