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- PDB-3pm5: Crystal Structure of BoxB in mixed valent state with bound benzoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 3pm5
TitleCrystal Structure of BoxB in mixed valent state with bound benzoyl-CoA
ComponentsBenzoyl-CoA oxygenase component B
KeywordsOXIDOREDUCTASE / diiron center / epoxidase / benzoyl coenzyme A
Function / homology
Function and homology information


benzoyl-CoA 2,3-epoxidase / phenylacetate catabolic process / dioxygenase activity / metal ion binding / cytosol
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
benzoyl coenzyme A / : / TRIETHYLENE GLYCOL / S-1,2-PROPANEDIOL / Benzoyl-CoA oxygenase component B
Similarity search - Component
Biological speciesAzoarcus evansii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWeinert, T. / Rather, L. / 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
DepositionNov 16, 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 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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_seq_id / _struct_conn.ptnr2_label_asym_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
C: Benzoyl-CoA oxygenase component B
D: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,05934
Polymers222,6734
Non-polymers5,38630
Water11,331629
1
A: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,08710
Polymers55,6681
Non-polymers1,4199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8046
Polymers55,6681
Non-polymers1,1365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0679
Polymers55,6681
Non-polymers1,3998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1019
Polymers55,6681
Non-polymers1,4338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Benzoyl-CoA oxygenase component B
B: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,89016
Polymers111,3362
Non-polymers2,55414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-112 kcal/mol
Surface area37830 Å2
MethodPISA
6
C: Benzoyl-CoA oxygenase component B
D: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,16918
Polymers111,3362
Non-polymers2,83216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-132 kcal/mol
Surface area37170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.180, 76.650, 148.200
Angle α, β, γ (deg.)90.00, 108.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4 / Fragment: BoxB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus evansii (bacteria) / Gene: Azoarcus evansii, boxB / Production host: Azoarcus evansii (bacteria) / References: UniProt: Q9AIX7, EC: 1.14.12.21

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Non-polymers , 8 types, 659 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical
ChemComp-BYC / benzoyl coenzyme A


Mass: 871.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H40N7O17P3S
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 4000, 0.1M sodium acetate, 0.1M Li2SO4, 18% glycerol, 5 mM benzoyl-CoA, 1 mM NADPH, 0.1 mg/ml BoxA 10 mM Pipes, 0.1 M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2137 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2010
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2137 Å / Relative weight: 1
ReflectionResolution: 2.3→49.4 Å / Num. all: 98025 / Num. obs: 98025 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.475 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.945 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22417 4887 5 %RANDOM
Rwork0.17417 ---
obs0.17665 93138 99.24 %-
all-98025 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.75 Å2
2--0.2 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15388 0 313 629 16330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02116305
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211174
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.94822149
X-RAY DIFFRACTIONr_angle_other_deg0.973326893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25551918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57123.526882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.874152630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.45915140
X-RAY DIFFRACTIONr_chiral_restr0.1030.22246
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023610
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_it0.8721.59479
X-RAY DIFFRACTIONr_mcbond_other0.221.53850
X-RAY DIFFRACTIONr_mcangle_it1.62215267
X-RAY DIFFRACTIONr_scbond_it2.64336826
X-RAY DIFFRACTIONr_scangle_it4.1254.56878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 376 -
Rwork0.251 6857 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08080.2267-0.06361.30520.07740.77030.0401-0.18790.04520.2223-0.02120.0784-0.0527-0.0817-0.01890.13280.0456-0.04360.25420.0030.0477-27.78126.622-10.657
20.9564-0.07420.07760.9213-0.1180.77820.07060.2564-0.1017-0.0974-0.00440.0607-0.0855-0.0011-0.06620.09430.0934-0.03870.2874-0.04820.0341-25.91119.257-49.738
31.1616-0.4106-0.09840.6732-0.17641.10090.0296-0.017-0.20060.08120.0120.10260.03690.0594-0.04170.140.0778-0.07830.1092-0.10350.222915.08-7.716-32.632
40.79330.25960.03240.1336-0.13951.0098-0.10070.14730.2277-0.0187-0.03020.134-0.12020.38870.13090.27310.0855-0.12770.2776-0.02690.309234.06426.057-44.942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 85
2X-RAY DIFFRACTION1A86 - 238
3X-RAY DIFFRACTION1A239 - 390
4X-RAY DIFFRACTION1A391 - 474
5X-RAY DIFFRACTION2B5 - 63
6X-RAY DIFFRACTION2B64 - 236
7X-RAY DIFFRACTION2B237 - 393
8X-RAY DIFFRACTION2B394 - 474
9X-RAY DIFFRACTION3C1 - 106
10X-RAY DIFFRACTION3C107 - 195
11X-RAY DIFFRACTION3C196 - 390
12X-RAY DIFFRACTION3C391 - 475
13X-RAY DIFFRACTION4D5 - 85
14X-RAY DIFFRACTION4D86 - 237
15X-RAY DIFFRACTION4D238 - 390
16X-RAY DIFFRACTION4A645 - 663
17X-RAY DIFFRACTION4C618 - 644
18X-RAY DIFFRACTION4B632 - 659
19X-RAY DIFFRACTION4D574 - 593

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