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- PDB-3vb0: Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase fr... -

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Entry
Database: PDB / ID: 3vb0
TitleCrystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading Sphingomonas wittichii strain RW1
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / translational non-crystallographic symmetry / hypersymmetry / unusual crystal packing / extradiol dioxygenase
Function / homology
Function and homology information


: / dioxygenase activity / ferrous iron binding
Similarity search - Function
Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / Glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesSphingomonas wittichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoksal, M. / Kumar, P. / Bolin, J.T.
CitationJournal: To be Published
Title: Crystal structure of a dibenzofuran-degrading dioxygenase: an unusual spatially heterogeneous crystal with a hypersymmetric intensity distribution
Authors: Koksal, M. / Kumar, P. / Fortin, P.D. / Eltis, L.D. / Bolin, J.T.
History
DepositionDec 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: 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_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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
C: Glyoxalase/bleomycin resistance protein/dioxygenase
D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,22712
Polymers129,2474
Non-polymers9808
Water2,846158
1
A: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7464
Polymers32,3121
Non-polymers4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7464
Polymers32,3121
Non-polymers4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3672
Polymers32,3121
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3672
Polymers32,3121
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.587, 131.587, 103.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23B

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 2 - 290 / Label seq-ID: 2 - 290

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
115BB
215AA
122CC
222AA
132DD
232BB

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 32311.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: pAHD1 is pVLT31 plasmid containing dbfB gene / Source: (gene. exp.) Sphingomonas wittichii (bacteria) / Strain: RW1 / Gene: dbfB, Swit_4902 / Plasmid: pAHD1 / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442
References: UniProt: A5VGW5, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.727 Å3/Da / Density % sol: 28.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4-2.0 M (NH4)2SO4, 2% PEG 400 and 0.1 M PIPES at pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 30, 2005
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→92.85 Å / Num. all: 53614 / Num. obs: 51572 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 14.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2 / Num. unique all: 4815 / Rsym value: 0.499 / % possible all: 91.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus globerulus strain P6

Resolution: 2.1→92.85 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.582 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28906 2647 5 %RANDOM
Rwork0.25378 ---
all0.25559 52592 --
obs0.25559 49806 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→92.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8952 0 52 158 9162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229208
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.94512490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56251152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98323.784444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.838151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1611560
X-RAY DIFFRACTIONr_chiral_restr0.0780.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027128
X-RAY DIFFRACTIONr_nbd_refined0.2060.22310
X-RAY DIFFRACTIONr_nbtor_refined0.30.24850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2313
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.212
X-RAY DIFFRACTIONr_mcbond_it0.5651.55883
X-RAY DIFFRACTIONr_mcangle_it0.96629136
X-RAY DIFFRACTIONr_scbond_it1.28433768
X-RAY DIFFRACTIONr_scangle_it2.0344.53354
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
2C1156tight positional0.030.05
3D1156tight positional0.030.05
1B1156medium positional0.040.5
2C1082medium positional0.30.5
3D1082medium positional0.290.5
1B1082loose positional0.225
2C1156tight thermal0.090.5
3D1156tight thermal0.090.5
1B1156medium thermal0.312
2C1082medium thermal0.852
3D1082medium thermal0.862
1B1082loose thermal1.0510
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 162 -
Rwork0.321 3351 -
obs--89.89 %

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