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- PDB-7rrl: Alternate Crystal Form of Human Malate Dehydrogenase I -

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Basic information

Entry
Database: PDB / ID: 7rrl
TitleAlternate Crystal Form of Human Malate Dehydrogenase I
ComponentsMalate dehydrogenase, cytoplasmic
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


diiodophenylpyruvate reductase activity / diiodophenylpyruvate reductase / hydroxyphenylpyruvate reductase activity / malate-aspartate shuttle / Malate-aspartate shuttle / malic enzyme activity / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / NADP metabolic process ...diiodophenylpyruvate reductase activity / diiodophenylpyruvate reductase / hydroxyphenylpyruvate reductase activity / malate-aspartate shuttle / Malate-aspartate shuttle / malic enzyme activity / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / NADP metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / centrosome / extracellular space / extracellular exosome / cytosol / cytoplasm
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
Malate dehydrogenase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMcCue, W. / Finzel, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Ph.D.Thesis,University of Minnesota / Year: 2021
Title: Structural Studies to Enable Drug Discovery
Authors: McCue, W.
History
DepositionAug 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,9422
Polymers72,9422
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-27 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.875, 62.593, 74.322
Angle α, β, γ (deg.)90.000, 91.219, 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P40925, malate dehydrogenase, diiodophenylpyruvate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 4000, 100 mM NaMalonate pH 7.2, and 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: 2.05→74.31 Å / Num. obs: 39122 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.06 / Rrim(I) all: 0.114 / Net I/σ(I): 8.4 / Num. measured all: 135782 / Scaling rejects: 61
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.601 / Num. unique obs: 5707 / CC1/2: 0.724 / Rpim(I) all: 0.359 / Rrim(I) all: 0.702 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
JDirectordata collection
PHASERphasing
AutoProcessdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDH

5mdh


Resolution: 2.05→46.01 Å / SU ML: 0.2794 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1979 5.06 %
Rwork0.1864 37113 -
obs0.1887 39092 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.77 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4878 0 0 180 5058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724961
X-RAY DIFFRACTIONf_angle_d0.84866734
X-RAY DIFFRACTIONf_chiral_restr0.0532801
X-RAY DIFFRACTIONf_plane_restr0.0063859
X-RAY DIFFRACTIONf_dihedral_angle_d6.4482684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.30931540.25752643X-RAY DIFFRACTION100
2.1-2.160.26891510.22672633X-RAY DIFFRACTION99.93
2.16-2.220.26511580.21552612X-RAY DIFFRACTION99.86
2.22-2.290.2681850.20882592X-RAY DIFFRACTION99.53
2.29-2.380.3071560.20372619X-RAY DIFFRACTION99.28
2.38-2.470.29491370.21042630X-RAY DIFFRACTION99.64
2.47-2.580.29871220.22032666X-RAY DIFFRACTION99.71
2.58-2.720.28011330.22042676X-RAY DIFFRACTION99.61
2.72-2.890.24311540.21462630X-RAY DIFFRACTION99.57
2.89-3.110.30241270.22112687X-RAY DIFFRACTION99.86
3.11-3.430.26791320.20042652X-RAY DIFFRACTION99.57
3.43-3.920.19091250.17362692X-RAY DIFFRACTION99.19
3.92-4.940.18551250.14072623X-RAY DIFFRACTION97.65
4.94-46.010.16011200.1462758X-RAY DIFFRACTION99.04

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