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- PDB-1nzo: The crystal structure of wild type penicillin-binding protein 5 f... -

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Basic information

Entry
Database: PDB / ID: 1nzo
TitleThe crystal structure of wild type penicillin-binding protein 5 from E. coli
ComponentsPenicillin-binding protein 5
KeywordsHYDROLASE / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE
Function / homology
Function and homology information


peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase / beta-lactamase activity / regulation of cell shape ...peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase / beta-lactamase activity / regulation of cell shape / outer membrane-bounded periplasmic space / cell division / protein homodimerization activity / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase ...Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / D-alanyl-D-alanine carboxypeptidase DacA / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNicholas, R.A. / Krings, S. / Tomberg, J. / Nicola, G. / Davies, C.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli: implications for deacylation of the acyl-enzyme complex.
Authors: Nicholas, R.A. / Krings, S. / Tomberg, J. / Nicola, G. / Davies, C.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN-BINDING PROTEIN 5 AT 2.3-A RESOLUTION
Authors: Davies, C. / White, S.W. / Nicholas, R.A.
History
DepositionFeb 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE SPBP 5, THE LAST ...SEQUENCE THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE CODONS, AN ADDITIONAL SIX AMINO ACIDS (GDPVID) WERE INTRODUCED AT THE C TERMINUS DUE TO READ-THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST 29 AMINO ACIDS OF THE PROTEIN ENCODED BY THE OPEN READING FRAME REPRESENT THE SIGNAL SEQUENCE, WHICH IS REMOVED DURING MATURATION AND TRANSPORT TO THE PERIPLASMIC SPACE AND IS NOT PRESENT IN THIS CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9973
Polymers39,8411
Non-polymers1562
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.35, 50.28, 84.53
Angle α, β, γ (deg.)90.00, 120.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Penicillin-binding protein 5 / D-alanyl-D-alanine carboxypeptidase fraction A / DD-peptidase / DD-carboxypeptidase / PBP-5


Mass: 39841.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DACA / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061
References: UniProt: P04287, UniProt: P0AEB2*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris pH 7.0, 8% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2002 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→54 Å / Num. all: 31624 / Num. obs: 31624 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2 / Num. unique all: 2269 / % possible all: 67.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HD8

1hd8


Resolution: 1.85→14.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.3 / SU ML: 0.126 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24503 1542 5.1 %RANDOM
Rwork0.20779 ---
all0.20964 30384 --
obs0.20964 30384 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.08 Å2
2---0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 8 190 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222773
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9553742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0213351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.06715510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022088
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.31254
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.5286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.352
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8120.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.51739
X-RAY DIFFRACTIONr_mcangle_it1.29422791
X-RAY DIFFRACTIONr_scbond_it2.10631034
X-RAY DIFFRACTIONr_scangle_it3.2644.5951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.388 72
Rwork0.297 1461
obs-1533

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