[English] 日本語
Yorodumi
- PDB-1pwd: Covalent acyl enzyme complex of the Streptomyces R61 DD-peptidase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pwd
TitleCovalent acyl enzyme complex of the Streptomyces R61 DD-peptidase with cephalosporin C
ComponentsD-alanyl-D-alanine carboxypeptidase precursor
KeywordsHYDROLASE/Antibiotic / BETA-LACTAM / ANTIBIOTICS / PENICILLIN BINDING PROTEIN / ENZYME / PEPTIDOGLYCAN / HYDROLASE / HYDROLASE-Antibiotic 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-0MU / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsSilvaggi, N.R. / Josephine, H.R. / Pratt, R.F. / Kelly, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin"
Authors: Silvaggi, N.R. / Josephine, H.R. / Kuzin, A.P. / Nagarajan, 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: 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.
#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
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-alanyl-D-alanine carboxypeptidase precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8402
Polymers37,4231
Non-polymers4171
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.00, 67.00, 100.00
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein D-alanyl-D-alanine carboxypeptidase precursor / 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-0MU / (2R)-5-(acetyloxymethyl)-2-[(1R)-1-[[(5R)-5-azanyl-6-oxidanyl-6-oxidanylidene-hexanoyl]amino]-2-oxidanylidene-ethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / CEPHALOSPORIN C, bound form


Type: D-peptide linking / Mass: 417.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N3O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE LIGAND 0MU REPRESENTS THE BOUND FORM OF THE ANTIBIOTIC CEPHALOSPORIN C. THE ACYLATION REACTION ...THE LIGAND 0MU REPRESENTS THE BOUND FORM OF THE ANTIBIOTIC CEPHALOSPORIN C. THE ACYLATION REACTION RESULTED IN THE REMOVAL OF THE COVALENT BOND BETWEEN ATOMS N5 AND C8 OF THE STARTING CEPHALOSPORIN C AND THE FORMATION OF THE COVALENT BOND BETWEEN ATOM OG OF SER A 62 AND ATOM C8 OF THE FINAL PRODUCT 0MU

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 8000, 50mM Sodium Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 15, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.2→60 Å / Num. all: 102353 / Num. obs: 102353 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4 / Num. unique all: 7443 / % possible all: 70

-
Processing

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

3pte


Resolution: 1.2→10 Å / Num. parameters: 28084 / Num. restraintsaints: 33924 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.024.
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 4946 5.1 %RANDOM
Rwork0.1238 ---
all0.125 97720 --
obs0.1238 97720 91 %-
Refine analyzeLuzzati coordinate error obs: 0.08 Å / Num. disordered residues: 11 / Occupancy sum hydrogen: 261 / Occupancy sum non hydrogen: 3061.9
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 24 456 3082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.032
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0324
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.031
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.089

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more