[English] 日本語
Yorodumi
- PDB-1mbt: OXIDOREDUCTASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mbt
TitleOXIDOREDUCTASE
ComponentsURIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME
Function / homology
Function and homology information


UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / flavin adenine dinucleotide binding / regulation of cell shape / cell division / cytosol / cytoplasm
Similarity search - Function
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 1 / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 ...Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 1 / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBenson, T.E. / Walsh, C.T. / Hogle, J.M.
Citation
Journal: Structure / Year: 1996
Title: The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls.
Authors: Benson, T.E. / Walsh, C.T. / Hogle, J.M.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: An Enzyme-Substrate Complex Involved in Bacterial Cell Wall Biosynthesis
Authors: Benson, T.E. / Filman, D.J. / Walsh, C.T. / Hogle, J.M.
#2: Journal: Protein Sci. / Year: 1994
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Udp-N-Acetyl Enolpyruvylglucosamine Reductase
Authors: Benson, T.E. / Walsh, C.T. / Hogle, J.M.
#3: Journal: Biochemistry / Year: 1993
Title: Overexpression, Purification, and Mechanistic Study of Udp-N-Acetylenolpyruvylglucosamine Reductase
Authors: Benson, T.E. / Marquardt, J.L. / Marquardt, A.C. / Etzkorn, F.A. / Walsh, C.T.
History
DepositionNov 28, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7743
Polymers37,8921
Non-polymers8822
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.400, 79.100, 90.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE / MURB


Mass: 37891.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BOUND FLAVIN-ADENINE DINUCLEOTIDE, PH 8.0 / Source: (natural) Escherichia coli (E. coli) / Strain: AB1157 (ATCC) / References: UniProt: P08373, EC: 1.1.1.158
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDENSITY. THE SECONDARY STRUCTURE ASSIGNMENT IN THIS PDB ENTRY REFLECTS THE RESULTS OF AN AUTOMATED ...DENSITY. THE SECONDARY STRUCTURE ASSIGNMENT IN THIS PDB ENTRY REFLECTS THE RESULTS OF AN AUTOMATED PROCEDURE. FOR SECONDARY STRUCTURE ASSIGNMENTS MADE BY THE AUTHORS BASED ON INSPECTION OF HYDROGEN BONDING PATTERNS, SEE THE ORIGINAL REFERENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal grow
*PLUS
Temperature: 25 unknown / pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
21 mMNADP11
3100 mMsodium HEPES11
41.4 Mlithium sulfate11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→12 Å / Num. obs: 7297 / % possible obs: 95.9 %
Reflection
*PLUS
Redundancy: 5 % / Num. measured all: 36458 / Rmerge(I) obs: 0.084

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→12 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.322 --
Rwork0.209 --
obs0.209 7271 95.9 %
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 58 4 2716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.6 Å2

+
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