[English] 日本語
Yorodumi
- PDB-4mdh: REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mdh
TitleREFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION
ComponentsCYTOPLASMIC MALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(NAD(A)-CHOH(D))
Function / homology
Function and homology information


diiodophenylpyruvate reductase / (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] activity / Malate-aspartate shuttle / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBirktoft, J.J. / Banaszak, L.J.
Citation
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.
#1: Journal: To be Published
Title: Comparison of the Molecular Structures of Cytoplasmic and Mitochondrial Malate Dehydrogenase
Authors: Birktoft, J.J. / Fu, Z. / Carnahan, G.E. / Rhodes, G. / Roderick, S.L. / 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
DepositionApr 12, 1989Processing site: BNL
SupersessionApr 19, 1989ID: 2MDH
Revision 1.0Apr 19, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET IN SHEET S2 THE REGULAR HYDROGEN BONDING PATTERN IS DISRUPTED BY A THREE RESIDUE BULGE ...SHEET IN SHEET S2 THE REGULAR HYDROGEN BONDING PATTERN IS DISRUPTED BY A THREE RESIDUE BULGE (RESIDUES 194 -196) IN STRAND 2. IN SHEET S1 A BETA BULGE IS FOUND IN STRAND 1 AT RESIDUE 64.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOPLASMIC MALATE DEHYDROGENASE
B: CYTOPLASMIC MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3076
Polymers72,7882
Non-polymers1,5194
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-87 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.200, 86.600, 58.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUES PRO A 131 AND PRO B 131 ARE CIS PROLINES. / 2: SEE REMARK 5.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.86554, 0.46781, -0.17888), (0.49979, 0.82988, -0.24802), (0.03242, -0.30407, -0.9521)
Vector: 55.214, -1.799, 89.133)

-
Components

#1: Protein CYTOPLASMIC MALATE DEHYDROGENASE


Mass: 36393.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P11708, malate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHREE DIFFERENT COMPOUNDS CONTAINING HEAVY ATOMS WERE FOUND TO BIND TO CMDH. EACH ASYMMETRIC UNIT ...THREE DIFFERENT COMPOUNDS CONTAINING HEAVY ATOMS WERE FOUND TO BIND TO CMDH. EACH ASYMMETRIC UNIT CONTAINING A DIMERIC CMDH MOLECULE BINDS P-HYDROXYMERCURIPHENYL SULFONIC ACID (PMS) AT THREE SITES, PLATINUM ETHYLENEDIAMINE DICHLORIDE (PED) AT EIGHT SITES AND URANOYL DIOXYGENATE (UO2) AT SEVEN SITES. THE COORDINATES OF THESE HEAVY ATOM SITES ARE AS FOLLOWS - PMS G 1 22.274 14.896 47.569 PMS G 2 36.054 9.960 41.219 PMS G 3 31.451 15.151 36.570 PED G 11 8.142 37.151 32.750 PED G 12 58.882 28.231 51.570 PED G 13 26.172 38.361 33.750 PED G 14 34.941 31.350 2.350 PED G 15 31.601 25.631 23.460 PED G 16 43.712 35.851 47.390 PED G 17 52.202 36.631 39.400 PED G 18 21.850 43.390 47.300 UO2 G 21 2.371 18.101 27.750 UO2 G 22 47.470 5.890 7.060 UO2 G 23 64.870 7.790 6.640 UO2 G 24 3.901 29.971 21.110 UO2 G 25 59.440 8.750 9.880 UO2 G 26 46.490 1.300 2.410 UO2 G 27 .003 43.302 .235 NOTE THAT THESE HEAVY-ATOM COORDINATES ARE NOT IDENTICAL TO THOSE PRESENTED IN TABLE 1 OF REFERENCE 10 ABOVE WHICH WERE DESCRIBED IN A LEFT-HANDED COORDINATE FRAME.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %

-
Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Num. all: 23373 / Num. obs: 22910

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.5→6 Å / Rfactor obs: 0.167
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 98 471 5675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.57
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Num. reflection obs: 22910 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_d2.57
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d

+
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