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- PDB-3dwk: Identification of Dynamic Structural Motifs Involved in Peptidogl... -

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Basic information

Entry
Database: PDB / ID: 3dwk
TitleIdentification of Dynamic Structural Motifs Involved in Peptidoglycan Glycosyltransfer
ComponentsPenicillin-binding protein 2
KeywordsTRANSFERASE / lysozyme-fold transpeptidase fold pi-helix / Cell shape / Cell wall biogenesis/degradation / Membrane / Peptidoglycan synthesis
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 / membrane => GO:0016020
Similarity search - Function
Penicillin-binding protein 2a (Domain 2) - #20 / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase ...Penicillin-binding protein 2a (Domain 2) - #20 / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DD-transpeptidase / DD-transpeptidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsLovering, A.L. / De Castro, L. / Strynadka, N.C.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Identification of dynamic structural motifs involved in peptidoglycan glycosyltransfer.
Authors: Lovering, A.L. / De Castro, L. / Strynadka, N.C.
History
DepositionJul 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 2
B: Penicillin-binding protein 2
C: Penicillin-binding protein 2
D: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,15651
Polymers278,5084
Non-polymers4,64847
Water0
1
A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,06816
Polymers69,6271
Non-polymers1,44115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,87614
Polymers69,6271
Non-polymers1,24913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,49110
Polymers69,6271
Non-polymers8659
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,72111
Polymers69,6271
Non-polymers1,09410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.352, 217.471, 95.735
Angle α, β, γ (deg.)90.000, 90.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Penicillin-binding protein 2


Mass: 69626.914 Da / Num. of mol.: 4 / Fragment: PBP2 (UNP residues 68-692)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pbp2, SACOL1490 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5HFX3, UniProt: Q8KHY3*PLUS
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM

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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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Hepes pH 7.5 2M Ammonium Sulphate 0.28mM LDAO, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.96649 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2006
RadiationMonochromator: Double crystal, Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96649 Å / Relative weight: 1
ReflectionResolution: 3.1→41.88 Å / Num. all: 63100 / Num. obs: 60450 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.119 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.9 / % possible all: 92.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OLV

2olv


Resolution: 3.1→41.88 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3155 -Random
Rwork0.218 ---
all0.218 63100 --
obs0.218 60450 95.8 %-
Displacement parametersBiso max: 317.12 Å2 / Biso mean: 72.405 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: LAST / Resolution: 3.1→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19228 0 246 0 19474

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