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- PDB-1fqt: CRYSTAL STRUCTURE OF THE RIESKE-TYPE FERREDOXIN ASSOCIATED WITH B... -

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Basic information

Entry
Database: PDB / ID: 1fqt
TitleCRYSTAL STRUCTURE OF THE RIESKE-TYPE FERREDOXIN ASSOCIATED WITH BIPHENYL DIOXYGENASE
ComponentsRIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE
KeywordsOXIDOREDUCTASE / RIESKE-TYPE FERREDOXIN / 2FE-2S CLUSTER / BETA SANDWICH
Function / homology
Function and homology information


: / : / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Biphenyl dioxygenase system ferredoxin subunit
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FE MAD / Resolution: 1.6 Å
AuthorsColbert, C.L. / Couture, M.M.-J. / Eltis, L.D. / Bolin, J.T.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: A cluster exposed: structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins.
Authors: Colbert, C.L. / Couture, M.M. / Eltis, L.D. / Bolin, J.T.
History
DepositionSep 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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_ref_seq_dif.details / _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: RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE
B: RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1307
Polymers24,5022
Non-polymers6285
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.400, 53.100, 64.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE / BIPHENYL DIOXYGENASE / BIPHENYL DIOXYGENASE SYSTEM FERREDOXIN COMPONENT / BIPHENYL DIOXYGENASE


Mass: 12250.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Plasmid: PEBRE12 / Production host: Escherichia coli (E. coli)
References: UniProt: P37332, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.7 Å3/Da / Density % sol: 52 % / Description: INVERSE BEAM GEOMETRY WAS USED
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG MME 5000, MES buffer, ammonium sulfate, pH 6.3, VAPOR DIFFUSION, SITTING DROP at 283K, pH 6.5
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
131 mg/mlprotein1drop
20.15 Msodium chloride1drop
31 mMdithiothreitol1drop
420 mMMOPS1drop
525 %mPEG50001reservoir
60.2 Mammonium sulfate1reservoir
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9537,1.742,1.737
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 10, 1998 / Details: BENT CYLINDRICAL: SI-MIRROR (RH COATING)
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL: MONOCHROMATOR / Protocol: MULTIPLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21.7421
31.7371
ReflectionResolution: 1.6→26 Å / Num. obs: 34971 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.95 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.91 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.2 / % possible all: 97.6
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FE MAD / Resolution: 1.6→26 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE GEOMETRY WITHIN THE FE-S CLUSTER AND THE BONDS WITH THE PROTEIN LIGANDS WERE RESTRAINED WITH FORCE CONSTANTS OF: 200 KCAL MOLE^-1 ANG.^2 APPLIED TO FE-S (TARGET=2.28 ANG.), FE-ND1 (2.05 ...Details: THE GEOMETRY WITHIN THE FE-S CLUSTER AND THE BONDS WITH THE PROTEIN LIGANDS WERE RESTRAINED WITH FORCE CONSTANTS OF: 200 KCAL MOLE^-1 ANG.^2 APPLIED TO FE-S (TARGET=2.28 ANG.), FE-ND1 (2.05 ANG.), AND FE-FE (2.68 ANG.) DISTANCES; 40 KCAL MOLE^-1 RAD^-2 APPLIED TO ANGLES S-FE-ND1 (115 DEG.), S-FE-S (105 DEG.), FE-S-FE (75 DEG.), ND1-FE-ND1 (90 DEG.), FE-ND1-CG (108 DEG.), AND FE-S-CB (109.5 DEG.) REFINEMENT TARGET EQUALS MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1761 5 %RANDOM
Rwork0.18 ---
obs0.18 34933 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.83 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å20 Å20 Å2
2--4.28 Å20 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 26 314 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.96
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.652.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 285 5.1 %
Rwork0.225 5333 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3FES.PARAMFES.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07

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