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

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Basic information

Entry
Database: PDB / ID: 1kbi
TitleCrystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: Comparison with the Intact Wild-type Enzyme
ComponentsCYTOCHROME B2
KeywordsOXIDOREDUCTASE / Flavocytochrome b2 / electron transfer
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 / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid 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. ...L-mandelate/L-lactate dehydrogenase, FMN-binding domain / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid 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 / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / PYRUVIC ACID / L-lactate dehydrogenase (cytochrome)
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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 / software / 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)115,63112
Polymers113,3282
Non-polymers2,30310
Water11,133618
1
A: CYTOCHROME B2
B: CYTOCHROME B2
hetero molecules

A: CYTOCHROME B2
B: CYTOCHROME B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,26224
Polymers226,6564
Non-polymers4,60620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area38190 Å2
ΔGint-312 kcal/mol
Surface area61660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)164.160, 164.160, 111.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-900-

PO4

DetailsThe enzyme is a homotetramer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME B2 / L-LCR


Mass: 56663.898 Da / Num. of mol.: 2
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)

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Non-polymers , 6 types, 628 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.2
Details: phosphate buffer, D,L-lactate, EDTA, MPD, pH 7.2, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-7.5 mg/mlprotein11
250 mMphosphate11pH7.2
350 mMD,L-lactate11
41 mMEDTA11
530-33 %(v/v)MPD12
670 mMphosphate12pH7.2
747 mMD,L-lactate12
81 mMEDTA12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 174544 / Num. obs: 157962 / % possible obs: 90.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 25.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.8 / % possible all: 73.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Num. obs: 65248 / Num. measured all: 157962 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 73.7 % / Rmerge(I) obs: 0.207

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
RefinementStarting model: PDB ENTRY 1FCB

1fcb


Resolution: 2.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 6138 -RANDOM
Rwork0.17 ---
all-77081 --
obs-62046 80.5 %-
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 0 154 618 7828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.3-2.460.2778010.228X-RAY DIFFRACTION8212
2.46-2.640.2768330.223X-RAY DIFFRACTION8427
2.64-2.90.2499350.197X-RAY DIFFRACTION9190
2.9-3.30.21510530.174X-RAY DIFFRACTION10617
3.3-4.240.19213580.153X-RAY DIFFRACTION13547
4.24-300.19411580.157X-RAY DIFFRACTION12153
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / Rfactor Rwork: 0.228

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