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- PDB-3pf7: Crystal structure of BoxB with malonate bound to the diiron center -

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Basic information

Entry
Database: PDB / ID: 3pf7
TitleCrystal structure of BoxB with malonate bound to the diiron center
ComponentsBenzoyl-CoA oxygenase component B
KeywordsOXIDOREDUCTASE / diiron center / epoxidase / benzoyl coenzyme A
Function / homology
Function and homology information


benzoyl-CoA 2,3-epoxidase / : / dioxygenase activity / metal ion binding
Similarity search - Function
Benzoyl-CoA oxygenase, B subunit / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / MALONIC ACID / HYDROXIDE ION / Benzoyl-CoA oxygenase component B
Similarity search - Component
Biological speciesAzoarcus evansii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsWeinert, T. / Rather, L.J. / Fuchs, G. / Ermler, U.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Mechanism of the Diiron Benzoyl-Coenzyme A Epoxidase BoxB.
Authors: Rather, L.J. / Weinert, T. / Demmer, U. / Bill, E. / Ismail, W. / Fuchs, G. / Ermler, U.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Benzoyl-CoA oxygenase component B
B: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,83711
Polymers111,3362
Non-polymers5019
Water17,889993
1
A: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9366
Polymers55,6681
Non-polymers2685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9015
Polymers55,6681
Non-polymers2334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.790, 213.490, 137.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-842-

HOH

31B-885-

HOH

41B-895-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Benzoyl-CoA oxygenase component B / Benzoyl-CoA 2 / 3-dioxygenase subunit B / Benzoyl-CoA dioxygenase oxygenase component


Mass: 55668.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus evansii (bacteria) / Gene: boxB / Production host: Azoarcus evansii (bacteria) / References: UniProt: Q9AIX7, EC: 1.14.12.21

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Non-polymers , 5 types, 1002 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 993 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE C-TERMINAL TAGGED BOXB WAS INTEGRATED INTO THE GENOME OF AZOARCUS EVANSII AS DESCRIBED ...THE C-TERMINAL TAGGED BOXB WAS INTEGRATED INTO THE GENOME OF AZOARCUS EVANSII AS DESCRIBED ELSEWHERE FOR THE HIS-TAG VERSION (ZAAR ET AL. 2004)

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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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.6 M sodium malonate 0.94 % MG8 (octanoyl-N-metylglucamide) 100 mM KCl 10 mM Pipes 5 mM Benzoyl-CoA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2009
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 124905 / Num. obs: 124905 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2.7 / Num. unique all: 15532 / Rsym value: 0.813 / % possible all: 84.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→46.864 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 6094 5 %RANDOM
Rwork0.1821 ---
obs0.1838 121927 94.43 %-
all-124905 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.639 Å2 / ksol: 0.434 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.5533 Å2-0 Å20 Å2
2---7.8379 Å2-0 Å2
3---0.2845 Å2
Refinement stepCycle: LAST / Resolution: 1.903→46.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7717 0 21 993 8731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098124
X-RAY DIFFRACTIONf_angle_d1.13311062
X-RAY DIFFRACTIONf_dihedral_angle_d13.3033010
X-RAY DIFFRACTIONf_chiral_restr0.0661126
X-RAY DIFFRACTIONf_plane_restr0.0051461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9035-1.92510.57811170.57812251X-RAY DIFFRACTION55
1.9251-1.94780.4497900.4311687X-RAY DIFFRACTION42
1.9478-1.97150.38531910.33523676X-RAY DIFFRACTION91
1.9715-1.99650.2962080.23843954X-RAY DIFFRACTION98
1.9965-2.02270.24092130.23954040X-RAY DIFFRACTION100
2.0227-2.05040.29092120.274029X-RAY DIFFRACTION99
2.0504-2.07970.42621910.36013608X-RAY DIFFRACTION89
2.0797-2.11080.29182070.26223930X-RAY DIFFRACTION97
2.1108-2.14380.21172120.17894024X-RAY DIFFRACTION100
2.1438-2.17890.21282150.18294086X-RAY DIFFRACTION100
2.1789-2.21650.22572120.19624028X-RAY DIFFRACTION100
2.2165-2.25680.4721790.38323449X-RAY DIFFRACTION85
2.2568-2.30020.371980.25453764X-RAY DIFFRACTION93
2.3002-2.34710.20162130.16144050X-RAY DIFFRACTION100
2.3471-2.39820.19482160.15734102X-RAY DIFFRACTION100
2.3982-2.4540.22792130.15364052X-RAY DIFFRACTION100
2.454-2.51530.18442150.15324068X-RAY DIFFRACTION100
2.5153-2.58330.19472130.15624049X-RAY DIFFRACTION100
2.5833-2.65930.22032130.16754050X-RAY DIFFRACTION99
2.6593-2.74520.23062110.16974013X-RAY DIFFRACTION98
2.7452-2.84330.19222140.14824060X-RAY DIFFRACTION100
2.8433-2.95710.1662170.14564124X-RAY DIFFRACTION100
2.9571-3.09160.19452160.14714092X-RAY DIFFRACTION100
3.0916-3.25460.1852150.15174083X-RAY DIFFRACTION100
3.2546-3.45850.21922130.16364046X-RAY DIFFRACTION98
3.4585-3.72540.1822100.15543995X-RAY DIFFRACTION97
3.7254-4.10010.17922110.14384007X-RAY DIFFRACTION97
4.1001-4.69290.13932190.12374154X-RAY DIFFRACTION100
4.6929-5.91070.17722200.15864184X-RAY DIFFRACTION100
5.9107-46.87840.18912200.18624178X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -23.5266 Å / Origin y: 23.8971 Å / Origin z: -4.5491 Å
111213212223313233
T0.1374 Å2-0.0149 Å2-0.0103 Å2-0.0972 Å20.0129 Å2--0.1088 Å2
L0.0909 °20.0806 °20.1236 °2--0.0163 °20.192 °2--0.1251 °2
S0.0265 Å °0.0272 Å °-0.0021 Å °0.0021 Å °0.0026 Å °0.0026 Å °-0.028 Å °0.0175 Å °-0.0182 Å °
Refinement TLS groupSelection details: all

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