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- PDB-3q1g: Crystal Structure of BoxB crystallized with PEG -

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Basic information

Entry
Database: PDB / ID: 3q1g
TitleCrystal Structure of BoxB crystallized with PEG
ComponentsBenzoyl-CoA oxygenase component B
KeywordsOXIDOREDUCTASE / DIIRON CENTER / EPOXIDASE / BENZOYL COENZYME A / benzoyl coenzyme A binding
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
: / HYDROXIDE ION / Benzoyl-CoA oxygenase component B
Similarity search - Component
Biological speciesAzoarcus evansii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionDec 17, 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 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)223,71424
Polymers222,6734
Non-polymers1,04120
Water4,936274
1
A: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9286
Polymers55,6681
Non-polymers2605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0257
Polymers55,6681
Non-polymers3566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9286
Polymers55,6681
Non-polymers2605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8325
Polymers55,6681
Non-polymers1644
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)111,95313
Polymers111,3362
Non-polymers61611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-114 kcal/mol
Surface area38210 Å2
MethodPISA
6
C: Benzoyl-CoA oxygenase component B
hetero molecules

D: Benzoyl-CoA oxygenase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,76111
Polymers111,3362
Non-polymers4249
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3630 Å2
ΔGint-102 kcal/mol
Surface area38150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.660, 76.770, 147.830
Angle α, β, γ (deg.)90.00, 109.43, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEARGARGBB8 - 518 - 51
21ILEILEARGARGAA8 - 518 - 51
31ILEILEARGARGCC8 - 518 - 51
41ILEILEARGARGDD8 - 518 - 51
12ASPASPPHEPHEBB63 - 47263 - 472
22ASPASPPHEPHEAA63 - 47263 - 472
32ASPASPPHEPHECC63 - 47263 - 472
42ASPASPPHEPHEDD63 - 47263 - 472

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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 / Mutation: c-terminal strep tag
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 , 5 types, 294 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 51.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 13% PEG 4000 0.1M sodium acetate, pH 4.6 0.1M Li2SO4 18% glycerol 5 mM benzoyl-CoA 0.1 mg/ml BoxA 0.1 M KCl 10 mM Pipes, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2010
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.5→43.7 Å / Num. all: 77107 / Num. obs: 76352 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.131 / Rsym value: 0.113 / Net I/σ(I): 8.56
Reflection shellResolution: 2.5→2.6 Å / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3PF7

3pf7


Resolution: 2.5→43.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 22.451 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23498 3824 5 %RANDOM
Rwork0.2059 ---
obs0.20735 72478 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.457 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20.15 Å2
2--1.73 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15298 0 36 274 15608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02215870
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210903
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.92921481
X-RAY DIFFRACTIONr_angle_other_deg0.94326236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63751889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37723.51866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.752152593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.37315136
X-RAY DIFFRACTIONr_chiral_restr0.0720.22202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117898
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023531
X-RAY DIFFRACTIONr_mcbond_it0.5711.59378
X-RAY DIFFRACTIONr_mcbond_other0.1031.53811
X-RAY DIFFRACTIONr_mcangle_it1.165215076
X-RAY DIFFRACTIONr_scbond_it2.20936492
X-RAY DIFFRACTIONr_scangle_it3.3074.56400
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2651TIGHT POSITIONAL0.050.05
2A2651TIGHT POSITIONAL0.040.05
3C2651TIGHT POSITIONAL0.040.05
4D2651TIGHT POSITIONAL0.040.05
1B3561LOOSE POSITIONAL0.045
2A3561LOOSE POSITIONAL0.045
3C3561LOOSE POSITIONAL0.045
4D3561LOOSE POSITIONAL0.045
1B2651TIGHT THERMAL0.10.5
2A2651TIGHT THERMAL0.10.5
3C2651TIGHT THERMAL0.090.5
4D2651TIGHT THERMAL0.080.5
1B3561LOOSE THERMAL0.110
2A3561LOOSE THERMAL0.110
3C3561LOOSE THERMAL0.0910
4D3561LOOSE THERMAL0.0810
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 269 -
Rwork0.402 5056 -
obs--94.15 %
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)
15.523-0.86093.3880.643-0.33995.40840.15350.6936-0.0157-0.2805-0.1139-0.42630.15240.705-0.03960.67280.0273-0.07650.483-0.03490.538920.244-13.439-52.666
21.05380.2440.2940.91410.33021.57270.08640.0933-0.09440.0820.005-0.07470.22170.0297-0.09140.521-0.0186-0.28520.0860.00870.21934.105-13.742-36.361
32.853-0.5673-0.96411.61610.8562.04910.0658-0.20910.0460.19230.1399-0.23750.10540.2317-0.20580.5743-0.059-0.29650.09040.02830.256413.123-8.686-23.497
43.35852.4072-1.55472.774-2.82384.3748-0.1418-0.28370.4310.3353-0.11090.0438-0.5875-0.3270.25260.84770.0547-0.37360.1752-0.10160.2314-5.50329.486-9.413
50.90350.21060.46940.48540.26271.8395-0.0895-0.06950.0915-0.013-0.10130.0985-0.1601-0.35990.19080.5962-0.0383-0.25490.1251-0.01840.1765-12.23919.706-29.184
61.56460.64050.82463.11852.16394.1359-0.25580.22440.0649-0.12220.051-0.1097-0.40510.22740.20480.7435-0.088-0.35080.0990.07930.20570.29724.341-38.854
75.23041.74170.36852.23070.15612.50570.17640.0809-0.55640.247-0.0608-0.20290.29770.1075-0.11560.6241-0.0353-0.30330.31170.09810.2214-2.9635.064-68.202
81.31560.06950.20371.1781-0.34711.22530.05810.22390.1240.03250.00330.1326-0.09640.1436-0.06140.4456-0.015-0.21080.35970.06910.1742-6.11223.227-81.773
91.19810.0503-0.11951.5958-1.02033.33980.2070.1620.1481-0.1614-0.1839-0.0909-0.08060.694-0.02310.477-0.0595-0.21840.53510.0230.195510.8626.821-83.443
101.40522.71010.010910.22580.3833.13620.4288-0.65110.23260.8361-0.38820.6994-0.2055-0.9012-0.04060.7193-0.11240.01231.0619-0.10830.350334.5823.187-10.562
111.37050.2086-0.01131.08690.22440.73170.1935-0.4129-0.03530.1998-0.1476-0.1093-0.0397-0.1846-0.04590.578-0.1495-0.23330.66540.02650.212253.50116.115-20.726
123.09370.5347-1.44571.11660.16942.80090.0778-0.1441-0.3620.1269-0.1789-0.11230.2432-0.22890.10110.5458-0.1373-0.29560.57990.10810.239547.8481.794-26.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 74
2X-RAY DIFFRACTION2A75 - 390
3X-RAY DIFFRACTION3A391 - 474
4X-RAY DIFFRACTION4B6 - 74
5X-RAY DIFFRACTION5B75 - 392
6X-RAY DIFFRACTION6B393 - 473
7X-RAY DIFFRACTION7C7 - 72
8X-RAY DIFFRACTION8C73 - 398
9X-RAY DIFFRACTION9C399 - 473
10X-RAY DIFFRACTION10D8 - 74
11X-RAY DIFFRACTION11D75 - 390
12X-RAY DIFFRACTION12D391 - 474

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