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- PDB-3wja: The crystal structure of human cytosolic NADP(+)-dependent malic ... -

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Basic information

Entry
Database: PDB / ID: 3wja
TitleThe crystal structure of human cytosolic NADP(+)-dependent malic enzyme in apo form
ComponentsNADP-dependent malic enzyme
KeywordsOXIDOREDUCTASE / NADP(+)-binding Rossmann-fold domains / oxidoreductase activity / metal ion binding
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / regulation of NADP metabolic process / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / nucleotide biosynthetic process / NFE2L2 regulating TCA cycle genes / oxaloacetate decarboxylase activity / Pyruvate metabolism / malate metabolic process / NADP metabolic process ...malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / regulation of NADP metabolic process / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / nucleotide biosynthetic process / NFE2L2 regulating TCA cycle genes / oxaloacetate decarboxylase activity / Pyruvate metabolism / malate metabolic process / NADP metabolic process / response to carbohydrate / NADH metabolic process / pyruvate metabolic process / response to hormone / PPARA activates gene expression / ADP binding / NAD binding / NADP binding / manganese ion binding / protein homotetramerization / carbohydrate metabolic process / electron transfer activity / magnesium ion binding / mitochondrion / identical protein binding / cytoplasm / cytosol
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: 2.548 Å
AuthorsLi, S.-Y. / Chen, M.-C. / Yang, P.-C. / Chan, N.-L. / Liu, J.-H. / Hung, H.-C.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Structural characteristics of the nonallosteric human cytosolic malic enzyme.
Authors: Hsieh, J.Y. / Li, S.Y. / Chen, M.C. / Yang, P.C. / Chen, H.Y. / Chan, N.L. / Liu, J.H. / Hung, H.C.
History
DepositionOct 8, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)130,5892
Polymers130,5892
Non-polymers00
Water4,792266
1
A: NADP-dependent malic enzyme
B: NADP-dependent malic enzyme

A: NADP-dependent malic enzyme
B: NADP-dependent malic enzyme


Theoretical massNumber of molelcules
Total (without water)261,1784
Polymers261,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area18340 Å2
ΔGint-83 kcal/mol
Surface area80050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.213, 116.138, 182.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21B-719-

HOH

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Components

#1: Protein NADP-dependent malic enzyme / cytosolic NADP(+)-dependent malic enzyme / NADP-ME / Malic enzyme 1


Mass: 65294.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ME1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P48163, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 250mM LiCl, 19% (w/v) PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2010
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.548→30 Å / Num. all: 49600 / Num. obs: 49232 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 18.944
Reflection shellResolution: 2.548→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.692 / Num. unique all: 4821 / Rsym value: 0.433 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQ2

1gq2


Resolution: 2.548→25.146 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8403 / SU ML: 0.27 / σ(F): 0 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1914 4.08 %RANDOM
Rwork0.1818 ---
all0.1835 49600 --
obs0.1835 46914 94.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.08 Å2 / Biso mean: 57.7521 Å2 / Biso min: 21.18 Å2
Refinement stepCycle: LAST / Resolution: 2.548→25.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8873 0 0 266 9139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049045
X-RAY DIFFRACTIONf_angle_d0.76512244
X-RAY DIFFRACTIONf_dihedral_angle_d12.2833404
X-RAY DIFFRACTIONf_chiral_restr0.0451378
X-RAY DIFFRACTIONf_plane_restr0.0031597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5481-2.61180.37041240.26282809293383
2.6118-2.68230.31751240.24062910303488
2.6823-2.76120.23321310.22562986311789
2.7612-2.85020.26861320.20643046317891
2.8502-2.95190.25171370.20783170330794
2.9519-3.06990.26431380.21793170330894
3.0699-3.20930.25411320.20963238337096
3.2093-3.37820.26731380.20513305344398
3.3782-3.58930.23591390.19783317345699
3.5893-3.86550.19031400.17343355349598
3.8655-4.25280.1891430.15863364350799
4.2528-4.86430.1951430.1463396353999
4.8643-6.11390.20461440.17053383352797
6.1139-25.14750.18861490.15373551370098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.13420.43381.18531.20650.39731.2103-0.1224-0.00810.19150.0650.06880.2419-0.2156-0.06760.02450.27250.02910.06530.28240.01850.21257.282.810119.6384
21.2022-0.6429-0.2511.44530.62440.76940.0714-0.06570.24720.04010.054-0.1763-0.18440.12940.10510.26980.00420.050.3147-0.04570.270828.23719.613122.6067
31.71850.00520.17311.3029-0.22320.3185-0.0605-0.66320.43310.35630.0291-0.2344-0.22310.0786-0.2320.42350.08060.04020.3922-0.20650.48426.720738.665444.3112
40.5120.35460.72120.61810.74961.3658-0.1192-0.13340.1868-0.03480.01770.2146-0.2338-0.33230.07340.32510.0990.0190.32160.00310.46087.056127.455921.0073
50.61960.2476-0.42931.45790.30260.6552-0.021-0.0758-0.0963-0.2110.0667-0.03210.0818-0.1310.08750.32950.06220.03130.4278-0.01680.248330.3238-2.780815.2945
61.5203-0.8409-0.01652.0533-0.27940.38490.03460.0126-0.19670.14130.07620.31490.164-0.05870.32640.27460.00880.02520.2660.05110.23728.6666-20.891820.8694
71.9224-0.00630.09291.6579-0.43322.33560.0567-0.2433-0.36410.0872-0.1020.01210.2677-0.0453-0.01070.32190.0375-0.01390.18370.06360.372614.5493-41.570433.8864
80.28660.3561-0.41640.3324-0.40650.7091-0.01620.053-0.1113-0.0128-0.0148-0.13820.06780.17560.00290.32640.04740.02820.4327-0.05040.371634.1463-19.0344-0.4254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 18:102 )A18 - 102
2X-RAY DIFFRACTION2chain 'A' and (resseq 103:298 )A103 - 298
3X-RAY DIFFRACTION3chain 'A' and (resseq 299:442 )A299 - 442
4X-RAY DIFFRACTION4chain 'A' and (resseq 443:579 )A443 - 579
5X-RAY DIFFRACTION5chain 'B' and (resseq 18:74 )B18 - 74
6X-RAY DIFFRACTION6chain 'B' and (resseq 75:298 )B75 - 298
7X-RAY DIFFRACTION7chain 'B' and (resseq 299:533 )B299 - 533
8X-RAY DIFFRACTION8chain 'B' and (resseq 534:580 )B534 - 580

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