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- PDB-1ikg: MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFI... -

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Basic information

Entry
Database: PDB / ID: 1ikg
TitleMICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE
KeywordsHYDROLASE / MICHAELIS COMPLEX / PEPTIDOGLYCAN / PENICILLIN BINDING PROTEIN
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
Chem-REX / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsMcdonough, M.A. / Anderson, J.W. / Silvaggi, N.R. / Pratt, R.F. / Knox, J.R. / Kelly, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins.
Authors: McDonough, M.A. / Anderson, J.W. / Silvaggi, N.R. / Pratt, R.F. / Knox, J.R. / Kelly, J.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A 1.2-A SNAPSHOT OF THE FINAL STEP OF BACTERIAL CELL WALL BIOSYNTHESIS
Authors: LEE, W. / MCDONOUGH, M.A. / KOTRA, L. / LI, Z.H. / SILVAGGI, N.R. / TAKEDA, Y. / KELLY, J.A. / MOBASHERY, S.
#2: Journal: Biochemistry / Year: 1995
Title: BINDING OF CEPHALOTHIN AND CEFOTAXIME TO D-ALA-D-ALA-PEPTIDASE REVEALS A FUNCTIONAL BASIS OF A NATURAL MUTATION IN A LOW-AFFINITY PENICILLIN-BINDING PROTEIN AND IN EXTENDED-SPECTRUM BETA-LACTAMASES
Authors: KUZIN, A.P. / LIU, H. / KELLY, J.A. / KNOX, J.R.
#3: 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.
History
DepositionMay 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7972
Polymers37,4231
Non-polymers3741
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.873, 66.828, 100.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / DD-PEPTIDASE


Mass: 37422.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. (bacteria) / Strain: R61
References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-REX / GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANYL-D-ALANINE


Mass: 374.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N4O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, SODIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMsodium phosphate1reservoirpH6.8
230 %(w/v)PEG80001reservoir
35 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 13, 1999 / Details: MIRRORS
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→28 Å / Num. all: 28134 / Num. obs: 26003 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 7.7 Å2 / Rsym value: 0.044 / Net I/σ(I): 22.5
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2.4 % / Num. unique all: 2978 / Rsym value: 0.086 / % possible all: 70
Reflection
*PLUS
Lowest resolution: 28 Å / % possible obs: 93 % / Num. measured all: 130497 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 70 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 10

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Processing

Software
NameClassification
FRAMBOdata collection
X-GENdata reduction
CNSrefinement
X-GENdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3PTE

3pte


Resolution: 1.9→27.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 155199.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1279 5 %RANDOM
Rwork0.15 ---
all0.1612 27606 --
obs0.15 25556 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.12 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 9.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å20 Å2
2--1.82 Å20 Å2
3---1.29 Å2
Refine analyzeNum. disordered residues: 3
FreeObs
Luzzati coordinate error0.2 Å0.15 Å
Luzzati d res low-30 Å
Luzzati sigma a0.14 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 26 355 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it2.161.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it3.142
X-RAY DIFFRACTIONc_scangle_it3.762.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.227 162 5.2 %
Rwork0.159 2978 -
obs--69.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3REX.PARAMREX.TOP
Refinement
*PLUS
Lowest resolution: 28 Å / Rfactor all: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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