[English] 日本語
Yorodumi
- PDB-6y91: Crystal structure of malate dehydrogenase from Plasmodium Falcipa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y91
TitleCrystal structure of malate dehydrogenase from Plasmodium Falciparum in complex with NADH
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


carboxylic acid metabolic process / L-lactate dehydrogenase activity
Similarity search - Function
Malate dehydrogenase, type 3 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRomero, A.R. / Calderone, V. / Gentili, M. / Lunev, S. / Groves, M. / Popowicz, G. / Domling, A. / Sattler, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission675555 Netherlands
Citation
Journal: Commun Biol / Year: 2021
Title: A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity.
Authors: Reyes Romero, A. / Lunev, S. / Popowicz, G.M. / Calderone, V. / Gentili, M. / Sattler, M. / Plewka, J. / Taube, M. / Kozak, M. / Holak, T.A. / Domling, A.S.S. / Groves, M.R.
#1: Journal: PLoS ONE / Year: 2018
Title: Oligomeric interfaces as a tool in drug discovery: Specific interference with activity of malate dehydrogenase of Plasmodium falciparum in vitro.
Authors: Lunev, S. / Butzloff, S. / Romero, A.R. / Linzke, M. / Batista, F.A. / Meissner, K.A. / Muller, I.B. / Adawy, A. / Wrenger, C. / Groves, M.R.
History
DepositionMar 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: 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
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1058
Polymers141,4524
Non-polymers2,6544
Water2,576143
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18730 Å2
ΔGint-90 kcal/mol
Surface area41770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.620, 107.420, 145.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Malate dehydrogenase


Mass: 35362.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6VVP7, malate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M trisodium citrate, 0.1 M Hepes, 10 mM NADH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 16, 2019
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→18.27 Å / Num. obs: 46208 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.3
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 16.3 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3249 / CC1/2: 0.61 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
PHENIX(dev_3753: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nfr

5nfr


Resolution: 2.5→18.27 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28
RfactorNum. reflection% reflection
Rfree0.286 2302 5 %
Rwork0.2386 --
obs0.241 46006 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→18.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9133 0 176 143 9452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079856
X-RAY DIFFRACTIONf_angle_d1.32313344
X-RAY DIFFRACTIONf_dihedral_angle_d12.7061348
X-RAY DIFFRACTIONf_chiral_restr0.0691592
X-RAY DIFFRACTIONf_plane_restr0.0051672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.33811370.272593X-RAY DIFFRACTION96
2.56-2.620.31341410.27322689X-RAY DIFFRACTION100
2.62-2.680.33421430.28662701X-RAY DIFFRACTION100
2.68-2.750.35941430.27232721X-RAY DIFFRACTION100
2.75-2.840.35471420.26352694X-RAY DIFFRACTION100
2.84-2.930.31621420.26092708X-RAY DIFFRACTION100
2.93-3.030.32661420.24862714X-RAY DIFFRACTION100
3.03-3.150.321430.25082716X-RAY DIFFRACTION100
3.15-3.290.29411440.2492728X-RAY DIFFRACTION100
3.29-3.470.33341440.24262724X-RAY DIFFRACTION100
3.47-3.680.27981440.22982742X-RAY DIFFRACTION100
3.68-3.960.25041440.22192728X-RAY DIFFRACTION100
3.96-4.360.22331450.21062747X-RAY DIFFRACTION100
4.36-4.980.27281470.20692791X-RAY DIFFRACTION100
4.98-6.230.2541470.24972803X-RAY DIFFRACTION100
6.23-18.270.25761540.22992905X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3016-0.1537-0.24670.243-0.05350.3777-0.0977-0.2310.08630.02420.0858-0.07420.02340.0706-0.00010.14280.0277-0.00060.23870.00180.1409-2.71957.558835.0408
20.1327-0.07010.14370.4013-0.15540.1597-0.0850.01890.02750.03010.08570.0339-0.0347-0.01630.00030.12270.0208-0.00130.1494-0.00830.0877-31.492124.68324.9087
30.2750.12890.01040.34520.00420.4044-0.09040.0925-0.0649-0.02790.0289-0.06650.0428-0.0511-0.04090.1067-0.03670.05160.0999-0.01830.1414-6.60781.9266-2.0147
40.3617-0.0841-0.22750.50320.11270.2787-0.20710.057-0.07050.04770.0905-0.05330.2351-0.0651-0.04210.1611-0.05360.04060.0585-0.00580.1658-35.5389-10.776912.8899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:313)
2X-RAY DIFFRACTION2(chain B and resseq 2:313)
3X-RAY DIFFRACTION3(chain C and resseq 1:313)
4X-RAY DIFFRACTION4(chain D and resseq 2:313)

+
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