[English] 日本語
Yorodumi
- PDB-1ez4: CRYSTAL STRUCTURE OF NON-ALLOSTERIC L-LACTATE DEHYDROGENASE FROM ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ez4
TitleCRYSTAL STRUCTURE OF NON-ALLOSTERIC L-LACTATE DEHYDROGENASE FROM LACTOBACILLUS PENTOSUS AT 2.3 ANGSTROM RESOLUTION
ComponentsLACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus pentosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsUchikoba, H. / Fushinobu, S. / Wakagi, T. / Konno, M. / Taguchi, H. / Matsuzawa, H.
Citation
Journal: Proteins / Year: 2002
Title: Crystal structure of non-allosteric L-lactate dehydrogenase from Lactobacillus pentosus at 2.3 A resolution: specific interactions at subunit interfaces.
Authors: Uchikoba, H. / Fushinobu, S. / Wakagi, T. / Konno, M. / Taguchi, H. / Matsuzawa, H.
#1: Journal: Eur.J.Biochem. / Year: 1992
Title: Unusual Amino Acid Substitution in the Anion-binding Site of Lactobacillus plantarum Non-allosteric L-lactate Dehydrogenase
Authors: Taguchi, H. / Ohta, T.
History
DepositionMay 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
C: LACTATE DEHYDROGENASE
D: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8048
Polymers136,1504
Non-polymers2,6544
Water14,142785
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-69 kcal/mol
Surface area39510 Å2
MethodPISA
2
A: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
hetero molecules

C: LACTATE DEHYDROGENASE
D: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8048
Polymers136,1504
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area14600 Å2
ΔGint-67 kcal/mol
Surface area44080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.351, 145.544, 111.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer constructed from chain A-D. The symmetry partners have three two-fold axes in total.

-
Components

#1: Protein
LACTATE DEHYDROGENASE


Mass: 34037.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus pentosus (bacteria) / Plasmid: PEXLP / Production host: Escherichia coli (E. coli) / References: UniProt: P56511, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, sodium acetate, NADH, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMacetate/NaOH1reservoir
21.2 Mammonium sulfate1reservoir
31 mMNADH1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
Detector
TypeIDDetectorDate
WEISSENBERG1DIFFRACTOMETERMar 7, 1998
2Jun 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 123693 / % possible obs: 99.3 % / Observed criterion σ(I): 0.1 / Redundancy: 8.7 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.367 / Num. unique all: 286006 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 1078131 / Rmerge(I) obs: 0.125

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.3→80 Å / σ(F): 2 / Stereochemistry target values: X-PLOR 3.851 param19.pro / Details: bulk solvent correction
RfactorNum. reflectionSelection details
Rfree0.241 6181 RANDOM
Rwork0.205 --
all-105490 -
obs-123624 -
Refinement stepCycle: LAST / Resolution: 2.3→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9392 0 176 785 10353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.692
X-RAY DIFFRACTIONx_bond_d0.016
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 80 Å / σ(F): 2 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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