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- PDB-2p8i: Crystal structure of putative dioxygenase (YP_555069.1) from Burk... -

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Basic information

Entry
Database: PDB / ID: 2p8i
TitleCrystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 A resolution
ComponentsPutative dioxygenase
KeywordsOXIDOREDUCTASE / YP_555069.1 / putative dioxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
Dopa 4,5-dioxygenase / DOPA-like superfamily / Dopa 4,5-dioxygenase family / DOPA-like domains / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative dioxygenase
B: Putative dioxygenase
C: Putative dioxygenase
D: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,71918
Polymers53,6944
Non-polymers1,02414
Water15,799877
1
A: Putative dioxygenase
B: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2689
Polymers26,8472
Non-polymers4207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-60 kcal/mol
Surface area10880 Å2
MethodPISA
2
C: Putative dioxygenase
D: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4519
Polymers26,8472
Non-polymers6047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-38 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.835, 138.772, 44.046
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number4
Space group name H-MP1211
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative dioxygenase


Mass: 13423.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: YP_555069.1, Bxeno_B2751, Bxe_B0224 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13JM0

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Non-polymers , 5 types, 891 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: NANODROP, 0.2M NaCl, 10.0% PEG 3000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98086 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98086 Å / Relative weight: 1
ReflectionResolution: 1.4→30.002 Å / Num. obs: 85722 / % possible obs: 85 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.21 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.442.20.4661.71321561210.46682.3
1.44-1.483.10.4321.81898960480.43283.1
1.48-1.523.20.3432.21901458600.34382.8
1.52-1.573.30.2912.61854956950.29183.1
1.57-1.623.30.25331808455340.25382.9
1.62-1.673.30.2183.41737853090.21883
1.67-1.743.30.18641671650920.18682.5
1.74-1.813.30.1484.91629349420.14882.8
1.81-1.893.30.11961565647470.11982.6
1.89-1.983.30.1026.71504845470.10283
1.98-2.093.30.0867.71441443230.08683
2.09-2.213.40.0758.81369340830.07583
2.21-2.373.40.0738.81306138910.07384.2
2.37-2.563.30.064101240737320.06486.4
2.56-2.83.30.05910.71155835180.05988.9
2.8-3.133.20.05411.41082833760.05493.3
3.13-3.613.20.04812.8984831010.04897.6
3.61-4.433.20.04514848226630.04598
4.43-6.263.20.0414.6656620490.0498.1
6.26-303.20.03715.6347410910.03795.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NYH

2nyh


Resolution: 1.4→30.002 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.758 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CL, PO4, CITRATE, AND ETHYLENE GLYCOL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. THERE IS UNMODELED DENSITY NEAR HIS 87 OF CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.173 4342 5.1 %RANDOM
Rwork0.144 ---
all0.145 ---
obs0.145 85675 84.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.313 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å2-0.25 Å2
2---0.21 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 57 877 4705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214042
X-RAY DIFFRACTIONr_bond_other_d0.0010.023460
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.8975529
X-RAY DIFFRACTIONr_angle_other_deg0.81437989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25822.93215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08715584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7391528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02926
X-RAY DIFFRACTIONr_nbd_refined0.2140.2765
X-RAY DIFFRACTIONr_nbd_other0.1920.23531
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21933
X-RAY DIFFRACTIONr_nbtor_other0.0870.22209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2627
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.278
X-RAY DIFFRACTIONr_mcbond_it1.86432793
X-RAY DIFFRACTIONr_mcbond_other0.4363973
X-RAY DIFFRACTIONr_mcangle_it2.34953776
X-RAY DIFFRACTIONr_scbond_it3.82981938
X-RAY DIFFRACTIONr_scangle_it5.656111738
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 290 -
Rwork0.242 5660 -
obs-5950 79.53 %
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)
10.4209-0.04260.25990.7698-0.19820.76750.00750.00830.03630.0531-0.0298-0.0047-0.0090.00830.0223-0.0364-0.01560.0072-0.01780.0012-0.007512.592-0.0738.29
20.30080.08350.09531.2745-0.160.41060.02150.0239-0.034-0.0947-0.0319-0.00710.05280.04030.0104-0.02020.00810.0052-0.02380.0011-0.00648.296-18.452.077
30.45560.0672-0.09220.5765-0.04550.4720.0173-0.0175-0.0268-0.055200.01970.034-0.0139-0.0172-0.0345-0.008-0.0073-0.0108-0.0023-0.008232.18710.375-10.972
40.29210.1454-0.10571.16020.030.41170.01280.03070.0616-0.1381-0.0068-0.0099-0.0348-0.0302-0.006-0.02040.01040.0046-0.02440.0053-0.002837.82928.815-15.812
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1161 - 117
22BB0 - 1161 - 117
33CC0 - 1151 - 116
44DD0 - 1161 - 117

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