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- PDB-3ks0: Crystal structure of the heme domain of flavocytochrome b2 in com... -

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Basic information

Entry
Database: PDB / ID: 3ks0
TitleCrystal structure of the heme domain of flavocytochrome b2 in complex with Fab B2B4
Components
  • Cytochrome b2, mitochondrial
  • Fragment Antigen Binding B2B4
  • heme domain of flavocytochrome b2
KeywordsOXIDOREDUCTASE / electron transfer / epitope / domain mobility / flavocytochrome b2 / antibody / Fab / heme domain / Electron transport / Flavoprotein / FMN / Heme / Metal-binding / Mitochondrion / Respiratory chain / Transit peptide / Transport
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-type TIM barrel / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / L-lactate dehydrogenase (cytochrome)
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsGolinelli-Pimpaneau, B. / Lederer, F. / Le, K.H.D.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Structural evidence for the functional importance of the heme domain mobility in flavocytochrome b2.
Authors: Diep Le, K.H. / Lederer, F. / Golinelli-Pimpaneau, B.
#1: Journal: Biochemistry / Year: 1998
Title: Probing intramolecular electron transfer within flavocytochrome b2 with a monoclonal antibody
Authors: Miles, C.S. / Le, K.H.D. / Lederer, F.
#2: Journal: BIOCHEM.J. / Year: 2003
Title: Epitope mapping for the monoclonal antibody that inhibits intramolecular electron transfer in flavocytochrome b2
Authors: Le, K.H.D. / Mayer, M. / Lederer, F.
History
DepositionNov 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: heme domain of flavocytochrome b2
H: Fragment Antigen Binding B2B4
A: Cytochrome b2, mitochondrial
J: heme domain of flavocytochrome b2
K: Fragment Antigen Binding B2B4
B: Cytochrome b2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8658
Polymers115,6326
Non-polymers1,2332
Water2,378132
1
A: Cytochrome b2, mitochondrial
J: heme domain of flavocytochrome b2
K: Fragment Antigen Binding B2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4324
Polymers57,8163
Non-polymers6161
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: heme domain of flavocytochrome b2
H: Fragment Antigen Binding B2B4
B: Cytochrome b2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4324
Polymers57,8163
Non-polymers6161
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.580, 83.680, 92.165
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody heme domain of flavocytochrome b2


Mass: 22876.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fragment Antigen Binding B2B4


Mass: 24475.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Cytochrome b2, mitochondrial / L-lactate dehydrogenase [Cytochrome] / L-lactate ferricytochrome C oxidoreductase / L-LCR


Mass: 10464.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CYB2, YML054C, YM9958.08C / Production host: Escherichia coli (E. coli)
References: UniProt: P00175, L-lactate dehydrogenase (cytochrome)
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 20 % PEG 4000, 0.1 M MES pH 6.5, 0.2 M MgCl2, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 29267 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
2.7-2.853.30.6661.20.66694.6
2.85-3.023.40.4591.70.45996.5
3.02-3.233.50.3322.30.33297.5
3.23-3.493.60.2253.40.22597.7
3.49-3.823.70.15350.15397.8
3.82-4.273.70.1057.20.10597.9
4.27-4.933.70.0769.60.07697.9
4.93-6.043.60.08390.08398
6.04-8.543.60.088.70.0898
8.54-71.983.10.066.80.0694.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.89 Å22.67 Å
Translation2.89 Å22.67 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
SCALA3.2.19data scaling
PHASER1.3.2phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→24.75 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.835 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.848 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28907 1487 5.1 %RANDOM
Rwork0.21399 ---
obs0.21771 27762 96.64 %-
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: 43.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20.22 Å2
2---0.15 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7803 0 86 132 8021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228125
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9911163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44951025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09324.744293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.179151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.3411517
X-RAY DIFFRACTIONr_chiral_restr0.1030.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0226155
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6881.55160
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2928397
X-RAY DIFFRACTIONr_scbond_it1.73232965
X-RAY DIFFRACTIONr_scangle_it2.8694.52766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 108 -
Rwork0.276 1987 -
obs--93.74 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4parallhdg.hemes

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