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- PDB-1hvb: CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1hvb
TitleCRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE
KeywordsHYDROLASE / Protein-cephalosporin complex
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-CEH / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.17 Å
AuthorsMcDonough, M.A. / Lee, W. / Silvaggi, N.R. / Mobashery, S. / Kelly, J.A.
Citation
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.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: The Refined Crystallographic Structure of a DD-Peptidase Penicillin-target Enzyme at 1.6 Angstrom Resolution
Authors: Kelly, J.A. / Kuzin, A.P.
History
DepositionJan 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 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)38,1732
Polymers37,4231
Non-polymers7511
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.778, 66.664, 100.928
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 / DD-CARBOXYPEPTIDASE


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-CEH / 5-{3-(S)-(4-(R)-ACETYLAMINO-4-CARBOXY-BUTYRYLAMINO)-3-[1-(R)-(1-(R)-CARBOXY-ETHYLCARBAMOYL)-ETHYLCARBAMOYL]-PROPYL}-2-( CARBOXY-PHENYLACETYLAMINO-METHYL)-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / CEPHALOSPORIN ANALOG


Mass: 750.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N6O13S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown / Details: Kuzin, A.P., (1995) Biochemistry, 34, 9532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG800011
250 mMphosphate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jan 29, 2000 / Details: Monochromator, Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.17→20 Å / Num. all: 2330719 / Num. obs: 111370 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25
Reflection shellResolution: 1.17→1.21 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4.6 / Num. unique all: 8392 / % possible all: 72.9
Reflection
*PLUS
Num. measured all: 2330719 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 73 %

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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: 1.17→10 Å / Num. parameters: 29978 / Num. restraintsaints: 36742 / Isotropic thermal model: ISOTROPIC / 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 0.032 ANGSTROMS DETERMINED BY INVERSION OF THE LEAST-SQUARES MATRIX. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) ...Details: THE ESTIMATED STANDARD DEVIATION OF ATOMIC COORDINATES FOR ALL ATOMS IS 0.032 ANGSTROMS DETERMINED BY INVERSION OF THE LEAST-SQUARES MATRIX. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.5%. WATER MOLECULES DESIGNATED AS B CONFORMATION ARE PRESENT IN UN-LIGAND BOUND MOLECULES IN THE CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.1528 5560 5 %RANDOM
Rwork0.1126 ---
all0.1141 111197 --
obs0.1141 111197 96.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 16.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.146 Å / Luzzati d res low obs: 20 Å / Num. disordered residues: 35 / Occupancy sum hydrogen: 268.92 / Occupancy sum non hydrogen: 3181.8
Refinement stepCycle: LAST / Resolution: 1.17→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 51 555 3213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0311
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.102
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_planar_d0.031
X-RAY DIFFRACTIONs_plane_restr0.082

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