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- PDB-1ltd: THE 2.6 ANGSTROMS REFINED STRUCTURE OF THE ESCHERICHIA COLI RECOM... -

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Entry
Database: PDB / ID: 1ltd
TitleTHE 2.6 ANGSTROMS REFINED STRUCTURE OF THE ESCHERICHIA COLI RECOMBINANT SACCHAROMYCES CEREVISIAE FLAVOCYTOCHROME B2-SULPHITE COMPLEX
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 / metal ion binding / nucleus / 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 / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / SULFITE ION / L-lactate dehydrogenase (cytochrome)
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsTegoni, M. / Cambillau, C.
Citation
Journal: Protein Sci. / Year: 1994
Title: The 2.6-A refined structure of the Escherichia coli recombinant Saccharomyces cerevisiae flavocytochrome b2-sulfite complex.
Authors: Tegoni, M. / Cambillau, C.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Molecular Structure of Flavocytochrome B2 at 2.4 Angstroms Resolution
Authors: Xia, Z. / Mathews, F.S.
#2: Journal: Biochem.J. / Year: 1989
Title: High Level Expression of Fully Active Yeast Flavocytochrome B2 in Escherichia Coli
Authors: Black, M. / White, S. / Reid, G. / Chapman, S.
History
DepositionJan 14, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,8507
Polymers112,1602
Non-polymers1,6895
Water3,711206
1
A: FLAVOCYTOCHROME B2
B: FLAVOCYTOCHROME B2
hetero molecules

A: FLAVOCYTOCHROME B2
B: FLAVOCYTOCHROME B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,70014
Polymers224,3214
Non-polymers3,37910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area31920 Å2
ΔGint-206 kcal/mol
Surface area58070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)164.500, 164.500, 114.000
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)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein FLAVOCYTOCHROME B2


Mass: 56080.242 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-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEACH SUBUNIT CONTAINS TWO DOMAINS, A CYTOCHROME DOMAIN COMPRISING RESIDUES 5 - 99 AND A FLAVIN- ...EACH SUBUNIT CONTAINS TWO DOMAINS, A CYTOCHROME DOMAIN COMPRISING RESIDUES 5 - 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: 3.97 Å3/Da / Density % sol: 69 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mM1dropNa2SO5
225 mg/mlenzyme1drop
312 %PEG40001reservoir
450 mMMES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 100 Å / Num. obs: 44282 / % possible obs: 81 % / Num. measured all: 452385 / Rmerge(I) obs: 0.147
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.9 Å / % possible obs: 55 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→6 Å / Rfactor Rwork: 0.173 / Rfactor obs: 0.173 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 113 206 7075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.37

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