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- PDB-3eby: Crystal structure of the beta subunit of a putative aromatic-ring... -

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Entry
Database: PDB / ID: 3eby
TitleCrystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution
Componentsbeta subunit of a putative Aromatic-ring-hydroxylating dioxygenase
Keywordsstructural genomics / unknown function / YP_001165631.1 / the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Dioxygenase
Function / homologyRing hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Nuclear Transport Factor 2; Chain: A, - #50 / dioxygenase activity / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Aromatic-ring-hydroxylating dioxygenase, beta subunit
Function and homology information
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1492
Polymers18,1141
Non-polymers351
Water3,117173
1
A: beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase
hetero molecules

A: beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase
hetero molecules

A: beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4486
Polymers54,3423
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5010 Å2
ΔGint-24 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.290, 80.290, 145.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-189-

HOH

21A-293-

HOH

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Components

#1: Protein beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase


Mass: 18113.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Gene: YP_001165631.1, Saro_3860 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4XDU4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2000M KCl, 20.0000% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97929,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 10, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
30.979151
ReflectionResolution: 1.75→26.764 Å / Num. obs: 18394 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 21.006 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.75-1.810.5771.993833316197.1
1.81-1.890.4592.5108363797199.5
1.89-1.970.2813.994213286199.7
1.97-2.070.1935.696613368199.5
2.07-2.20.1377.9101653537199.5
2.2-2.370.09910.4102283536199.5
2.37-2.610.07613.2102383529199.3
2.61-2.990.05218.4102723538199.5
2.99-3.760.03128.3102123494199.3
3.76-26.7640.02536.3102603517199

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→26.764 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.993 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CHLORIDE ANION FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 939 5.1 %RANDOM
Rwork0.168 ---
obs0.17 18393 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.4 Å2 / Biso mean: 23.605 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.33 Å20 Å2
2---0.67 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 1 173 1344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221261
X-RAY DIFFRACTIONr_bond_other_d0.0040.02810
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9551728
X-RAY DIFFRACTIONr_angle_other_deg0.69731972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15223.62158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18215199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3521511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
X-RAY DIFFRACTIONr_nbd_refined0.2140.3224
X-RAY DIFFRACTIONr_nbd_other0.2180.3858
X-RAY DIFFRACTIONr_nbtor_refined0.1740.5620
X-RAY DIFFRACTIONr_nbtor_other0.0840.5672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.5202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.528
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0010.51
X-RAY DIFFRACTIONr_mcbond_it2.7333887
X-RAY DIFFRACTIONr_mcbond_other0.6873330
X-RAY DIFFRACTIONr_mcangle_it3.46251312
X-RAY DIFFRACTIONr_scbond_it4.2838491
X-RAY DIFFRACTIONr_scangle_it5.65511416
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 71 -
Rwork0.236 1255 -
all-1326 -
obs--99.18 %
Refinement TLS params.Method: refined / Origin x: 10.6003 Å / Origin y: 11.2447 Å / Origin z: 36.5233 Å
111213212223313233
T-0.0347 Å2-0.0051 Å20.0071 Å2--0.0294 Å2-0.0072 Å2---0.0267 Å2
L1.1025 °20.2899 °2-0.2721 °2-0.9786 °20.1267 °2--0.4557 °2
S0.0325 Å °0.0118 Å °0.131 Å °0.0139 Å °0.0555 Å °-0.1004 Å °-0.0303 Å °-0.0092 Å °-0.088 Å °

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