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- PDB-4uuo: Apo Trichomonas vaginalis malate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4uuo
TitleApo Trichomonas vaginalis malate dehydrogenase
ComponentsCYTOSOLIC MALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / malate metabolic process / carbohydrate metabolic process
Similarity search - Function
Malate dehydrogenase, type 2 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 Rossmann-like Domain ...Malate dehydrogenase, type 2 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytosolic malate dehydrogenase
Similarity search - Component
Biological speciesTRICHOMONAS VAGINALIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.842 Å
AuthorsSteindel, P.A. / Chen, E.H. / Theobald, D.L.
CitationJournal: Protein Sci. / Year: 2016
Title: Gradual Neofunctionalization in the Convergent Evolution of Trichomonad Lactate and Malate Dehydrogenases.
Authors: Steindel, P.A. / Chen, E.H. / Wirth, J.D. / Theobald, D.L.
History
DepositionJul 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection / Derived calculations / Refinement description
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Jul 6, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOSOLIC MALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)36,8351
Polymers36,8351
Non-polymers00
Water34219
1
A: CYTOSOLIC MALATE DEHYDROGENASE

A: CYTOSOLIC MALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)73,6712
Polymers73,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554x,-y,-z-1/21
Buried area3530 Å2
ΔGint-18.2 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.000, 155.000, 155.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein CYTOSOLIC MALATE DEHYDROGENASE / MALATE DEHYDROGENASE


Mass: 36835.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOMONAS VAGINALIS (eukaryote) / Plasmid: PET-21B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q27819, malate dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.06 Å3/Da / Density % sol: 69.7 % / Description: NONE
Crystal growDetails: 8.3 MG/ML PROTEIN, 4.0 M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.84→49 Å / Num. obs: 19501 / % possible obs: 99.5 % / Observed criterion σ(I): 0.25 / Redundancy: 41.7 % / Biso Wilson estimate: 91.74 Å2 / Rmerge(I) obs: 0.188 / Net I/σ(I): 27.83
Reflection shellResolution: 2.84→2.92 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.25 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON TRICHOMONAS VAGINALIS LDH

Resolution: 2.842→49.015 Å / SU ML: 0.52 / σ(F): 1.34 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 743 5.06 %
Rwork0.2062 --
obs0.2088 14688 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.8 Å2
Refinement stepCycle: LAST / Resolution: 2.842→49.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 0 19 2509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042555
X-RAY DIFFRACTIONf_angle_d0.7973465
X-RAY DIFFRACTIONf_dihedral_angle_d11.44925
X-RAY DIFFRACTIONf_chiral_restr0.029397
X-RAY DIFFRACTIONf_plane_restr0.003445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8422-3.06170.41731470.33892750X-RAY DIFFRACTION99
3.0617-3.36970.3641470.26392767X-RAY DIFFRACTION100
3.3697-3.85710.24161490.2062746X-RAY DIFFRACTION99
3.8571-4.85890.21471460.18212799X-RAY DIFFRACTION100
4.8589-49.02260.24871540.19112883X-RAY DIFFRACTION100
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)
11.63390.69740.90312.47350.92133.60280.042-0.04530.3246-0.229-0.17730.3165-0.4357-0.50630.14780.80160.04950.07290.7261-0.07740.725834.65315.1941-31.4887
20.81720.35880.58050.53730.67540.88110.1589-0.56980.01580.883-0.24030.74880.2454-0.66350.25111.0143-0.21990.2120.9895-0.05720.828830.09731.5097-14.646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 152 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 153 THROUGH 336 )

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