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

+
Open data


ID or keywords:

Loading...

-
Basic information

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


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / carboxylic acid metabolic process
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
2-ETHOXYETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)68,2066
Polymers66,6992
Non-polymers1,5074
Water1,15364
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,41212
Polymers133,3984
Non-polymers3,0148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area19380 Å2
ΔGint-60 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.900, 87.900, 231.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Malate dehydrogenase /


Mass: 33349.500 Da / Num. of mol.: 2 / Fragment: UNP residues 2-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula (archaea) / Strain: DSM 5348 / Gene: HA72_0455 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_T1R(DE3) / References: UniProt: A0A088E2H7, malate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.36 Å3/Da / Density % sol: 63.34 % / Mosaicity: 0.861 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 35 %(v/v) 2-ethoxyethanol, 0.1M sodium cacodylate / hydrochloric acid pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 28, 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: 2.3→50 Å / Num. obs: 40297 / % possible obs: 97.7 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Rrim(I) all: 0.078 / Χ2: 2.716 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.345.30.27119100.8580.1140.2961.53895.1
2.34-2.386.50.26919480.8880.1020.291.76496.3
2.38-2.436.90.26519590.880.0970.2841.84196.9
2.43-2.487.40.23719540.9430.0830.2521.90197.1
2.48-2.537.40.23319720.9430.0810.2481.95297.2
2.53-2.598.10.21219790.9650.070.2251.99597.2
2.59-2.668.60.19919680.9730.0640.212.08297.5
2.66-2.739.30.17819820.9830.0550.1872.13297.4
2.73-2.819.40.1719660.9870.0520.1792.2297.4
2.81-2.910.10.1519840.990.0440.1572.28397.7
2.9-311.40.1319930.9940.0360.1352.48197.8
3-3.1211.80.11920300.9950.0330.1242.49698
3.12-3.26130.10320280.9960.0270.1072.6598.6
3.26-3.4414.10.09120040.9970.0230.0942.8798.7
3.44-3.6514.90.08220580.9980.020.0843.12298.8
3.65-3.9315.80.07420420.9980.0180.0763.27298.8
3.93-4.33160.06720540.9990.0160.0693.33498.8
4.33-4.9516.40.06120980.9980.0150.0633.39198.9
4.95-6.2416.40.05721410.9990.0140.0582.74699.5
6.24-50150.05822270.9980.0160.063.74196.3

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLH

4plh


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.772 / SU ML: 0.156 / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.202
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 2006 5 %RANDOM
Rwork0.1841 ---
obs0.1869 38270 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.64 Å2 / Biso mean: 53.705 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 100 64 4794
Biso mean--54.89 47.78 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194825
X-RAY DIFFRACTIONr_bond_other_d0.0020.024740
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9936518
X-RAY DIFFRACTIONr_angle_other_deg1.076310967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.235600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.63725.138181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87915869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2171517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02983
LS refinement shellResolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 139 -
Rwork0.321 2669 -
all-2808 -
obs--94.42 %

+
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