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- PDB-1fcb: MOLECULAR STRUCTURE OF FLAVOCYTOCHROME B2 AT 2.4 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1fcb
TitleMOLECULAR STRUCTURE OF FLAVOCYTOCHROME B2 AT 2.4 ANGSTROMS RESOLUTION
ComponentsFLAVOCYTOCHROME B2
KeywordsOXIDOREDUCTASE (CH-OH(D)-CYTOCHROME(A))
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 / PYRUVIC ACID / L-lactate dehydrogenase (cytochrome)
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMathews, F.S. / Xia, Z.-X.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Molecular structure of flavocytochrome b2 at 2.4 A resolution.
Authors: Xia, Z.X. / Mathews, F.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Three-Dimensional Structure of Flavocytochrome B2 from Baker,S Yeast at 3.0-Angstroms Resolution
Authors: Xia, Z.-X. / Shamala, N. / Bethge, P.H. / Lim, L.W. / Bellamy, H.D. / Xuong, N.H. / Lederer, F. / Mathews, F.S.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: Crystallographic Study of Bakers, Yeast Cytochrome B2
Authors: Mathews, F.S. / Lederer, F.
History
DepositionJan 16, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEETS PRESENTED AS *BRA* AND *BRB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BRA* AND *BRB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)114,9456
Polymers113,3282
Non-polymers1,6174
Water5,098283
1
A: FLAVOCYTOCHROME B2
B: FLAVOCYTOCHROME B2
hetero molecules

A: FLAVOCYTOCHROME B2
B: FLAVOCYTOCHROME B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,89012
Polymers226,6564
Non-polymers3,2348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area32800 Å2
ΔGint-206 kcal/mol
Surface area61120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)165.510, 165.510, 113.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.247, 0.4353, -0.8657), (0.4312, 0.7507, 0.5005), (0.8678, -0.4969, -0.0023)
Vector: -0.0427, -0.0266, -0.3895)

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Components

#1: Protein FLAVOCYTOCHROME B2


Mass: 56663.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00175, L-lactate dehydrogenase (cytochrome)
#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-PYR / PYRUVIC ACID


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


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEACH SUBUNIT CONTAINS TWO DOMAINS, A CYTOCHROME DOMAIN COMPRISING RESIDUES 1 - 99 AND A FLAVIN- ...EACH SUBUNIT CONTAINS TWO DOMAINS, A CYTOCHROME DOMAIN COMPRISING RESIDUES 1 - 99 AND A FLAVIN-BINDING DOMAIN COMPRISING RESIDUES 100 - 511.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.98 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMphosphate1buttom
20.5 %protein1buttom
350 mMD,L-lactate1buttom
41 mMEDTA1buttom
530 %(v/v)MPD1reservoir
670 mMphosphate1reservoir
747 mMD,L-lactate1reservoir
81 mMEDTA1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.4→5 Å
Details: SOME BOND ANGLES DIFFER SIGNIFICANTLY FROM EXPECTED VALUES AND SOME RESIDUES FALL OUTSIDE THE ALLOWED REGIONS OF A PHI-PSI PLOT. FURTHER REFINEMENT IS IN PROGRESS AND REVISED COORDINATES ...Details: SOME BOND ANGLES DIFFER SIGNIFICANTLY FROM EXPECTED VALUES AND SOME RESIDUES FALL OUTSIDE THE ALLOWED REGIONS OF A PHI-PSI PLOT. FURTHER REFINEMENT IS IN PROGRESS AND REVISED COORDINATES WILL BE DEPOSITED WITH THE PROTEIN DATA BANK IN THE FUTURE.
RfactorNum. reflection
obs0.188 61365
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6948 0 111 283 7342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 5 Å / Num. reflection obs: 61365 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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