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- PDB-1iki: COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A S... -

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Basic information

Entry
Database: PDB / ID: 1iki
TitleCOMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE
KeywordsHYDROLASE / PRODUCTS 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
D-ALANINE / GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
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 1.6Nov 6, 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)37,8153
Polymers37,4231
Non-polymers3922
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.859, 66.799, 100.263
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-REY / GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE


Mass: 303.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O6
#3: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, SODIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K
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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Aug 26, 2000 / Details: MONOCHROMATOR, MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. all: 95204 / Num. obs: 92030 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rsym value: 0.069 / Net I/σ(I): 17.2
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Num. unique all: 7323 / Rsym value: 0.178 / % possible all: 77.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 95204 / % possible obs: 97 % / Num. measured all: 973583 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 78 % / Rmerge(I) obs: 0.178

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3PTE

3pte


Resolution: 1.25→10 Å / Num. parameters: 29573 / Num. restraintsaints: 35362 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE ESTIMATED STANDARD DEVIATION OF ATOMIC COORDINATES FOR ALL ATOMS IS 0.045 ANGSTROMS DETERMINED BY INVERSION OF THE LEAST-SQUARES MATRIX.
RfactorNum. reflection% reflectionSelection details
Rfree0.154 4463 5 %RANDOM
Rwork0.1112 ---
obs0.1094 84590 89.1 %-
all-89053 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3215
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 27 587 3216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.1
LS refinement shellResolution: 1.25→1.29 Å
RfactorNum. reflection% reflection
Rwork0.172 --
Rfree-284 -
obs-5677 67 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor all: 0.111 / Rfactor Rfree: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.2

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