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- PDB-1llq: Crystal Structure of Malic Enzyme from Ascaris suum Complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1llq
TitleCrystal Structure of Malic Enzyme from Ascaris suum Complexed with Nicotinamide Adenine Dinucleotide
ComponentsNAD-dependent malic enzyme
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / oxaloacetate decarboxylase activity / metabolic process / NAD binding / mitochondrial matrix / metal ion binding
Similarity search - Function
Hemocyanin, N-terminal domain - #30 / arginine biosynthesis bifunctional protein fold / arginine biosynthesis bifunctional protein fold - #10 / 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 ...Hemocyanin, N-terminal domain - #30 / arginine biosynthesis bifunctional protein fold / arginine biosynthesis bifunctional protein fold - #10 / 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 / Hemocyanin, N-terminal domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Other non-globular / Special / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsColeman, D.E. / Jagannatha, G.S. / Goldsmith, E.J. / Cook, P.F. / Harris, B.G.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal structure of the malic enzyme from Ascaris suum complexed with nicotinamide adenine dinucleotide at 2.3 A resolution.
Authors: Coleman, D.E. / Rao, G.S. / Goldsmith, E.J. / Cook, P.F. / Harris, B.G.
History
DepositionApr 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The numbering system used for the coordinates corresponds to the numbering system used in ...SEQUENCE The numbering system used for the coordinates corresponds to the numbering system used in published mutational studies, where residue 1 (LYS) is the first residue present in the fully processed protein chain. A 12 residue mitochondrial transport sequence is present in the unprocessed protein, but is absent from processed protein and the protein present in the crystals.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,4404
Polymers137,1132
Non-polymers1,3272
Water1,33374
1
A: NAD-dependent malic enzyme
B: NAD-dependent malic enzyme
hetero molecules

A: NAD-dependent malic enzyme
B: NAD-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,8798
Polymers274,2264
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area26040 Å2
ΔGint-115 kcal/mol
Surface area89140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.62, 130.62, 149.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe Biological assembly is a tetramer generated from the dimer in the asymmetric unit by appling the following rotation and translation operators to the A and B subunits: -0.500000 0.866025 0.0 0.000 0.866025 0.500000 0.0 0.000 0.000000 0.000000 -1.0 149.230

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Components

#1: Protein NAD-dependent malic enzyme / NAD-ME


Mass: 68556.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm)
References: UniProt: P27443, malate dehydrogenase (oxaloacetate-decarboxylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, tartronate, magnesium sulfate, TRIS, NAD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Clancy, L.L., (1992) J. Mol. Biol., 226, 565.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.947 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 65007 / Num. obs: 65007 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 30
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 6.3 / Num. unique all: 5384 / % possible all: 99.3
Reflection
*PLUS
Num. obs: 62146 / % possible obs: 94.6 % / Num. measured all: 308683 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Rmerge(I) obs: 0.224

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QR6

1qr6


Resolution: 2.3→24.51 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Bulk solvent correction used throughout refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3171 -random
Rwork0.247 ---
all-65007 --
obs-62146 94.6 %-
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9494 0 88 74 9656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.249
LS refinement shellResolution: 2.3→2.37 Å
RfactorNum. reflection% reflection
Rfree0.339 247 -
Rwork0.31 --
obs-4863 87 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor obs: 0.247 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.339 / Rfactor Rwork: 0.31 / Rfactor obs: 0.31

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