[English] 日本語
Yorodumi
- PDB-1d2f: X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d2f
TitleX-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHOSPHATE-DEPENDENT ENZYME ACTING AS A MODULATOR IN MAL GENE EXPRESSION
ComponentsMALY PROTEIN
KeywordsTRANSFERASE / AMINOTRANSFERASE FOLD / LARGE PLP-BINDING DOMAIN / SMALL C-TERMINAL DOMAIN / OPEN ALPHA-BETA STRUCTURE.
Function / homology
Function and homology information


cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / : / L-cysteine desulfhydrase activity / methionine biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor binding / protein homodimerization activity
Similarity search - Function
Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Protein MalY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsClausen, T.
Citation
Journal: EMBO J. / Year: 2000
Title: X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression.
Authors: Clausen, T. / Schlegel, A. / Peist, R. / Schneider, E. / Steegborn, C. / Chang, Y.S. / Haase, A. / Bourenkov, G.P. / Bartunik, H.D. / Boos, W.
#1: Journal: J.Bacteriol. / Year: 1995
Title: Maly of Escherichia-Coli Is an Enzyme With the Activity of a Beta-C-S Lyase (Cystathionase).
Authors: Zdych, E. / Peist, R. / Reidl, J. / Boos, W.
History
DepositionSep 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MALY PROTEIN
B: MALY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8644
Polymers87,3692
Non-polymers4942
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-30 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.510, 107.190, 256.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein MALY PROTEIN


Mass: 43684.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PJR115 / Production host: Escherichia coli (E. coli) / References: UniProt: P23256
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: AMMONIUM SULPHATE, MES, TRIS, DITHITHREITOL, pH 7.0, VAPOR DIFFUSION, SITTING DROP
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
23 mMdithiothreitol1drop
310 mMTris-HCl1drop
40.020 mMPLP1drop
5100 mMMES/Tris1reservoir
61.8 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 94388 / Num. obs: 24839 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.303 / % possible all: 88.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 94388
Reflection shell
*PLUS
% possible obs: 88.7 % / Mean I/σ(I) obs: 3.3

-
Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.5→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER / Details: ENERGY RESTRAINED CRYSTALLOGRAPHIC REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1242 -RANDOM
Rwork0.201 ---
all0.204 94388 --
obs0.204 24839 94.9 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 30 167 5914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d2.7
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d0.008
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.42
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.42
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_deg1.2

+
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