[English] 日本語
Yorodumi
- PDB-5mdh: CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALAT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mdh
TitleCRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALATE DEHYDROGENASE ALPHA-KETOMALONATE AND TNAD AT 2.4 ANGSTROMS RESOLUTION
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / (NAD(A)-CHOH(D))
Function / homology
Function and homology information


diiodophenylpyruvate reductase / hydroxyphenylpyruvate reductase activity / Malate-aspartate shuttle / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / NAD binding / cytosol
Similarity search - Function
Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / 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 ...Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / 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
ALPHA-KETOMALONIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChapman, A.D.M. / Cortes, A. / Dafforn, T.R. / Clarke, A.R. / Brady, R.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.
Authors: Chapman, A.D. / Cortes, A. / Dafforn, T.R. / Clarke, A.R. / Brady, R.L.
#1: Journal: Biochemistry / Year: 1989
Title: Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-A Resolution
Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J.
#2: Journal: Biochemistry / Year: 1987
Title: Structure of Porcine Heart Cytoplasmic Malate Dehydrogenase. Combining X-Ray Diffraction and Chemical Sequence Data in Structural Studies
Authors: Birktoft, J.J. / Bradshaw, R.A. / Banaszak, L.J.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: The Presence of a Histidine-Aspartic Acid Pair in the Active Site of 2-Hydroxyacid Dehydrogenases. X-Ray Refinement of Cytoplasmic Malate Dehydrogenase
Authors: Birktoft, J.J. / Banaszak, L.J.
#4: Journal: MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY / Year: 1982
Title: The Interactions of Nad/Nadh with 2-Hydroxy Acid Dehydrogenases
Authors: Birktoft, J.J. / Fernley, R.T. / Bradshaw, R.A. / Banaszak, L.J.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Amino Acid Sequence Homology Among the 2-Hydroxy Acid Dehydrogenases. Mitochondrial and Cytoplasmic Malate Dehydrogenases Form a Homologous System with Lactate Dehydrogenase
Authors: Birktoft, J.J. / Fernley, R.T. / Bradshaw, R.A. / Banaszak, L.J.
#6: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: Nicotinamide Adenine Dinucleotide and the Active Site of Cytoplasmic Malate Dehydrogenase
Authors: Banaszak, L.J. / Webb, L.E.
#7: Journal: Biochemistry / Year: 1973
Title: Conformation of Nicotinamide Adenine Dinucleotide Bound to Cytoplasmic Malate Dehydrogenase
Authors: Webb, L.E. / Hill, E.J. / Banaszak, L.J.
#8: Journal: J.Mol.Biol. / Year: 1972
Title: Polypeptide Conformation of Cytoplasmic Malate Dehydrogenase from an Electron Density Map at 3.0 Angstroms Resolution
Authors: Hill, E. / Tsernoglou, D. / Webb, L. / Banaszak, L.J.
#9: Journal: Biochem.Biophys.Res.Commun. / Year: 1972
Title: The Identification of an Asymmetric Complex of Nicotinamide Adenine Dinucleotide and Pig Heart Cytoplasmic Malate Dehydrogenase
Authors: Glatthaar, B.E. / Banaszak, L.J. / Bradshaw, R.A.
#10: Journal: J.Mol.Biol. / Year: 1972
Title: Cytoplasmic Malate Dehydrogenase--Heavy Atom Derivatives and Low Resolution Structure
Authors: Tsernoglou, D. / Hill, E. / Banaszak, L.J.
#11: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Structural Studies on Heart Muscle Malate Dehydrogenases
Authors: Tsernoglou, D. / Hill, E. / Banaszak, L.J.
History
DepositionOct 8, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 17, 2011Group: Derived calculations
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2996
Polymers72,7362
Non-polymers1,5634
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-40 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.700, 144.432, 59.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. ALTHOUGH THE TWO SUBUNITS ARE CHEMICALLY EQUIVALENT, THEY ARE RELATED BY A NON-CRYSTALLOGRAPHIC SYMMETRY AXIS WITH A ROTATION ANGLE OF 174.9 DEGREES WHICH IS SIGNIFICANTLY DIFFERENT FROM A TRUE TWO-FOLD SYMMETRY OPERATION.

-
Components

#1: Protein MALATE DEHYDROGENASE


Mass: 36367.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: MUSCLE / Cellular location: CYTOPLASM / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P11708, malate dehydrogenase
#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-MAK / ALPHA-KETOMALONIC ACID


Mass: 118.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.78 Å3/Da / Density % sol: 57.1 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.15 mMammonium acetate1reservoir
216 %(v/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 26268 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Biso Wilson estimate: 42.44 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 12.34
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.72 / Rsym value: 0.32 / % possible all: 91.6

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MDH

4mdh


Resolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.67 / ESU R Free: 0.3
Details: ATOMS WITH ZERO OCCUPANCIES HAVE NO ELECTRON DENSITY IN THE MAPS, THEREFORE THE POSITIONS OF THESE RESIDUES CANNOT BE DETERMINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1492 5 %RANDOM
Rwork0.1994 ---
obs-29520 84.3 %-
Displacement parametersBiso mean: 46.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 104 354 5558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0650.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3162
X-RAY DIFFRACTIONp_mcangle_it2.1193
X-RAY DIFFRACTIONp_scbond_it1.4292
X-RAY DIFFRACTIONp_scangle_it2.1733
X-RAY DIFFRACTIONp_plane_restr0.022
X-RAY DIFFRACTIONp_chiral_restr0.128
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor7.87
X-RAY DIFFRACTIONp_staggered_tor20.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.25378 / Rfactor Rwork: 0.19946
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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