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- PDB-6urf: Malic enzyme from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6urf
TitleMalic enzyme from Mycobacterium tuberculosis
ComponentsNAD-dependent malic enzyme
KeywordsOXIDOREDUCTASE / Malic enzyme / Fatty acid synthesis / Glucose metabolism / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / malate metabolic process / pyruvate metabolic process / NAD binding / metal ion binding / cytosol
Similarity search - Function
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Malate oxidoreductase / Putative malate oxidoreductase [NAD]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsCuthbert, B.J. / Burley, K.H. / Goulding, C.W. / Mathews, E.I. / Beste, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095208 United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target.
Authors: Burley, K.H. / Cuthbert, B.J. / Basu, P. / Newcombe, J. / Irimpan, E.M. / Quechol, R. / Foik, I.P. / Mobley, D.L. / Beste, D.J.V. / Goulding, C.W.
History
DepositionOct 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)248,6259
Polymers248,1644
Non-polymers4605
Water1,802100
1
A: NAD-dependent malic enzyme
B: NAD-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4516
Polymers124,0822
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-24 kcal/mol
Surface area45900 Å2
MethodPISA
2
C: NAD-dependent malic enzyme
D: NAD-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1743
Polymers124,0822
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-22 kcal/mol
Surface area45450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.548, 143.178, 117.617
Angle α, β, γ (deg.)90.000, 109.773, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
NAD-dependent malic enzyme / [NAD]-dependent malate oxidoreductase


Mass: 62041.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: mez, mez_2, DSI35_04950, ERS007657_00054, ERS007661_01303, ERS007665_00385, ERS007670_00245, ERS007672_00340, ERS007681_00703, ERS007703_00793, ERS007720_02108, ERS007722_00150, ERS007741_ ...Gene: mez, mez_2, DSI35_04950, ERS007657_00054, ERS007661_01303, ERS007665_00385, ERS007670_00245, ERS007672_00340, ERS007681_00703, ERS007703_00793, ERS007720_02108, ERS007722_00150, ERS007741_00458, ERS023446_00378, ERS024276_00123, ERS027644_00794, ERS027646_00126, ERS027651_00016, ERS027652_00738, ERS027654_00055, ERS027659_00902, ERS027661_00290, ERS027666_00475, ERS031537_00346, ERS124361_01639, FDK60_04380, SAMEA2682835_05736, SAMEA2682864_03296, SAMEA2683035_01163
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045JP82, UniProt: P9WK25*PLUS, malate dehydrogenase (oxaloacetate-decarboxylating)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 200mM NaCl, 2mM Glycine, 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→47.17 Å / Num. obs: 34246 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 101.5 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.1368 / Rpim(I) all: 0.1368 / Rrim(I) all: 0.1934 / Net I/σ(I): 4.43
Reflection shellResolution: 3.6→3.729 Å / Redundancy: 2 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 3417 / CC1/2: 0.491 / CC star: 0.811 / Rpim(I) all: 0.777 / Rrim(I) all: 1.099 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
pointless1.11.19data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AW5

2aw5


Resolution: 3.6→47.17 Å / SU ML: 0.6422 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.327 1995 5.84 %
Rwork0.3053 32190 -
obs0.3065 34185 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.86 Å2
Refinement stepCycle: LAST / Resolution: 3.6→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13482 0 30 100 13612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003813738
X-RAY DIFFRACTIONf_angle_d0.821918874
X-RAY DIFFRACTIONf_chiral_restr0.05682287
X-RAY DIFFRACTIONf_plane_restr0.00722551
X-RAY DIFFRACTIONf_dihedral_angle_d12.34368048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.690.42371420.40632285X-RAY DIFFRACTION99.43
3.69-3.790.37621490.36952323X-RAY DIFFRACTION99.84
3.79-3.90.37581380.38752231X-RAY DIFFRACTION98.59
3.9-4.030.3331350.35632300X-RAY DIFFRACTION99.96
4.03-4.170.36541470.33212276X-RAY DIFFRACTION99.88
4.17-4.340.34251360.31642314X-RAY DIFFRACTION99.92
4.34-4.540.30981480.29132296X-RAY DIFFRACTION99.96
4.54-4.770.31021440.29012287X-RAY DIFFRACTION99.96
4.77-5.070.31071400.29312276X-RAY DIFFRACTION99.79
5.07-5.460.32631410.31432317X-RAY DIFFRACTION99.88
5.46-6.010.32661440.31992306X-RAY DIFFRACTION100
6.01-6.880.35721470.30592323X-RAY DIFFRACTION99.96
6.88-8.660.28821350.28152314X-RAY DIFFRACTION100
8.66-47.170.29061490.24622342X-RAY DIFFRACTION99.24

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