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- PDB-2aw5: Crystal structure of a human malic enzyme -

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Basic information

Entry
Database: PDB / ID: 2aw5
TitleCrystal structure of a human malic enzyme
ComponentsNADP-dependent malic enzyme
KeywordsOXIDOREDUCTASE / Rossmann fold / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / NFE2L2 regulating TCA cycle genes / nucleotide biosynthetic process / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / NADP metabolic process ...malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / NFE2L2 regulating TCA cycle genes / nucleotide biosynthetic process / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / NADP metabolic process / pyruvate metabolic process / response to carbohydrate / NADH metabolic process / response to hormone / ADP binding / PPARA activates gene expression / NAD binding / NADP binding / manganese ion binding / protein homotetramerization / electron transfer activity / carbohydrate metabolic process / magnesium ion binding / mitochondrion / identical protein binding / cytosol / cytoplasm
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
NADP-dependent malic enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPapagrigoriou, E. / Berridge, G. / Smee, C. / Bray, J. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U. / Gileadi, O. ...Papagrigoriou, E. / Berridge, G. / Smee, C. / Bray, J. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U. / Gileadi, O. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of a human malic enzyme
Authors: Papagrigoriou, E. / Berridge, G. / Smee, C. / Bray, J. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U. / Gileadi, O. / von Delft, F.
History
DepositionAug 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: NADP-dependent malic enzyme
B: NADP-dependent malic enzyme
C: NADP-dependent malic enzyme


Theoretical massNumber of molelcules
Total (without water)193,4003
Polymers193,4003
Non-polymers00
Water0
1
A: NADP-dependent malic enzyme

A: NADP-dependent malic enzyme


Theoretical massNumber of molelcules
Total (without water)128,9332
Polymers128,9332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
2
B: NADP-dependent malic enzyme
C: NADP-dependent malic enzyme


Theoretical massNumber of molelcules
Total (without water)128,9332
Polymers128,9332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-19 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.505, 136.963, 117.840
Angle α, β, γ (deg.)90.00, 121.75, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22C
32A
42C
52A
62C
72A
82C
92A
102C
112A
122C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYGLNGLN3AA280 - 551291 - 562
211GLYGLYILEILE3BB280 - 552291 - 563
321LEULEUALAALA5AA44 - 27955 - 290
421LEULEUALAALA5BB44 - 27955 - 290
112GLYGLYSERSER3AA280 - 407291 - 418
212GLYGLYSERSER3CC280 - 407291 - 418
322CYSCYSLEULEU3AA420 - 441431 - 452
422CYSCYSLEULEU3CC420 - 441431 - 452
532SERSERTHRTHR3AA455 - 547466 - 558
632SERSERTHRTHR3CC455 - 547466 - 558
742LEULEUALAALA5AA44 - 27955 - 290
842LEULEUALAALA5CC44 - 27955 - 290
952SERSERGLNGLN5AA407 - 419418 - 430
1052SERSERGLNGLN5CC407 - 419418 - 430
1162PROPROASNASN5AA442 - 454453 - 465
1262PROPROASNASN5CC442 - 454453 - 465

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a tetramer generated from the chain A molecule of the asu by the operations (there are three olecules in the asu): ROTATION MATRIX: -1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS 62.00893 -0.00001-100.20600, ROTATION MATRIX: -0.23721 -0.72192 -0.65005 -0.77206 -0.26605 0.57719 -0.58963 0.63879 -0.49426 TRANSLATION VECTOR IN AS 43.48327 94.22293 -59.04757, ROTATION MATRIX: 0.30283 -0.76600 0.56705 0.73573 -0.19031 -0.64999 0.60580 0.61403 0.50594 TRANSLATION VECTOR IN AS 93.06689 -18.36662 -46.28003,

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Components

#1: Protein NADP-dependent malic enzyme / ME1 / NADP-ME / Malic enzyme 1


Mass: 64466.535 Da / Num. of mol.: 3 / Fragment: residues 15-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 R3
References: UniProt: P48163, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)

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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: 2.5 Å3/Da / Density % sol: 54.519791 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG 1K, Glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→37.45 Å / Num. all: 71047 / Num. obs: 69400 / % possible obs: 97.8 %
Reflection shellResolution: 2.5→2.64 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 23.171 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 3520 5.1 %RANDOM
Rwork0.2074 ---
all0.20984 ---
obs0.20984 65880 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.395 Å2
Baniso -1Baniso -2Baniso -3
1--4.82 Å20 Å2-3.12 Å2
2--2.28 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11920 0 0 0 11920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212156
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211122
X-RAY DIFFRACTIONr_angle_refined_deg1.431.96716541
X-RAY DIFFRACTIONr_angle_other_deg0.91325600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96551595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73924.306497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.007151879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7151566
X-RAY DIFFRACTIONr_chiral_restr0.090.21924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022428
X-RAY DIFFRACTIONr_nbd_refined0.2280.22934
X-RAY DIFFRACTIONr_nbd_other0.180.211618
X-RAY DIFFRACTIONr_nbtor_refined0.1870.26172
X-RAY DIFFRACTIONr_nbtor_other0.0890.27169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.83738086
X-RAY DIFFRACTIONr_mcbond_other0.60233249
X-RAY DIFFRACTIONr_mcangle_it3.06512702
X-RAY DIFFRACTIONr_scbond_it5.40674489
X-RAY DIFFRACTIONr_scangle_it7.723113839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11570tight positional0.050.05
21402tight positional0.090.05
11389medium positional0.380.5
21533medium positional1.010.5
14084loose positional0.475
24247loose positional0.875
11570tight thermal4.9110
21402tight thermal4.0510
11389medium thermal12
21533medium thermal1.232
14084loose thermal3.5110
24247loose thermal3.1110
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 280 -
Rwork0.301 4771 -
obs--97.28 %

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