[English] 日本語
Yorodumi
- PDB-7xqn: InDel-mutant malate dehydrogenase from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xqn
TitleInDel-mutant malate dehydrogenase from E. coli
ComponentsMalate dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / InDel design / oxidoreductase mutant / Rossmann divergence / modified coenzyme-binding / coenzyme-switch
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 domain superfamily
Similarity search - Domain/homology
Malate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsToledo-Patino, S. / Laurino, P.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other government Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Insertions and deletions mediated functional divergence of Rossmann fold enzymes.
Authors: Toledo-Patino, S. / Pascarelli, S. / Uechi, G.I. / Laurino, P.
History
DepositionMay 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)64,4282
Polymers64,4282
Non-polymers00
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-25 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.640, 98.350, 118.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

-
Components

#1: Protein Malate dehydrogenase


Mass: 32213.967 Da / Num. of mol.: 2 / Mutation: V5N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SRV3, malate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 35% (v/v) MPD, 100 mM sodium cacodylate/hydrochloric acid pH 6.5, 50 mM zinc acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→49.17 Å / Num. obs: 43701 / % possible obs: 100 % / Redundancy: 27.1 % / Biso Wilson estimate: 22.09 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.55
Reflection shellResolution: 1.98→2.13 Å / Num. unique obs: 6971 / CC1/2: 0.83

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158model building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1emd

1emd


Resolution: 1.98→49.17 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.1576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 2000 4.58 %RANDOM
Rwork0.1776 41688 --
obs0.178 43688 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.59 Å2
Refinement stepCycle: LAST / Resolution: 1.98→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 0 485 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994578
X-RAY DIFFRACTIONf_angle_d1.28536202
X-RAY DIFFRACTIONf_chiral_restr0.079752
X-RAY DIFFRACTIONf_plane_restr0.005808
X-RAY DIFFRACTIONf_dihedral_angle_d13.20421680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.2741410.27292952X-RAY DIFFRACTION99.94
2.03-2.080.25861400.21612913X-RAY DIFFRACTION100
2.08-2.150.23321420.19422947X-RAY DIFFRACTION99.97
2.15-2.210.21071390.18852911X-RAY DIFFRACTION100
2.21-2.290.22211430.18192975X-RAY DIFFRACTION100
2.29-2.390.19611400.17252926X-RAY DIFFRACTION100
2.39-2.490.17861420.17132952X-RAY DIFFRACTION99.97
2.49-2.630.18261430.17352972X-RAY DIFFRACTION100
2.63-2.790.19711410.17392957X-RAY DIFFRACTION100
2.79-3.010.19931420.18272959X-RAY DIFFRACTION99.97
3.01-3.310.17731440.17932993X-RAY DIFFRACTION100
3.31-3.790.16121450.16513009X-RAY DIFFRACTION99.97
3.79-4.770.13991450.15233038X-RAY DIFFRACTION99.94
4.77-49.170.18191530.17943184X-RAY DIFFRACTION99.85

+
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