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- PDB-3tg9: The crystal structure of penicillin binding protein from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 3tg9
TitleThe crystal structure of penicillin binding protein from Bacillus halodurans
ComponentsPenicillin-binding protein
Keywordspenicillin binding protein / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Z. / Satyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. ...Zhang, Z. / Satyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: The crystal structure of penicillin binding protein from Bacillus halodurans
Authors: Zhang, Z. / Satyanarayana, L. / Almo, S.C. / Swaminathan, S.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Penicillin-binding protein
B: Penicillin-binding protein


Theoretical massNumber of molelcules
Total (without water)80,7692
Polymers80,7692
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-10 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.241, 79.800, 74.443
Angle α, β, γ (deg.)90.00, 100.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Penicillin-binding protein


Mass: 40384.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2267 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIP / References: UniProt: Q9KAM0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, 0.8% 1,4- butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38211 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.5 / Num. unique all: 3781 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QMI

2qmi


Resolution: 2.2→49.999 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.19 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1852 5.01 %RANDOM
Rwork0.1929 ---
obs0.1948 36966 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.334 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4378 Å20 Å2-18.7625 Å2
2---7.1143 Å2-0 Å2
3---9.9797 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 0 267 5404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065295
X-RAY DIFFRACTIONf_angle_d1.0387200
X-RAY DIFFRACTIONf_dihedral_angle_d17.5231823
X-RAY DIFFRACTIONf_chiral_restr0.074766
X-RAY DIFFRACTIONf_plane_restr0.004925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1998-2.25930.31481370.23392468X-RAY DIFFRACTION89
2.2593-2.32580.27131450.21052555X-RAY DIFFRACTION92
2.3258-2.40080.25681340.19592624X-RAY DIFFRACTION94
2.4008-2.48660.27711230.21092648X-RAY DIFFRACTION95
2.4866-2.58620.31631320.20082667X-RAY DIFFRACTION96
2.5862-2.70390.26141260.2152720X-RAY DIFFRACTION97
2.7039-2.84640.28591520.21372722X-RAY DIFFRACTION98
2.8464-3.02470.25921320.22052743X-RAY DIFFRACTION98
3.0247-3.25820.28151410.2112781X-RAY DIFFRACTION99
3.2582-3.5860.21551560.19242766X-RAY DIFFRACTION99
3.586-4.10470.20091470.17292787X-RAY DIFFRACTION100
4.1047-5.17070.17621630.15252794X-RAY DIFFRACTION100
5.1707-50.01140.18411640.17972839X-RAY DIFFRACTION99

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