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- PDB-1qr6: HUMAN MITOCHONDRIAL NAD(P)-DEPENDENT MALIC ENZYME -

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Basic information

Entry
Database: PDB / ID: 1qr6
TitleHUMAN MITOCHONDRIAL NAD(P)-DEPENDENT MALIC ENZYME
ComponentsMALIC ENZYME 2
KeywordsOXIDOREDUCTASE / FOUR DOMAINS / ROSSMANN FOLD
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / NAD binding ...malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / NAD binding / electron transfer activity / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain ...Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsXu, Y. / Bhargava, G. / Wu, H. / Loeber, G. / Tong, L.
CitationJournal: Structure / Year: 1999
Title: Crystal structure of human mitochondrial NAD(P)(+)-dependent malic enzyme: a new class of oxidative decarboxylases.
Authors: Xu, Y. / Bhargava, G. / Wu, H. / Loeber, G. / Tong, L.
History
DepositionJun 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALIC ENZYME 2
B: MALIC ENZYME 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0106
Polymers132,3562
Non-polymers2,6544
Water13,691760
1
A: MALIC ENZYME 2
B: MALIC ENZYME 2
hetero molecules

A: MALIC ENZYME 2
B: MALIC ENZYME 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,01912
Polymers264,7124
Non-polymers5,3078
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area22130 Å2
ΔGint-94 kcal/mol
Surface area77450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)204.4, 107.0, 59.2
Angle α, β, γ (deg.)90, 90, 101.9
Int Tables number5
Cell settingmonoclinic
Space group name H-MB112

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Components

#1: Protein MALIC ENZYME 2 / / E.C.1.1.1.39


Mass: 66177.977 Da / Num. of mol.: 2 / Mutation: METHIONINES REPLACED BY SELENOMETHIONINES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P23368, malate dehydrogenase (decarboxylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 MM HEPES, 8% PEG 8000, 5% MPD, 6 MM MGSO4, 10 MM TARTRONATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
230 mMTris1drop
3125 mM1dropKCl
43 mMNAD+1drop
510 mMdithiothreitol1drop
6100 mMHEPES1reservoir
78 %PEG80001reservoir
85 %MPD1reservoir
96 mM1reservoirMgSO4
1010 mMtartronate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS F210.9
SYNCHROTRONNSLS X4A20.98
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 5, 1998
RIGAKU RAXIS IV2IMAGE PLATEAug 25, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.981
ReflectionResolution: 2.1→20 Å / Num. obs: 70337 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 20
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.108 / % possible all: 69
Reflection
*PLUS
Num. measured all: 343811

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Processing

Software
NameVersionClassification
MADSYSphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.287 -7.5 %RANDOM
Rwork0.228 ---
obs0.228 64039 87 %-
all-70337 --
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8684 0 176 760 9620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4

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