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- PDB-1kbj: Crystallographic Study of the Recombinant Flavin-binding Domain o... -

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Basic information

Entry
Database: PDB / ID: 1kbj
TitleCrystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: comparison with the Intact Wild-type Enzyme
ComponentsCYTOCHROME B2
KeywordsOXIDOREDUCTASE / flavin-binding domain of flavocytochrome b2
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 / metal ion binding / nucleus / 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
FLAVIN MONONUCLEOTIDE / L-lactate dehydrogenase (cytochrome)
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCunane, L.M. / Barton, J.D. / Chen, Z.W. / Welsh, F.E. / Chapman, S.K. / Reid, G.A. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme.
Authors: Cunane, L.M. / Barton, J.D. / Chen, Z.W. / Welsh, F.E. / Chapman, S.K. / Reid, G.A. / Mathews, F.S.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Molecular Structure of Flavocytochrome b2 at 2.4 A Resolution
Authors: Xia, Z.X. / Mathews, F.S.
#2: Journal: BIOCHEM.J. / Year: 1995
Title: Isolation and Characterization of the Flavin-binding Domain of Flavocytochrome b2 Expressed Independently in Escherichia coli
Authors: Blame, A. / Brunt, C.E. / Pallister, R.L. / Chapman, S.K. / Reid, G.A.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: CYTOCHROME B2
B: CYTOCHROME B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4196
Polymers91,3832
Non-polymers1,0374
Water6,666370
1
A: CYTOCHROME B2
B: CYTOCHROME B2
hetero molecules

A: CYTOCHROME B2
B: CYTOCHROME B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,83912
Polymers182,7654
Non-polymers2,0748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area30850 Å2
ΔGint-162 kcal/mol
Surface area52080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.730, 147.620, 64.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-787-

HOH

DetailsThe enzyme is a tetramer.

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Components

#1: Protein CYTOCHROME B2


Mass: 45691.297 Da / Num. of mol.: 2 / Fragment: FMN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: P00175, L-lactate dehydrogenase (cytochrome)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG, sodium citrate, ethylene glycol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MTris1droppH7.5
326 %PEG40001reservoir
40.17 Msodium citrate1reservoirpH5.6
53 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 37593 / Num. obs: 34160 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 5.2 / % possible all: 96.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Num. obs: 36688 / Num. measured all: 240788
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 96.2 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FCB

1fcb


Resolution: 2.5→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3470 -RANDOM
Rwork0.157 ---
all-37593 --
obs-34160 90.9 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 70 370 6562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.670.2485130.183X-RAY DIFFRACTION5119
2.67-2.870.2364790.183X-RAY DIFFRACTION5066
2.87-3.150.2645550.191X-RAY DIFFRACTION5397
3.15-3.580.2126120.17X-RAY DIFFRACTION5757
3.58-4.430.1726140.138X-RAY DIFFRACTION5917
4.43-400.1826970.138X-RAY DIFFRACTION6904
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.5 Å

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