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- PDB-2aum: Active site Ser115Ala mutant of LD-carboxypeptidase -

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Basic information

Entry
Database: PDB / ID: 2aum
TitleActive site Ser115Ala mutant of LD-carboxypeptidase
Componentshypothetical protein
KeywordsHYDROLASE / LD-carboxypeptidase / peptidoglycan hydrolase / serine peptidase / serine-histidine-glutamate triad / nucleophilic elbow
Function / homology
Function and homology information


muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / peptidoglycan turnover / peptidoglycan biosynthetic process / serine-type peptidase activity / cell wall organization / regulation of cell shape / proteolysis / cytoplasm
Similarity search - Function
Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 ...Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 / Class I glutamine amidotransferase-like / 3-Layer(bba) Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Murein tetrapeptide carboxypeptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKorza, H.J. / Bochtler, M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow.
Authors: Korza, H.J. / Bochtler, M.
History
DepositionAug 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 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: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)69,2432
Polymers69,2432
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-10 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.455, 77.843, 71.154
Angle α, β, γ (deg.)90.00, 104.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein


Mass: 34621.352 Da / Num. of mol.: 2 / Mutation: S115A mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET15bmod / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HTZ1, muramoyltetrapeptide carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 1.98 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: citric acid , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2005 / Details: Max-Flux
RadiationMonochromator: Osmic Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. all: 21396 / Num. obs: 21396 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.43 Å / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3.6 / Num. unique all: 806 / Rsym value: 0.226 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZRS

1zrs


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.8 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24723 1082 5.1 %RANDOM
Rwork0.24198 ---
all0.24224 20302 --
obs0.24224 20302 98.57 %-
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: 20.915 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20.24 Å2
2---0.06 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 0 310 4813
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 82
Rwork0.28 1439

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