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- PDB-1vbi: Crystal structure of type 2 malate/lactate dehydrogenase from the... -

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Basic information

Entry
Database: PDB / ID: 1vbi
TitleCrystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus HB8
ComponentsType 2 malate/lactate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / NAD(P) binding protein / thermus thermophilus HB8 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich ...Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate/L-lactate dehydrogenase family protein / Dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus HB8
Authors: Mizutani, H. / Kunishima, N.
History
DepositionFeb 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 2 malate/lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1979
Polymers36,9971
Non-polymers1,2008
Water6,161342
1
A: Type 2 malate/lactate dehydrogenase
hetero molecules

A: Type 2 malate/lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,39418
Polymers73,9952
Non-polymers2,40016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area11830 Å2
ΔGint-112 kcal/mol
Surface area24470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.320, 78.320, 253.213
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is dimer generated by the operation:x-y+1,-y+2,-z.

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Components

#1: Protein Type 2 malate/lactate dehydrogenase


Mass: 36997.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q746L8, UniProt: Q53W84*PLUS, L-lactate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.67 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: 1.58M ammonium sulfate, 0.1M sodium acetate, 1mM NAD, pH 4.6, microbatch, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97900, 0.97931, 1.0000
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 3, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979311
311
ReflectionResolution: 1.8→30 Å / Num. all: 43745 / Num. obs: 43745 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 11.53 / Num. unique all: 4275 / Rsym value: 0.124 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2925735.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2162 5 %RANDOM
Rwork0.187 ---
all0.188 43745 --
obs0.188 43635 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4969 Å2 / ksol: 0.366908 e/Å3
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å21.04 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 75 342 2996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.216 202 4.8 %
Rwork0.188 4027 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4NAD.PARAMNAD.TOP
X-RAY DIFFRACTION5EGL.PARAMEGL.TOP

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