[English] 日本語
Yorodumi
- PDB-2dfd: Crystal Structure of Human Malate Dehydrogenase Type 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dfd
TitleCrystal Structure of Human Malate Dehydrogenase Type 2
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / Citric acid cycle / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


malate-aspartate shuttle / L-malate dehydrogenase (NADP+) activity / Malate-aspartate shuttle / Citric acid cycle (TCA cycle) / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle ...malate-aspartate shuttle / L-malate dehydrogenase (NADP+) activity / Malate-aspartate shuttle / Citric acid cycle (TCA cycle) / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / aerobic respiration / gluconeogenesis / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / membrane / nucleus / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 ...Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE / HISTIDINE / D-MALATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsUgochukwu, E. / Shafqat, N. / Rojkova, A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Malate Dehydrogenase Type 2
Authors: Ugochukwu, E. / Shafqat, N. / Rojkova, A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U.
History
DepositionFeb 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)148,96723
Polymers144,9714
Non-polymers3,99619
Water14,394799
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,58812
Polymers72,4862
Non-polymers2,10310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-60 kcal/mol
Surface area21890 Å2
MethodPISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,37911
Polymers72,4862
Non-polymers1,8939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-70 kcal/mol
Surface area22330 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14920 Å2
ΔGint-139 kcal/mol
Surface area42510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.943, 152.526, 154.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 6 - 319 / Label seq-ID: 28 - 341

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Malate dehydrogenase / Malate Dehydrogenase Type 2


Mass: 36242.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDH2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P40926, malate dehydrogenase

-
Non-polymers , 6 types, 818 molecules

#2: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MMT, 30% PEG1000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99806 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99806 Å / Relative weight: 1
ReflectionResolution: 1.9→6.01 Å / Num. obs: 112689 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLD

1mld


Resolution: 1.9→6.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.372 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19416 5642 5 %RANDOM
Rwork0.15583 ---
all0.15774 106859 --
obs0.15774 106859 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--0.75 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9160 0 254 799 10213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229670
X-RAY DIFFRACTIONr_bond_other_d0.0020.026295
X-RAY DIFFRACTIONr_angle_refined_deg1.5422.00813196
X-RAY DIFFRACTIONr_angle_other_deg0.987315655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93651269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15225.446314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98151585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6511528
X-RAY DIFFRACTIONr_chiral_restr0.0880.21615
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021643
X-RAY DIFFRACTIONr_nbd_refined0.2150.22051
X-RAY DIFFRACTIONr_nbd_other0.1870.26424
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24752
X-RAY DIFFRACTIONr_nbtor_other0.0880.24579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2725
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.220
X-RAY DIFFRACTIONr_mcbond_it0.8661.56852
X-RAY DIFFRACTIONr_mcbond_other0.2451.52557
X-RAY DIFFRACTIONr_mcangle_it1.16210201
X-RAY DIFFRACTIONr_scbond_it2.07233630
X-RAY DIFFRACTIONr_scangle_it2.994.52987
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1824medium positional0.150.5
2B1824medium positional0.120.5
3C1824medium positional0.170.5
4D1824medium positional0.130.5
1A1828loose positional0.445
2B1828loose positional0.365
3C1828loose positional0.485
4D1828loose positional0.385
1A1824medium thermal1.0810
2B1824medium thermal1.1210
3C1824medium thermal1.2110
4D1824medium thermal110
1A1828loose thermal1.3610
2B1828loose thermal1.3210
3C1828loose thermal1.6410
4D1828loose thermal1.3210
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 396 -
Rwork0.253 7681 -
obs--97.91 %
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)
10.9381-0.41050.05471.55740.50021.0843-0.05840.0295-0.09350.0575-0.0271-0.00320.0115-0.02170.0855-0.04970.0407-0.0624-0.1266-0.0897-0.111829.1224136.908835.0246
21.3943-0.25250.04171.13470.14671.0257-0.00890.23220.1845-0.1636-0.09790.0925-0.2935-0.18430.10680.11660.1146-0.143-0.0571-0.053-0.077616.3932169.216229.6236
30.9576-0.24210.0272.1164-0.2080.65130.00290.1304-0.03550.093-0.04370.2793-0.1211-0.00930.0407-0.20160.00670.0008-0.1594-0.0356-0.148226.3376177.277567.9295
41.1655-0.49410.12081.6138-0.11891.27270.10530.0919-0.20990.0107-0.1118-0.0350.2220.35450.0065-0.18490.0755-0.0215-0.0112-0.073-0.131349.9564151.134666.7504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 31928 - 341
2X-RAY DIFFRACTION2BB6 - 31928 - 341
3X-RAY DIFFRACTION3CC6 - 31928 - 341
4X-RAY DIFFRACTION4DD6 - 31928 - 341

+
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