[English] 日本語
Yorodumi
- PDB-6ihe: Crystal structure of Malate dehydrogenase from Metallosphaera sedula -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ihe
TitleCrystal structure of Malate dehydrogenase from Metallosphaera sedula
ComponentsMalate dehydrogenase (NAD)
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


L-lactate dehydrogenase activity / lactate metabolic process / pyruvate metabolic process / nucleotide binding
Similarity search - Function
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Malate dehydrogenase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, D. / Kim, K.J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula
Authors: Lee, D. / Hong, J. / Kim, K.J.
History
DepositionSep 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malate dehydrogenase (NAD)
B: Malate dehydrogenase (NAD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,67821
Polymers66,2982
Non-polymers3,37919
Water4,071226
1
A: Malate dehydrogenase (NAD)
B: Malate dehydrogenase (NAD)
hetero molecules

A: Malate dehydrogenase (NAD)
B: Malate dehydrogenase (NAD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,35542
Polymers132,5974
Non-polymers6,75838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area12840 Å2
ΔGint-52 kcal/mol
Surface area43440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.194, 134.194, 81.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Malate dehydrogenase (NAD)


Mass: 33149.242 Da / Num. of mol.: 2 / Fragment: UNP residues 2-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula (archaea) / Gene: Msed_0455 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_T1R(DE3) / References: UniProt: A0A088E2H7, malate dehydrogenase

-
Non-polymers , 8 types, 245 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.21 Å3/Da / Density % sol: 61.71 % / Mosaicity: 0.678 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 40 % (v/v) polyethylene glycol (PEG) 300, 0.1 M CHES / sodium hydroxide pH 9.5, 0.2 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 17, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 65061 / % possible obs: 96.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Χ2: 1.97 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.934.40.33332320.7540.1620.3731.0397.4
1.93-1.974.50.31532280.8030.1510.3521.11696.7
1.97-2.014.80.2832390.8970.1280.311.23396.7
2.01-2.0550.27632170.8960.1240.3051.24196.7
2.05-2.095.10.25131940.9260.110.2751.28795.9
2.09-2.145.60.22332480.950.0930.2431.44897.5
2.14-2.195.60.20332360.9650.0830.2211.48696.4
2.19-2.255.90.18232150.9740.0730.1971.52296.9
2.25-2.326.30.16732210.9810.0650.181.58595.9
2.32-2.396.40.14631880.9880.0550.1571.68995.1
2.39-2.486.60.13632080.9890.0510.1461.72595.9
2.48-2.586.80.12232020.9920.0450.131.85195.3
2.58-2.77.30.10732110.9940.0380.1141.88196.3
2.7-2.847.60.09832270.9950.0350.1041.94895.4
2.84-3.0280.08432300.9960.0290.0892.08796.1
3.02-3.258.40.07732730.9970.0260.0812.25297
3.25-3.5890.06633230.9980.0210.0692.51197.6
3.58-4.099.50.05833200.9980.0190.0612.68498.1
4.09-5.169.60.05433720.9980.0180.0572.75398.2
5.16-509.10.05234770.9960.0180.0552.77998

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.139 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 3181 4.9 %RANDOM
Rwork0.1922 ---
obs0.1938 61878 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.44 Å2 / Biso mean: 36.481 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 220 226 5098
Biso mean--49.71 42.65 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194949
X-RAY DIFFRACTIONr_bond_other_d0.0020.024879
X-RAY DIFFRACTIONr_angle_refined_deg1.9772.0076646
X-RAY DIFFRACTIONr_angle_other_deg1.067311295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5815604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33325.055182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93315872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0091518
X-RAY DIFFRACTIONr_chiral_restr0.1190.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215306
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02990
LS refinement shellResolution: 1.898→1.947 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 217 -
Rwork0.439 4526 -
all-4743 -
obs--95.78 %

+
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