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- PDB-1szg: A198G:L230A flavocytochrome b2 with sulfite bound -

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Basic information

Entry
Database: PDB / ID: 1szg
TitleA198G:L230A flavocytochrome b2 with sulfite bound
ComponentsCytochrome b2, mitochondrial
KeywordsOXIDOREDUCTASE / flavocytochrome / L-lactate dehydrogenase / sulfite
Function / homology
Function and homology information


L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / lactate metabolic process / : / mitochondrial intermembrane space / mitochondrial inner membrane / heme binding / mitochondrion / nucleus / metal ion binding / cytosol
Similarity search - Function
L-mandelate/L-lactate dehydrogenase, FMN-binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily ...L-mandelate/L-lactate dehydrogenase, FMN-binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-SULFO-FLAVIN MONONUCLEOTIDE / L-lactate dehydrogenase (cytochrome)
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMowat, C.G. / Wehenkel, A. / Green, A.J. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
CitationJournal: Biochemistry / Year: 2004
Title: Altered Substrate Specificity in Flavocytochrome b(2): Structural Insights into the Mechanism of l-Lactate Dehydrogenation
Authors: Mowat, C.G. / Wehenkel, A. / Green, A.J. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: 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

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Assembly

Deposited unit
A: Cytochrome b2, mitochondrial
B: Cytochrome b2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2884
Polymers113,2162
Non-polymers1,0732
Water2,360131
1
A: Cytochrome b2, mitochondrial
B: Cytochrome b2, mitochondrial
hetero molecules

A: Cytochrome b2, mitochondrial
B: Cytochrome b2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,5778
Polymers226,4314
Non-polymers2,1464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area29250 Å2
ΔGint-146 kcal/mol
Surface area51470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)163.966, 163.966, 112.508
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
Detailsto generate other half of tetramer use two-fold axis: y, x, -z

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Components

#1: Protein Cytochrome b2, mitochondrial / E.C.1.1.2.3 / L-lactate dehydrogenase [Cytochrome] / L-lactate ferricytochrome C oxidoreductase / L-LCR


Mass: 56607.789 Da / Num. of mol.: 2 / Fragment: residues 81-591 / Mutation: A198G:L230A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CYB2 / Plasmid: pDSb2 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
References: UniProt: P00175, L-lactate dehydrogenase (cytochrome)
#2: Chemical ChemComp-FNS / N-SULFO-FLAVIN MONONUCLEOTIDE


Mass: 536.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O12PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 5 Å3/Da / Density % sol: 75.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 12-15% PEG4000, 18-21% glycerol, 50 mM sodium sulfite, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→24 Å / Num. all: 48197 / Num. obs: 43777 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 11.44
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.66 / Num. unique all: 4362 / % possible all: 92

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1LTD

1ltd


Resolution: 2.7→24 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.228 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26567 2233 5.1 %RANDOM
Rwork0.22276 ---
obs0.22495 41515 91 %-
all-48197 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.452 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.85 Å20 Å2
2--1.69 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 70 131 6255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226226
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9968428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485773
X-RAY DIFFRACTIONr_chiral_restr0.1230.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.024610
X-RAY DIFFRACTIONr_nbd_refined0.2260.23111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2321
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.2132
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.220
X-RAY DIFFRACTIONr_mcbond_it0.6961.53858
X-RAY DIFFRACTIONr_mcangle_it1.3926234
X-RAY DIFFRACTIONr_scbond_it2.5132368
X-RAY DIFFRACTIONr_scangle_it4.1624.52194
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 177
Rwork0.299 2992

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