[English] 日本語
Yorodumi
- PDB-1sjd: x-ray structure of o-succinylbenzoate synthase complexed with n-s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sjd
Titlex-ray structure of o-succinylbenzoate synthase complexed with n-succinyl phenylglycine
ComponentsN-acylamino acid racemase
KeywordsLYASE / ISOMERASE / racemase
Function / homology
Function and homology information


O-succinylbenzoate synthase activity / o-succinylbenzoate synthase / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding
Similarity search - Function
o-Succinylbenzoate synthase, MenC type 2 / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...o-Succinylbenzoate synthase, MenC type 2 / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-SUCCINYL PHENYLGLYCINE / N-succinylamino acid racemase
Similarity search - Component
Biological speciesAmycolatopsis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.87 Å
AuthorsThoden, J.B. / Taylor-Ringia, E.A. / Garrett, J.B. / Gerlt, J.A. / Holden, H.M. / Rayment, I.
CitationJournal: Biochemistry / Year: 2004
Title: Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous o-Succinylbenzoate Synthase from Amycolatopsis
Authors: Thoden, J.B. / Taylor-Ringia, E.A. / Garrett, J.B. / Gerlt, J.A. / Holden, H.M. / Rayment, I.
History
DepositionMar 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acylamino acid racemase
B: N-acylamino acid racemase
C: N-acylamino acid racemase
D: N-acylamino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,30010
Polymers157,7934
Non-polymers1,5076
Water20,9331162
1
A: N-acylamino acid racemase
B: N-acylamino acid racemase
C: N-acylamino acid racemase
D: N-acylamino acid racemase
hetero molecules

A: N-acylamino acid racemase
B: N-acylamino acid racemase
C: N-acylamino acid racemase
D: N-acylamino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,60120
Polymers315,5868
Non-polymers3,01512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)215.200, 215.200, 257.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein
N-acylamino acid racemase / o-succinylbenzoate synthase


Mass: 39448.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. (bacteria) / Gene: AAAR / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q44244
#2: Chemical
ChemComp-NPG / N-SUCCINYL PHENYLGLYCINE


Mass: 251.235 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H13NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 3.64 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 298 K / Method: batch / pH: 8
Details: PEG 8000, HEPES, MgCl2, n-succinylphenylglycine, pH 8.0, batch, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.6525 Å
DetectorDetector: CCD / Date: Apr 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6525 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 186822 / Num. obs: 186822 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rsym value: 0.085 / Net I/σ(I): 40.1
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.377 / % possible all: 99.2

-
Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1sjb

1sjb


Resolution: 1.87→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 18681 -RANDOM
Rwork0.196 ---
obs0.202 186821 99.7 %-
all-186821 --
Refinement stepCycle: LAST / Resolution: 1.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11067 0 108 1162 12337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.3

+
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