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- PDB-3pte: THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILL... -

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Basic information

Entry
Database: PDB / ID: 3pte
TitleTHE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6 A RESOLUTION
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE
KeywordsHYDROLASE / TRANSPEPTIDASE
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / extracellular region
Similarity search - Function
: / 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
D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsKelly, J.A. / Kuzin, A.P.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution.
Authors: Kelly, J.A. / Kuzin, A.P.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic Mapping of Beta-Lactams Bound to a D-Alanyl-D-Alanine Peptidase Target Enzyme
Authors: Kelly, J.A. / Knox, J.R. / Zhao, H. / Frere, J.M. / Ghuysen, J.M.
#2: Journal: Science / Year: 1986
Title: On the Origin of Bacterial Resistance to Penicillins. Comparison of a Beta-Lactamase, a Penicillin Target
Authors: Kelly, J.A. / Dideberg, O. / Charlier, P. / Wery, J.P. / Libert, M. / Moews, P.C. / Knox, J.R. / Duez, C. / Fraipont, Cl. / Joris, B. / Dusart, J. / Frere, J.F. / Ghuysen, J.M.
#3: Journal: J.Biol.Chem. / Year: 1985
Title: 2.8 Angstroms Structure of a Penicillin-Sensitive D-Alanyl Carboxypeptidase-Transpeptidase from Streptomyces R61, Complexes with Beta-Lactams
Authors: Kelly, J.A. / Knox, J.R. / Moews, P.C. / Hite, G.J. / Bartolone, J.B. / Zhao, H. / Joris, B. / Frere, J.M. / Ghuysen, J.M.
History
DepositionAug 5, 1994Processing site: BNL
SupersessionAug 15, 1995ID: 1PTE
Revision 1.0Aug 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650HELIX H7 (RESIDUES 235 - 237) AND RESIDUES 61 AND 62 OF H2 ARE 3/10 HELIX.
Remark 700SHEET AP1 IN *SHEET* RECORDS BELOW IS A MAJOR ANTIPARALLEL SHEET. AP2 IS A SHORT ANTIPARALLEL SHEET. ...SHEET AP1 IN *SHEET* RECORDS BELOW IS A MAJOR ANTIPARALLEL SHEET. AP2 IS A SHORT ANTIPARALLEL SHEET. M1 IS A SHORT MIXED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)37,4231
Polymers37,4231
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.060, 67.310, 102.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 201

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Components

#1: Protein D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE


Mass: 37422.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: R61
References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ACTIVE SITE CONSISTS OF EIGHT RESIDUES IN THREE GROUPS. THREE SHORT SEQUENCE SEGMENTS ARE FOUND ...THE ACTIVE SITE CONSISTS OF EIGHT RESIDUES IN THREE GROUPS. THREE SHORT SEQUENCE SEGMENTS ARE FOUND IN ALL PENICILLIN-INTERACTIVE ENZYMES. THOSE FOR STREPTOMYCES R61 ARE LISTED IN THE *SITE* RECORDS BELOW.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal grow
*PLUS
pH: 6.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
250 mMsodium phosphate11
315 %(w/v)PEG800011
420 %PEG800012

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Data collection

ReflectionNum. obs: 41176 / % possible obs: 88 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.158

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.211 --
Rwork0.148 --
obs0.148 38808 82 %
Displacement parametersBiso mean: 9.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 0 254 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d1.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.3191
X-RAY DIFFRACTIONx_mcangle_it1.9571.5
X-RAY DIFFRACTIONx_scbond_it1.9521
X-RAY DIFFRACTIONx_scangle_it2.8791.5
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.030.035
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_planar_d0.040.049
X-RAY DIFFRACTIONx_plane_restr0.020.019
X-RAY DIFFRACTIONx_chiral_restr0.150.167

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