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- PDB-1gz4: molecular mechanism of the regulation of human mitochondrial NAD(... -

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Basic information

Entry
Database: PDB / ID: 1gz4
Titlemolecular mechanism of the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate
ComponentsNAD-DEPENDENT MALIC ENZYME
KeywordsOXIDOREDUCTASE / ALLOSTERIC REGULATION / ENERGY METABOLISM / KINETICS
Function / homologyNAD(P)-binding domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzyme, NAD-binding / Citric acid cycle (TCA cycle) / Malic enzymes signature. / Malic enzyme, N-terminal domain / Malic oxidoreductase / Malic enzyme, N-terminal domain superfamily / Malic enzyme, NAD binding domain ...NAD(P)-binding domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzyme, NAD-binding / Citric acid cycle (TCA cycle) / Malic enzymes signature. / Malic enzyme, N-terminal domain / Malic oxidoreductase / Malic enzyme, N-terminal domain superfamily / Malic enzyme, NAD binding domain / regulation of NADP metabolic process / malate dehydrogenase (oxaloacetate-decarboxylating) / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / malate dehydrogenase (decarboxylating) (NAD+) activity / oxaloacetate decarboxylase activity / malate metabolic process / pyruvate metabolic process / tricarboxylic acid cycle / NAD binding / mitochondrial matrix / electron transfer activity / mitochondrion / metal ion binding / NAD-dependent malic enzyme, mitochondrial
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.2 Å resolution
AuthorsYang, Z. / Lanks, C.W. / Tong, L.
CitationJournal: Structure / Year: 2002
Title: Molecular Mechanism for the Regulation of Human Mitochondrial Nad(P)(+)-Dependent Malic Enzyme by ATP and Fumarate
Authors: Yang, Z. / Lanks, C.W. / Tong, L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 15, 2002 / Release: Jul 25, 2002
RevisionDateData content typeGroupProviderType
1.0Jul 25, 2002Structure modelrepositoryInitial release
1.1Nov 23, 2011Structure modelDerived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-DEPENDENT MALIC ENZYME
B: NAD-DEPENDENT MALIC ENZYME
C: NAD-DEPENDENT MALIC ENZYME
D: NAD-DEPENDENT MALIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,42424
Polyers250,2114
Non-polymers5,21420
Water10,305572
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)24790
ΔGint (kcal/M)-87.3
Surface area (Å2)75500
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)224.944, 117.454, 111.610
Angle α, β, γ (deg.)90.00, 109.33, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
NAD-DEPENDENT MALIC ENZYME / HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME / NAD-ME / MALIC ENZYME 2


Mass: 62552.656 Da / Num. of mol.: 4 / Source: (natural) HOMO SAPIENS (human) / Organelle: MITOCHONDRION
References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)

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Non-polymers , 5 types, 592 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical
ChemComp-TTN / TARTRONATE


Mass: 118.045 Da / Num. of mol.: 4 / Formula: C3H2O5
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Formula: Mn / Manganese
#5: Chemical
ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 4 / Formula: C4H4O4 / Fumaric acid
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Formula: H2O / Water

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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: 2.78 / Density percent sol: 55.76 %
Crystal growpH: 6 / Details: 10% PEG20K, PH6.0 MES, 5% MPD, pH 6.00
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
18 mg/mlproteindrop
230 mMTrisdroppH7.4
370 mMdropKCl
410 mMATPdrop
55 mMfumaratedrop
65 mMdropMnCl2
72 mMdithiothreitoldrop
85 mMtartronatedropor oxalate
9100 mMMESreservoirpH6.0
108-10 %(w/v)PEG20000reservoir
115 %(v/v)MPDreservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 32-ID / Synchrotron site: APS / Beamline: 32-ID / Wavelength: 0.97
DetectorCollection date: Jun 15, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionD resolution high: 2.2 Å / D resolution low: 2 Å / Number obs: 123880 / Rmerge I obs: 0.092 / NetI over sigmaI: 13.8 / Redundancy: 3.1 % / Percent possible obs: 95
Reflection shellRmerge I obs: 0.213 / Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / MeanI over sigI obs: 1 / Redundancy: 2.5 % / Percent possible all: 82
Reflection
*PLUS
D resolution low: 2 Å / Number measured all: 379495 / Percent possible obs: 95
Reflection shell
*PLUS
Percent possible obs: 82 / Rmerge I obs: 0.21

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DO8_D

Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 54.3 / Solvent model param ksol: 0.44
Displacement parametersAniso B11: 8.25 Å2 / Aniso B12: 0 Å2 / Aniso B13: -1.84 Å2 / Aniso B22: -4.99 Å2 / Aniso B23: 0 Å2 / Aniso B33: -3.26 Å2
Least-squares processR factor R free: 0.245 / R factor R work: 0.209 / R factor obs: 0.209 / Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Number reflection obs: 123880 / Percent reflection R free: 7.5 / Percent reflection obs: 95
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.29 Å / Luzzati sigma a obs: 0.27 Å
Refine hist #LASTHighest resolution: 2.2 Å / Lowest resolution: 20 Å
Number of atoms included #LASTProtein: 17401 / Nucleic acid: 0 / Ligand: 316 / Solvent: 572 / Total: 18289
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints ncsNcs model details: RESTRAINTS
Refine LS shellHighest resolution: 2.2 Å / R factor R free: 0.301 / R factor R free error: 0.024 / R factor R work: 0.278 / Lowest resolution: 2.21 Å / Number reflection R free: 152 / Number reflection R work: 1948 / Total number of bins used: 50 / Percent reflection R free: 7.2 / Percent reflection obs: 77
Least-squares process
*PLUS
R factor R free: 0.242 / R factor R work: 0.206 / Lowest resolution: 2 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
Refine LS shell
*PLUS
R factor R free: 0.271 / R factor R work: 0.244

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