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- PDB-1qcw: Flavocytochrome B2, ARG289LYS mutant -

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Basic information

Entry
Database: PDB / ID: 1qcw
TitleFlavocytochrome B2, ARG289LYS mutant
ComponentsFLAVOCYTOCHROME B2
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN ELECTRON TRANSFER MUTAGENISIS
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 / Resolution: 2.75 Å
AuthorsMowat, C.G. / Durley, R.C.E. / Pike, A.D. / Barton, J.D. / Chen, Z.-W. / Mathews, F.S. / Lederer, F. / Reid, G.A. / Chapman, S.K.
CitationJournal: Biochemistry / Year: 2000
Title: Kinetic and crystallographic studies on the active site Arg289Lys mutant of flavocytochrome b2 (yeast L-lactate dehydrogenase)
Authors: Mowat, C.G. / Beaudoin, I. / Durley, R.C.E. / Barton, J.D. / Pike, A.D. / Chen, Z.-W. / Reid, G.A. / Chapman, S.K. / Mathews, F.S. / Lederer, F.
History
DepositionMay 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAVOCYTOCHROME B2
B: FLAVOCYTOCHROME B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1274
Polymers91,0542
Non-polymers1,0732
Water1,38777
1
A: FLAVOCYTOCHROME B2
B: FLAVOCYTOCHROME B2
hetero molecules

A: FLAVOCYTOCHROME B2
B: FLAVOCYTOCHROME B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,2548
Polymers182,1094
Non-polymers2,1464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area29150 Å2
ΔGint-156 kcal/mol
Surface area49260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.569, 162.569, 112.011
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein FLAVOCYTOCHROME B2 / E.C.1.1.2.3


Mass: 45527.176 Da / Num. of mol.: 2 / Mutation: R289K, P304F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Strain (production host): TGI
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.: 77 / 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: 4.69 Å3/Da / Density % sol: 73.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
210 mMTris-HCl1drop
320 mMMES1reservoir
450 mMsodium sulfite1reservoir
512 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 36062 / % possible obs: 80.8 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 2.75→2.87 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.416 / Num. unique all: 36062 / % possible all: 75.2
Reflection
*PLUS
Num. obs: 36062
Reflection shell
*PLUS
% possible obs: 75.2 % / Mean I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2.75→8 Å / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.257 -8 %
Rwork0.204 --
obs-28442 -
Refinement stepCycle: LAST / Resolution: 2.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6024 0 70 77 6171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.52
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_d1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.67
LS refinement shell
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 2.88 Å / Rfactor Rfree: 0.338 / Rfactor Rwork: 0.299

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