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- PDB-7qoz: Crystal structure of NAD-bound glycosomal malate dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 7qoz
TitleCrystal structure of NAD-bound glycosomal malate dehydrogenase from Trypanosoma cruzi
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Glycosomal enzyme / Trypanosoma cruzi
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 1 / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / malate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSonani, R.R. / Dubin, G.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: To Be Published
Title: Crystal structure of NAD-bound glycosomal malate dehydrogenase from Trypanosoma cruzi
Authors: Sonani, R.R. / Dubin, G.
History
DepositionDec 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,05623
Polymers281,1048
Non-polymers5,95215
Water21,1861176
1
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,75814
Polymers140,5524
Non-polymers3,20610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17890 Å2
ΔGint-85 kcal/mol
Surface area45170 Å2
MethodPISA
2
E: Malate dehydrogenase
G: Malate dehydrogenase
hetero molecules

H: Malate dehydrogenase
hetero molecules

F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2989
Polymers140,5524
Non-polymers2,7465
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_444x-1,y-1,z-11
Buried area16110 Å2
ΔGint-82 kcal/mol
Surface area45780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.481, 84.802, 113.459
Angle α, β, γ (deg.)97.600, 100.440, 110.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Malate dehydrogenase /


Mass: 35137.980 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_2g261, ECC02_003170 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2XLH9, malate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus B3 10% PEG 4000, 20% glycerol, 0.03M of each halide - Sodium floride, Sodium bromide, Sodium Iodide, 0.1M MES-imidazole pH6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.033184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033184 Å / Relative weight: 1
ReflectionResolution: 1.85→46.84 Å / Num. obs: 211514 / % possible obs: 91.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 6
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.88 / Num. unique obs: 10690

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NRZ

7nrz


Resolution: 1.85→46.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.448 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.208 10332 4.9 %RANDOM
Rwork0.174 ---
obs0.176 201182 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.76 Å2 / Biso mean: 40.55 Å2 / Biso min: 19.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20.27 Å2-0.35 Å2
2--1.75 Å2-1.45 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.85→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19102 0 394 1176 20672
Biso mean--38.19 43.94 -
Num. residues----2582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01319944
X-RAY DIFFRACTIONr_bond_other_d0.0070.01719874
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.64627218
X-RAY DIFFRACTIONr_angle_other_deg1.4771.57345801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05652590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60321.303783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.171153273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.915129
X-RAY DIFFRACTIONr_chiral_restr0.0940.22727
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222178
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023984
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 742 -
Rwork0.271 15196 -
all-15938 -
obs--93.21 %
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)
10.4721-0.1-0.14720.1688-0.03590.1393-0.0160.1166-0.00010.0327-0.0068-0.015-0.0210.01120.02290.2806-0.04710.0070.23980.01030.219223.7194-5.519820.2311
20.5820.0407-0.18440.1976-0.05230.11330.00910.04120.09610.05710.00790.0672-0.01330.0272-0.01690.3034-0.01210.01380.16670.0040.2692-13.49138.345235.9886
30.60140.179-0.14460.19810.00980.1392-0.0637-0.1027-0.10290.0251-0.0122-0.0292-0.0190.05350.07590.3052-0.00210.01290.20690.03970.233618.9098-23.295549.611
40.6312-0.13520.08320.0965-0.02070.0661-0.04350.1021-0.17910.0473-0.00710.0515-0.0433-0.01380.05060.253-0.03760.03760.2099-0.05750.2841-18.374-25.139628.5294
51.32110.06950.22060.19650.06420.07970.0129-0.03510.16970.0317-0.0082-0.04650.09140.0097-0.00460.2490.0007-0.01430.25030.00730.220610.7043-51.0118-7.3821
60.64690.00220.25090.2887-0.03090.21810.05090.0562-0.0158-0.0109-0.08280.03520.0715-0.02660.03190.288-0.0268-0.00890.2744-0.02250.15354.4127-8.308185.3975
71.1980.0034-0.03070.2117-0.10770.10510.029-0.02850.5725-0.0516-0.07090.00220.11820.02050.0420.2053-0.02630.01090.2159-0.04970.477-31.5596-31.2876-14.7352
82.1136-0.36090.37320.0774-0.02850.14450.01831.09930.84930.0543-0.1882-0.13750.12810.18010.16990.2026-0.00850.04030.62450.51910.4713-14.8926-55.18873.338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 403
2X-RAY DIFFRACTION2B1 - 402
3X-RAY DIFFRACTION3C1 - 404
4X-RAY DIFFRACTION4D1 - 401
5X-RAY DIFFRACTION5E1 - 401
6X-RAY DIFFRACTION6F1 - 402
7X-RAY DIFFRACTION7G1 - 401
8X-RAY DIFFRACTION8H1 - 401

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