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

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Basic information

Entry
Database: PDB / ID: 2nyh
TitleCrystal structure of putative dioxygenase (YP_555069.1) from Burkholderia Xenovorans LB400 at 1.70 A resolution
ComponentsPutative dioxygenase
KeywordsOXIDOREDUCTASE / YP_555069.1 / putative Dioxygenase / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyDopa 4,5-dioxygenase / DOPA-like superfamily / Dopa 4,5-dioxygenase family / DOPA-like domains / dioxygenase activity / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Dioxygenase
Function and homology information
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 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 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 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 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3287
Polymers26,8472
Non-polymers4805
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-86 kcal/mol
Surface area10890 Å2
MethodPISA
2
A: Putative dioxygenase
hetero molecules

A: Putative dioxygenase
hetero molecules

B: Putative dioxygenase
hetero molecules

B: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,65514
Polymers53,6944
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area5980 Å2
ΔGint-155 kcal/mol
Surface area23030 Å2
MethodPISA
3
A: Putative dioxygenase
B: Putative dioxygenase
hetero molecules

A: Putative dioxygenase
B: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,65514
Polymers53,6944
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7850 Å2
ΔGint-188 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.970, 88.304, 88.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-163-

HOH

21A-243-

HOH

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Components

#1: Protein Putative dioxygenase


Mass: 13423.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Gene: YP_555069.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13JM0
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 277 K / pH: 6.4
Details: 0.2M Li2SO4, 20.0% PEG-3350, No Buffer, pH 6.4, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9795, 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2006
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97921
ReflectionResolution: 1.7→27.692 Å / Num. obs: 30205 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.743.50.9161.7758321760.91697.4
1.74-1.793.50.7411755521620.74197.5
1.79-1.843.50.6081.3730320980.60897.3
1.84-1.93.50.4521.7702120200.45297.8
1.9-1.963.50.3612.1684019700.36197.7
1.96-2.033.50.2982.6666119190.29898.2
2.03-2.113.50.2243.4639018430.22497.4
2.11-2.193.50.23.9609317630.298.4
2.19-2.293.40.1674.6590617160.16798
2.29-2.43.40.1465.1564916430.14698.2
2.4-2.533.40.1256531315530.12598
2.53-2.693.40.1067512014980.10698.5
2.69-2.873.40.0967.5468813880.09698.6
2.87-3.13.30.0788.9439613130.07898.3
3.1-3.43.30.0669401112160.06698.5
3.4-3.83.20.069.5358211090.0699
3.8-4.393.10.04712.529919570.04797.5
4.39-5.383.30.0371627228260.03798.8
5.38-7.63.40.03121.822526650.03198.8
7.6-27.693.20.02131.111923700.02196.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.692 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.442 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.108
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. 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. 3. SULFATES MODELED BASED ON CRYSTALLIZATION CONDITIONS. 4. DIFFERENCE ELECTRON DENSITY COINCIDENT WITH AN ANOMALOUS DIFFERENCE DENSITY PEAK IS LOCATED NEAR THE SIDE CHAIN OF HIS A47. X-RAY FLOURESCENCE EXPERIMENTS WERE UNSUCCESSFUL IN IDENTIFYING THE SCATTERING ELEMENT. THIS DENSITY WAS LEFT UNMODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1538 5.1 %RANDOM
Rwork0.176 ---
obs0.179 30193 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.044 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.58 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 25 363 2272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211973
X-RAY DIFFRACTIONr_bond_other_d0.0020.021271
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.8982700
X-RAY DIFFRACTIONr_angle_other_deg0.96733052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65322.549102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59915281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.111514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_nbd_refined0.1940.2353
X-RAY DIFFRACTIONr_nbd_other0.2040.21349
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2898
X-RAY DIFFRACTIONr_nbtor_other0.0890.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.226
X-RAY DIFFRACTIONr_mcbond_it2.11931392
X-RAY DIFFRACTIONr_mcbond_other0.5623470
X-RAY DIFFRACTIONr_mcangle_it2.70251842
X-RAY DIFFRACTIONr_scbond_it4.3958958
X-RAY DIFFRACTIONr_scangle_it6.2411855
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 119 -
Rwork0.265 2047 -
obs-2166 96.7 %

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