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- PDB-2xsh: CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURK... -

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Basic information

Entry
Database: PDB / ID: 2xsh
TitleCRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400 IN COMPLEX WITH 2,6 DI CHLOROBIPHENYL
Components(BIPHENYL DIOXYGENASE SUBUNIT ...) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / : / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2,6-DICHLOROBIPHENYL / : / FE2/S2 (INORGANIC) CLUSTER / Biphenyl dioxygenase subunit alpha / Biphenyl dioxygenase subunit beta
Similarity search - Component
Biological speciesBURKHOLDERIA XENOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKumar, P. / Bolin, J.T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Insight Into the Expanded Pcb-Degrading Abilities of a Biphenyl Dioxygenase Obtained by Directed Evolution.
Authors: Kumar, P. / Mohammadi, M. / Viger, J.F. / Barriault, D. / Gomez-Gil, L. / Eltis, L.D. / Bolin, J.T. / Sylvestre, M.
History
DepositionSep 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
B: BIPHENYL DIOXYGENASE SUBUNIT BETA
C: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
D: BIPHENYL DIOXYGENASE SUBUNIT BETA
E: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
F: BIPHENYL DIOXYGENASE SUBUNIT BETA
G: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
H: BIPHENYL DIOXYGENASE SUBUNIT BETA
I: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
J: BIPHENYL DIOXYGENASE SUBUNIT BETA
K: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
L: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,91327
Polymers441,85312
Non-polymers2,05915
Water17,889993
1
A: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
B: BIPHENYL DIOXYGENASE SUBUNIT BETA
C: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
D: BIPHENYL DIOXYGENASE SUBUNIT BETA
E: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
F: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,29115
Polymers220,9276
Non-polymers1,3649
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32440 Å2
ΔGint-189.1 kcal/mol
Surface area55680 Å2
MethodPISA
2
G: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
H: BIPHENYL DIOXYGENASE SUBUNIT BETA
I: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
J: BIPHENYL DIOXYGENASE SUBUNIT BETA
K: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
L: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,62212
Polymers220,9276
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32670 Å2
ΔGint-189.7 kcal/mol
Surface area56530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.728, 276.762, 92.317
Angle α, β, γ (deg.)90.00, 117.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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BIPHENYL DIOXYGENASE SUBUNIT ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
BIPHENYL DIOXYGENASE SUBUNIT ALPHA / BIPHENYL 2\ / 3-DIOXYGENASE / BIPHENYL DIOXYGENASE VARIANT P4


Mass: 51528.383 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: P4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37333, biphenyl 2,3-dioxygenase
#2: Protein
BIPHENYL DIOXYGENASE SUBUNIT BETA / BIPHENYL 2\ / 3-DIOXYGENASE


Mass: 22113.846 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: P4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37334, biphenyl 2,3-dioxygenase

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Non-polymers , 4 types, 1008 molecules

#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-DC5 / 2,6-DICHLOROBIPHENYL / Polychlorinated biphenyl


Mass: 223.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H8Cl2
#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

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN C, THR 335 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN C, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN E, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN G, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN I, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN K, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN C, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN E, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN G, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN I, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN K, PHE 336 TO MET

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6 / Details: PEG 8K, PIPES PH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→125 Å / Num. obs: 177300 / % possible obs: 86 % / Observed criterion σ(I): 1.5 / Redundancy: 4 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 51.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XR8

2xr8


Resolution: 2.29→138.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.517 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24456 7632 5 %RANDOM
Rwork0.18571 ---
obs0.18863 144572 87.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.16 Å2
2---0.83 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.29→138.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29538 0 72 993 30603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02130423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.93641238
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07153660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67223.321554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.209154908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.60315252
X-RAY DIFFRACTIONr_chiral_restr0.0780.24224
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0223874
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.213579
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.220205
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.21601
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4131.518773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.718229280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.064313554
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6914.511946
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.286→2.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 358 -
Rwork0.233 6779 -
obs--55.89 %
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)
10.77620.1499-0.00210.5951-0.00320.66180.0383-0.025-0.04040.03650.0285-0.15410.04830.2138-0.0668-0.17220.0342-0.03750.0074-0.033-0.013420.5373-6.5026-1.4748
21.0148-0.2776-0.11940.53450.0510.78080.0164-0.13080.22370.07720.0116-0.0343-0.1642-0.0118-0.0281-0.0844-0.0013-0.0121-0.0481-0.0864-0.0121-1.85114.88136.5784
30.53570.0290.10590.57280.02540.7798-0.02410.1624-0.0086-0.21070.02080.0597-0.0613-0.06210.0033-0.0619-0.0003-0.03090.0004-0.0118-0.0741-9.97090.3502-36.2216
40.8603-0.0915-0.14090.4080.1350.92990.02020.03880.1775-0.0479-0.01230.1344-0.1963-0.2492-0.0079-0.10390.0757-0.0095-0.0025-0.00480.0317-22.456515.0592-10.5992
50.76370.08510.11110.7342-0.04440.8420.0564-0.0651-0.24890.10880.00240.12260.2518-0.1571-0.0588-0.0761-0.07440.0074-0.09150.0160.0388-20.1675-29.8149-1.8803
60.7194-0.18180.1420.86870.13120.8392-0.0116-0.18330.04490.1901-0.02130.11890.0165-0.17940.0328-0.1286-0.00270.06170.0187-0.0218-0.0315-23.1727-0.710811.0774
71.0002-0.2872-0.02342.39121.09591.22620.17510.09720.04310.4012-0.68321.06170.1012-0.67140.5081-0.15510.00550.26760.1209-0.35770.287356.088455.2977-40.6622
80.9757-0.2721-0.29672.65391.1521.48580.10060.2526-0.1365-0.0374-0.32310.27850.1227-0.27220.2226-0.110.05460.0478-0.0743-0.1051-0.060978.480540.2201-57.7377
91.004-0.3271-0.06952.39321.31881.65270.22850.12690.416-1.0241-0.1165-0.2913-1.1838-0.1643-0.11190.6180.20640.2298-0.29470.12180.023186.458385.3009-59.7904
100.9764-0.4718-0.09522.56471.03191.63860.19170.19050.1645-0.53720.1027-0.5956-0.32630.1679-0.29440.00410.06670.2236-0.132-0.00330.005498.966656.2345-64.1727
110.94740.099-0.44142.52451.00652.06360.1867-0.34910.30861.350.1334-0.47620.37350.3439-0.320.52120.058-0.1966-0.154-0.2151-0.092996.961764.3196-19.1672
120.98720.0437-0.38672.59061.3981.3248-0.0032-0.0528-0.01980.73670.2514-0.57580.50470.2113-0.24820.09440.1548-0.1132-0.163-0.0598-0.02499.927641.7873-41.68
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 459
2X-RAY DIFFRACTION2B9 - 188
3X-RAY DIFFRACTION3C18 - 459
4X-RAY DIFFRACTION4D9 - 188
5X-RAY DIFFRACTION5E18 - 459
6X-RAY DIFFRACTION6F9 - 188
7X-RAY DIFFRACTION7G18 - 459
8X-RAY DIFFRACTION8H9 - 188
9X-RAY DIFFRACTION9I18 - 459
10X-RAY DIFFRACTION10J9 - 188
11X-RAY DIFFRACTION11K18 - 459
12X-RAY DIFFRACTION12L9 - 188

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