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- PDB-7rm9: Human Malate Dehydrogenase I (MDHI) -

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Basic information

Entry
Database: PDB / ID: 7rm9
TitleHuman Malate Dehydrogenase I (MDHI)
ComponentsMalate dehydrogenase, cytoplasmic
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


diiodophenylpyruvate reductase activity / diiodophenylpyruvate reductase / malic enzyme activity / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / NADP metabolic process / oxaloacetate metabolic process / Gluconeogenesis / NADH metabolic process ...diiodophenylpyruvate reductase activity / diiodophenylpyruvate reductase / malic enzyme activity / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / NADP metabolic process / oxaloacetate metabolic process / Gluconeogenesis / NADH metabolic process / tricarboxylic acid cycle / centrosome / extracellular space / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 domain superfamily
Similarity search - Domain/homology
MALONATE ION / Malate dehydrogenase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMcCue, W. / Finzel, B.C.
CitationJournal: Acs Omega / Year: 2022
Title: Structural Characterization of the Human Cytosolic Malate Dehydrogenase I.
Authors: McCue, W.M. / Finzel, B.C.
History
DepositionJul 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase, cytoplasmic
B: Malate dehydrogenase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0443
Polymers72,9422
Non-polymers1021
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-21 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.503, 84.312, 77.652
Angle α, β, γ (deg.)90.000, 91.223, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Malate dehydrogenase, cytoplasmic / Cytosolic malate dehydrogenase / Diiodophenylpyruvate reductase


Mass: 36471.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDH1, MDHA / Production host: Escherichia coli (E. coli)
References: UniProt: P40925, malate dehydrogenase, diiodophenylpyruvate reductase
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 28% PEG 4000, 100 mM Malonate pH 7.25, 0.15 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→77.634 Å / Num. obs: 73795 / % possible obs: 92.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 13.8
Reflection shellResolution: 1.65→1.678 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3944 / CC1/2: 0.88 / Rpim(I) all: 0.209 / Rrim(I) all: 0.385

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
AutoProcessdata processing
JDirectordata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mdh

5mdh


Resolution: 1.65→38.82 Å / SU ML: 0.1613 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.4183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 3685 4.99 %
Rwork0.166 70101 -
obs0.1674 73786 92.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 7 388 5374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625093
X-RAY DIFFRACTIONf_angle_d0.91046898
X-RAY DIFFRACTIONf_chiral_restr0.0635812
X-RAY DIFFRACTIONf_plane_restr0.0062878
X-RAY DIFFRACTIONf_dihedral_angle_d6.4949696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.22811560.18642859X-RAY DIFFRACTION100
1.67-1.690.2231500.18352918X-RAY DIFFRACTION99.97
1.69-1.720.20561530.17042910X-RAY DIFFRACTION99.97
1.72-1.740.19461430.15732892X-RAY DIFFRACTION100
1.74-1.770.21441530.15772907X-RAY DIFFRACTION100
1.77-1.80.1931620.16062887X-RAY DIFFRACTION99.93
1.8-1.830.21011520.16592931X-RAY DIFFRACTION100
1.83-1.870.20571580.172867X-RAY DIFFRACTION99.97
1.87-1.90.2358230.1828866X-RAY DIFFRACTION29.09
1.9-1.940.23441010.1891914X-RAY DIFFRACTION65.83
1.94-1.980.2132800.1671147X-RAY DIFFRACTION39.92
1.98-2.030.21371820.17592806X-RAY DIFFRACTION99.83
2.03-2.080.2251720.17242923X-RAY DIFFRACTION99.74
2.08-2.140.19311770.17622892X-RAY DIFFRACTION99.87
2.14-2.20.22871660.17152856X-RAY DIFFRACTION99.44
2.2-2.270.19891490.17242895X-RAY DIFFRACTION99.64
2.27-2.350.22131580.17172945X-RAY DIFFRACTION99.71
2.35-2.440.22191280.17252891X-RAY DIFFRACTION99.54
2.44-2.560.18591720.17542899X-RAY DIFFRACTION99.77
2.56-2.690.2241580.18842886X-RAY DIFFRACTION99.51
2.69-2.860.22131260.19122948X-RAY DIFFRACTION99.77
2.86-3.080.21281510.18172905X-RAY DIFFRACTION99.61
3.08-3.390.20341570.17062920X-RAY DIFFRACTION99.58
3.39-3.880.12971150.15262411X-RAY DIFFRACTION82.28
3.88-4.880.14141190.12632799X-RAY DIFFRACTION94.01
4.89-38.820.16741240.15043027X-RAY DIFFRACTION99.84

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