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- PDB-1mpl: CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE ... -

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Basic information

Entry
Database: PDB / ID: 1mpl
TitleCRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE
ComponentsD-alanyl-D-alanine carboxypeptidase
KeywordsHYDROLASE / TRANSITION STATE ANALOG / 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-RE1 / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.12 Å
AuthorsSilvaggi, N.R. / Anderson, J.W. / Brinsmade, S.R. / Pratt, R.F. / Kelly, J.A.
Citation
Journal: Biochemistry / Year: 2003
Title: The Crystal Structure of Phosphonate-Inhibited d-Ala-d-Ala Peptidase Reveals an Analogue of a Tetrahedral Transition State.
Authors: Silvaggi, N.R. / Anderson, J.W. / Brinsmade, S.R. / Pratt, R.F. / Kelly, J.A.
#1: 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.
#2: 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
DepositionSep 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)38,2217
Polymers37,4231
Non-polymers7996
Water8,017445
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.900, 66.760, 100.011
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 / D-ALANYL-D-ALANINE TRANSPEPTIDASE / DD- peptidase / DD-carboxypeptidase


Mass: 37422.574 Da / Num. of mol.: 1 / Fragment: DD-Peptidase / 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-RE1 / GLYCYL-L-A-AMINOPIMELYL-E-(D-2-AMINOETHYL)PHOSPHONATE


Mass: 338.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H21N3O7P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, SODIUM PHOSPHATE, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlenzyme1drop
215 %PEG80001drop
350 mMsodium phosphate1droppH6.8
420 %PEG80001reservoir
550 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2001 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.99991
ReflectionResolution: 1.12→50 Å / Num. all: 701505 / Num. obs: 127013 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 27.2
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3 / % possible all: 75.1
Reflection
*PLUS
Num. measured all: 701505
Reflection shell
*PLUS
% possible obs: 75.1 %

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Processing

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

3pte


Resolution: 1.12→10 Å / Num. parameters: 28853 / Num. restraintsaints: 36144 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.029
RfactorNum. reflection% reflectionSelection details
Rfree0.14 6231 5 %RANDOM
Rwork0.1143 ---
all0.1143 123545 --
obs0.1128 123545 94.2 %-
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 225 / Occupancy sum non hydrogen: 3081.77
Refinement stepCycle: LAST / Resolution: 1.12→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 51 445 3097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0334
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.094
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9999 Å / Num. reflection Rfree: 6242 / Rfactor Rfree: 0.139 / Rfactor Rwork: 0.113
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.5

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