[English] 日本語
Yorodumi
- PDB-8rs5: Crystal structure of Methanopyrus kandleri malate dehydrogenase m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rs5
TitleCrystal structure of Methanopyrus kandleri malate dehydrogenase mutant 4
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / Rossmann-like motif / NAD(P)H binding site
Function / homology
Function and homology information


malate dehydrogenase [NAD(P)+] / L-malate dehydrogenase (NADP+) activity / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle
Similarity search - Function
L-lactate dehydrogenase, active site / 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
: / Chem-NDP / Malate dehydrogenase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCoquille, S. / Engilberge, S. / Madern, D.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0011 France
Agence Nationale de la Recherche (ANR)ANR-21-CE44-0034-01 France
CitationJournal: To Be Published
Title: Navigating the conformational landscape of an enzyme. Stabilization of a low populated conformer by evolutionary mutations triggers Allostery into a non-allosteric enzyme.
Authors: Coquille, S. / Simoes Pereira, C. / Brochier-Armanet, C. / Roche, J. / Santoni, G. / Coquelle, N. / Girard, E. / Sterpone, F. / Madern, D.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9819
Polymers69,3062
Non-polymers1,6757
Water4,432246
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,96218
Polymers138,6124
Non-polymers3,35114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18370 Å2
ΔGint-115 kcal/mol
Surface area43220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.360, 74.360, 267.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Malate dehydrogenase


Mass: 34652.887 Da / Num. of mol.: 2 / Mutation: D51H, R85Q, L146S, S228T, P232I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mdh, MK1069 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TWG5, malate dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium citrate tribasic monohydrate, 13-16% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 55448 / % possible obs: 99 % / Redundancy: 7.39 % / Biso Wilson estimate: 31.96 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.16
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.68 % / Num. unique obs: 4057 / CC1/2: 0.401 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.92 Å / SU ML: 0.3391 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283 2765 5 %
Rwork0.258 52566 -
obs0.2593 55331 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.48 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 101 246 4986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864857
X-RAY DIFFRACTIONf_angle_d0.89266602
X-RAY DIFFRACTIONf_chiral_restr0.0486797
X-RAY DIFFRACTIONf_plane_restr0.0059843
X-RAY DIFFRACTIONf_dihedral_angle_d14.55561817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.35881360.35392597X-RAY DIFFRACTION99.82
1.98-2.020.38841370.33072600X-RAY DIFFRACTION99.89
2.02-2.060.34951370.32032610X-RAY DIFFRACTION99.78
2.06-2.10.29561350.31842590X-RAY DIFFRACTION99.78
2.1-2.150.30181370.29532597X-RAY DIFFRACTION99.67
2.15-2.20.35651370.28912607X-RAY DIFFRACTION99.64
2.2-2.250.3341380.28262608X-RAY DIFFRACTION99.53
2.25-2.310.30691370.27382604X-RAY DIFFRACTION99.56
2.31-2.380.28971370.26832606X-RAY DIFFRACTION99.64
2.38-2.460.28811370.26992607X-RAY DIFFRACTION99.42
2.46-2.540.30041380.26442615X-RAY DIFFRACTION99.42
2.54-2.650.27111380.25892630X-RAY DIFFRACTION99.21
2.65-2.770.34651380.26692633X-RAY DIFFRACTION99.11
2.77-2.910.29631370.26682604X-RAY DIFFRACTION98.99
2.91-3.090.28431410.27182661X-RAY DIFFRACTION98.91
3.09-3.330.29681370.26172610X-RAY DIFFRACTION98.71
3.33-3.660.28961390.23672632X-RAY DIFFRACTION97.78
3.66-4.190.22971400.21872657X-RAY DIFFRACTION97.73
4.19-5.260.22481410.21212694X-RAY DIFFRACTION97.06
5.26-19.920.2891480.27552804X-RAY DIFFRACTION96.22

+
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://pdbjlvh1.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