[English] 日本語
Yorodumi
- PDB-1uof: Deacetoxycephalosporin C synthase complexed with Penicillin G -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uof
TitleDeacetoxycephalosporin C synthase complexed with Penicillin G
ComponentsDEACETOXYCEPHALOSPORIN C SYNTHETASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


deacetoxycephalosporin-C synthase / deacetoxycephalosporin-C synthase activity / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / antibiotic biosynthetic process / iron ion binding
Similarity search - Function
Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / : / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. ...Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / : / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / PENICILLIN G / Deacetoxycephalosporin C synthase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsValegard, K. / Terwisscha Van scheltinga, A.C. / Dubus, A. / Oster, L.M. / Rhangino, G. / Hajdu, J. / Andersson, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The Structural Basis of Cephalosporin Formation in a Mononuclear Ferrous Enzyme
Authors: Valegard, K. / Terwisscha Van Scheltinga, A.C. / Dubus, A. / Ranghino, G. / Oster, L.M. / Hajdu, J. / Andersson, I.
History
DepositionSep 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9823
Polymers34,5921
Non-polymers3902
Water2,558142
1
A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9469
Polymers103,7753
Non-polymers1,1716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.500, 106.500, 72.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein DEACETOXYCEPHALOSPORIN C SYNTHETASE / DAOCS / EXPANDASE


Mass: 34591.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P18548, deacetoxycephalosporin-C synthase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PNN / PENICILLIN G


Mass: 334.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O4S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Description: THE DATA WERE COLLECTED FROM A MEROHEDRALLY TWINNED CRYSTAL
Crystal growpH: 7.5
Details: 1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPESPH7.5, pH 7.50
Crystal grow
*PLUS
Method: unknown / Details: Valegard, K., (1998) Nature, 394, 805. / PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.75 Mammonium sulfate11
25 mM2-oxoglutarate11
30.1 MHEPES11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.886
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.6→32 Å / Num. obs: 39909 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.134 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 207167 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.134

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RXF

1rxf


Resolution: 1.6→56.8 Å / SU B: 1.725 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095
Details: REFINED AGAINST DETWINNED DATA THE RESIDUES MISSING IN THE PDB ENTRY (81-96,165-178 AND 311) ARE DISORDERED, AND THEREFORE OMITTED FROM THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.231 753 2 %RANDOM
Rwork0.196 ---
obs0.197 36578 92.8 %-
Displacement parametersBiso mean: 25.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å20 Å2
2---1.06 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.6→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 24 142 2260

+
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