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- PDB-7nrz: Crystal structure of malate dehydrogenase from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 7nrz
TitleCrystal structure of 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / malate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSonani, R.R. / Kurpiewska, K. / Lewinski, K. / 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: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Distinct sequence and structural feature of trypanosoma malate dehydrogenase.
Authors: Sonani, R.R. / Kurpiewska, K. / Lewinski, K. / Dubin, G.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)279,01397
Polymers272,8558
Non-polymers6,15889
Water7,188399
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,50834
Polymers68,2142
Non-polymers2,29532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,75524
Polymers68,2142
Non-polymers1,54222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,63122
Polymers68,2142
Non-polymers1,41820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,11817
Polymers68,2142
Non-polymers90415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.040, 148.331, 251.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Malate dehydrogenase /


Mass: 34106.832 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053506503.69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DRD8, malate dehydrogenase

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Non-polymers , 6 types, 488 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density meas: 53.82 Mg/m3 / Density % sol: 55.09 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM Sodium nitrate, 30 mM Sodium Phosphate 30 mM Ammonium Sulphate, 0.1 M bicine/Trizma pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→23.319 Å / Num. obs: 91983 / % possible obs: 98.86 % / Redundancy: 11.8 % / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 15.18
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8774 / CC1/2: 0.512 / CC star: 0.823 / % possible all: 95.83

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFD

2dfd


Resolution: 2.6→23.319 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 4647 5.05 %
Rwork0.2031 87323 -
obs0.2038 91970 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.61 Å2 / Biso mean: 57.4447 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.6→23.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19043 0 398 399 19840
Biso mean--65.21 51.72 -
Num. residues----2584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.62950.31471590.3005274395
2.6295-2.66040.35491260.3101282096
2.6604-2.69280.31111610.3043276396
2.6928-2.72690.31521590.2886280097
2.7269-2.76270.32421370.2833287397
2.7627-2.80050.30351670.2737278797
2.8005-2.84040.29431710.2681281298
2.8404-2.88270.28461510.2601282798
2.8827-2.92770.24891460.2545287698
2.9277-2.97560.30091710.2434288399
2.9756-3.02680.26151520.2272888100
3.0268-3.08170.24421410.23832928100
3.0817-3.14090.24591430.2342914100
3.1409-3.20480.2411610.22422941100
3.2048-3.27430.25281510.22192877100
3.2743-3.35030.24251560.21912948100
3.3503-3.43380.22071320.21692944100
3.4338-3.52640.23781280.21562960100
3.5264-3.62970.20681690.19992922100
3.6297-3.74640.21661630.20282944100
3.7464-3.87980.21771630.18932903100
3.8798-4.03430.19411430.18262973100
4.0343-4.21690.19511560.18252965100
4.2169-4.43780.16651480.1792948100
4.4378-4.71370.20931620.17272969100
4.7137-5.07420.18251640.17282950100
5.0742-5.57850.22071570.19142972100
5.5785-6.37130.21291550.20073017100
6.3713-7.97350.16911760.17793038100
7.9735-23.30.151790.153138100
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)
10.8776-0.0372-0.21990.83340.24080.89150.0506-0.06730.05690.1394-0.1264-0.0916-0.12280.07610.00010.3195-0.0477-0.03710.3520.03070.3324-11.993823.1873-17.5084
20.40580.06270.09240.9293-0.08671.29360.07320.03010.0498-0.0733-0.21130.1764-0.2571-0.2134-0.00020.32810.1-0.03030.4202-0.08040.384-36.05218.5977-41.8166
30.43230.1321-0.07441.12220.32071.30830.03660.0378-0.04050.0382-0.1055-0.1980.22030.2689-0.00140.30780.1296-0.00760.45430.0740.401-1.1679-11.4709-38.1866
40.599-0.07760.09931.4487-0.24180.85090.10240.0258-0.08740.3641-0.17170.21560.2736-0.09610.00010.4614-0.0830.07620.3678-0.06180.3819-31.2198-18.6292-22.8922
51.3262-0.2477-0.73850.421-0.15481.0662-0.17810.08460.3485-0.05020.0696-0.1328-0.07220.0983-0.00020.4641-0.0624-0.17880.38720.03370.4893-6.749215.863224.6197
61.4349-0.14030.53680.4594-0.39980.6831-0.3987-0.0484-0.1846-0.0510.1518-0.07240.07750.1372-0.00060.49910.08310.1130.30020.03480.3225-2.926-14.306940.2798
70.78270.3017-0.29150.5158-0.03591.3366-0.20740.00110.15670.04670.01130.0913-0.0334-0.3481-0.00090.3810.1246-0.12130.451-0.09670.4244-43.38958.297243.8413
81.1906-0.28950.26211.158-0.32720.7322-0.30810.1304-0.1678-0.22410.11860.2310.1739-0.3428-0.00020.6519-0.1860.02880.4919-0.09450.4273-39.6163-16.598319.9063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:2201)A1 - 2201
2X-RAY DIFFRACTION2(chain B and resseq 1:2201)B1 - 2201
3X-RAY DIFFRACTION3(chain C and resseq 1:1801)C1 - 1801
4X-RAY DIFFRACTION4(chain D and resseq 1:1901)D1 - 1901
5X-RAY DIFFRACTION5(chain E and resseq 1:1001)E1 - 1001
6X-RAY DIFFRACTION6(chain F and resseq 1:1101)F1 - 1101
7X-RAY DIFFRACTION7(chain G and resseq 1:1601)G1 - 1601
8X-RAY DIFFRACTION8(chain H and resseq 1:901)H1 - 901

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