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- PDB-1gz3: Molecular mechanism for the regulation of human mitochondrial NAD... -

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Entry
Database: PDB / ID: 1gz3
TitleMolecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate
ComponentsNAD-dependent malic enzyme, mitochondrial
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 / 2.3 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 14, 2002 / Release: May 22, 2003
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 22, 2003Structure modelrepositoryInitial release
1.1Nov 23, 2011Structure modelDatabase references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
1.2Sep 19, 2018Structure modelData collection / Database references / Source and taxonomy / Structure summarycitation / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq_dif_citation.page_last / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent malic enzyme, mitochondrial
B: NAD-dependent malic enzyme, mitochondrial
C: NAD-dependent malic enzyme, mitochondrial
D: NAD-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,70620
Polyers248,6424
Non-polymers3,06516
Water20,8431157
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)22690
ΔGint (kcal/M)-83.8
Surface area (Å2)76370
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)71.815, 192.653, 110.161
Angle α, β, γ (deg.)90.00, 89.77, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
NAD-dependent malic enzyme, mitochondrial / NAD-ME / Malic enzyme 2


Mass: 62160.414 Da / Num. of mol.: 4 / Fragment: RESIDUES 20-573 / Mutation: YES / Source: (gene. exp.) Homo sapiens (human) / Gene: ME2 / Organelle: MITOCHONDRION / Production host: Escherichia coli (E. coli)
References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating)

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Non-polymers , 5 types, 1173 molecules

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


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Formula: C2O4 / Oxalate
#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.: 1157 / Formula: H2O / Water

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 542 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN A, ARG 556 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN B, ARG 556 TO GLN ENGINEERED RESIDUE IN CHAIN C, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN C, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN C, ARG 556 TO GLN ENGINEERED RESIDUE IN CHAIN D, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN D, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN D, ARG 556 TO GLN

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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: 3.06 / Density percent sol: 59.87 %
Crystal growpH: 6 / Details: 9% PEG20K, PH 5.5 NA CITRATE, 5% MPD

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: NSLS BEAMLINE X8C / Synchrotron site: NSLS / Beamline: X8C / Wavelength: 0.979
DetectorCollection date: Feb 15, 2001
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 21.4 Å2 / D resolution high: 2.3 Å / D resolution low: 2 Å / Number obs: 250429 / Rmerge I obs: 0.05 / NetI over sigmaI: 18 / Redundancy: 2.1 % / Percent possible obs: 91
Reflection shellRmerge I obs: 0.087 / Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / MeanI over sigI obs: 11 / Percent possible all: 78

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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

R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 2
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 50.1 / Solvent model param ksol: 0.442
Displacement parametersB iso mean: 27.2 Å2 / Aniso B11: 4.61 Å2 / Aniso B12: 0 Å2 / Aniso B13: -0.74 Å2 / Aniso B22: -6.14 Å2 / Aniso B23: 0 Å2 / Aniso B33: 1.53 Å2
Least-squares processR factor R free: 0.233 / R factor R free error: 0.002 / R factor R work: 0.194 / R factor obs: 0.194 / Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Number reflection R free: 8984 / Number reflection obs: 119325 / Percent reflection R free: 7.5 / Percent reflection obs: 91
Refine analyzeLuzzati coordinate error free: 0.3 Å / Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.21 Å / Luzzati sigma a obs: 0.12 Å
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 20 Å
Number of atoms included #LASTProtein: 17477 / Nucleic acid: 0 / Ligand: 184 / Solvent: 1157 / Total: 18818
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_d23.1
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: 2.3 Å / R factor R free: 0.255 / R factor R free error: 0.2 / R factor R work: 0.213 / Lowest resolution: 2.32 Å / Number reflection R free: 156 / Number reflection R work: 1762 / Total number of bins used: 50 / Percent reflection R free: 8.1 / Percent reflection obs: 72.4

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