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- PDB-6vdi: Crystal structure of ancestral apicomplexan lactate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 6vdi
TitleCrystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate.
Componentslactate dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide Binding / Rossman Fold / Ancestral Reconstruction
Function / homologyL-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesApicomplexa sp. (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTheobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM096053 United States
CitationJournal: To Be Published
Title: Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase
Authors: Theobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0034
Polymers71,8112
Non-polymers1922
Water1,54986
1
A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules

A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0068
Polymers143,6224
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area17130 Å2
ΔGint-146 kcal/mol
Surface area42520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.700, 84.700, 196.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein lactate dehydrogenase


Mass: 35905.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ancestral apicomplexan lactate dehydrogenase with sulfate bound
Source: (gene. exp.) Apicomplexa sp. (eukaryote) / Plasmid: pET24a(+) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20mg/mL protein, 2mM NADH4; well solution: 7% v/v 2-Propanol, 1.8M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 1.686→48.975 Å / Num. obs: 85995 / % possible obs: 83.4 % / Redundancy: 2.66 % / Biso Wilson estimate: 48.77 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.11 / Χ2: 0.79 / Net I/σ(I): 2.71
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 1.55 % / Mean I/σ(I) obs: 0.04 / Num. unique obs: 30551 / CC1/2: 0.013 / Rrim(I) all: 11.516 / % possible all: 34.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLG

4plg


Resolution: 2.1→48.79 Å / SU ML: 0.3627 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.0001
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2731 1101 2.32 %
Rwork0.2426 46277 -
obs0.2433 47378 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.61 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 10 86 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724839
X-RAY DIFFRACTIONf_angle_d0.97076547
X-RAY DIFFRACTIONf_chiral_restr0.0492768
X-RAY DIFFRACTIONf_plane_restr0.0064839
X-RAY DIFFRACTIONf_dihedral_angle_d4.9493661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.41761230.39785093X-RAY DIFFRACTION87.71
2.2-2.310.53031330.51535618X-RAY DIFFRACTION96.03
2.31-2.460.31761370.31565823X-RAY DIFFRACTION99.85
2.46-2.650.33621400.29525860X-RAY DIFFRACTION99.92
2.65-2.910.32631400.28025870X-RAY DIFFRACTION99.9
2.91-3.330.31621370.26015887X-RAY DIFFRACTION99.67
3.33-4.20.24851430.22495917X-RAY DIFFRACTION99.23
4.2-48.790.22281480.19176209X-RAY DIFFRACTION99.84
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)
11.940289346680.923198885934-0.682825794322.06568504345-0.3922210421892.167417828410.161924321174-0.1450085288240.3824973942140.3803799172950.01696913254930.185469352844-0.253673536997-0.481762163026-0.07910964258550.6145061443010.041748074610.100841466830.463074378250.00159380703380.4728166051937.00776310139.75981969939-17.0935564897
22.60427072969-0.2859063191070.6891657276261.36290173785-0.1380763448692.00172828714-0.02672300632310.0725019914843-0.2770732824360.47741027919-0.00547813435120.3743748046790.435791879398-1.22936985385-0.08549052080730.750712715019-0.1665631191180.1706327268860.7782218452610.04454657623420.60414208231330.9802210844-3.25231260377-9.07277798107
31.97059537111-0.1660340256430.01247199144971.601052215410.642611399242.361438329620.125186390332-0.37441954002-0.2283769318170.341323607898-0.05888896371940.007332219016280.5050374424180.314527624184-0.1505581762890.782034437328-0.0657663423033-0.09499518172520.4729332392930.04677361016470.46768897050456.3941318706-15.051538502-9.85726810131
41.68378640029-0.4654820764720.6809095458621.0296221808-0.7028014558532.476340013030.163203238093-0.291981034653-0.000477890366250.331612066135-0.048307728830.213288131682-0.0294945436936-0.123515326649-0.1025363873330.653036548203-0.08753514015460.07185641030230.360877788357-0.02163513690090.44645992313645.0967347428-2.89875619556-13.5348144642
50.979861205735-0.307085824338-0.6034741878771.266411313220.3661606562221.82268375583-0.0516673097336-0.291639102013-0.2006956067220.4487092848040.01125355686670.2099371944820.538238913111-0.124709224087-0.1025615395160.838834123063-0.239661176480.1030174037650.6150724914660.03701267798110.55879204519935.8160883877-13.7429379532-4.16512620259
61.537706930120.4425884980010.1215932270771.53011680826-0.455506668791.945672706660.144689886889-0.09334607565380.08013198518320.376481181223-0.0911903750401-0.0956465685039-0.06544492811960.262482763974-0.137500394380.625094110444-0.0869850503782-0.04226163797020.426869249125-0.05728063784050.45240293392762.24343545915.56019063459-17.1539714564
72.831773143410.6359506371811.09777631031.18450725824-0.08277817496642.561615021260.0987511251335-0.07623637781720.5032716115750.204598669974-0.0830323869108-0.235645783452-0.7027935966790.521417670657-0.08566414765430.689632862026-0.1651675053880.06414379616050.420415164167-0.09401678178670.53592876242966.480980281119.9378855641-21.5207076761
82.096247122630.181336551175-0.2797240318541.925313747650.6574891822332.017175584890.130994628945-0.1290782375140.516343227877-0.328713434709-0.06049215339360.173990478447-1.360140078620.0887549234304-0.03825380825370.8918634417230.08104128135840.06772425766870.3123009468860.001300218453850.60581777415147.58057541527.8173988434-39.2864888144
91.77949700448-0.8993473567510.4915690279121.613655060850.03602692498682.497921464760.0404477235488-0.08785266162350.2605084377720.02351284372960.149989546306-0.0248948734441-0.639572340740.238392709068-0.1086982093540.6912986568-0.1303248780370.06347977541550.29906449813-0.07030857206420.51197159527158.7276370818.68109929-27.9524302902
100.494832264874-0.1221559467260.720873257541.388120433760.5791597873041.82928540108-0.04115981863090.1993485330290.6366975089130.02263413423020.00910314805733-0.428199609863-0.9172440415220.415727043978-0.08797987204920.98832231997-0.2546710795010.1362617307180.627805374429-0.01940130802960.70556585818967.781670561431.5800191857-34.9788368712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 226 )
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 271 )
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 326 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 58 )
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 171 )
8X-RAY DIFFRACTION8chain 'B' and (resid 172 through 226 )
9X-RAY DIFFRACTION9chain 'B' and (resid 227 through 271 )
10X-RAY DIFFRACTION10chain 'B' and (resid 272 through 325 )

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