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- PDB-3on7: Crystal structure of a Putative oxygenase (SO_2589) from Shewanel... -

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Entry
Database: PDB / ID: 3on7
TitleCrystal structure of a Putative oxygenase (SO_2589) from Shewanella oneidensis at 2.20 A resolution
ComponentsOxidoreductase, iron/ascorbate family
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2OG-Fe(II) oxygenase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative oxygenase (SO_2589) from Shewanella oneidensis at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, iron/ascorbate family
B: Oxidoreductase, iron/ascorbate family
C: Oxidoreductase, iron/ascorbate family
D: Oxidoreductase, iron/ascorbate family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,26715
Polymers128,6374
Non-polymers63111
Water12,376687
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-99 kcal/mol
Surface area43370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.189, 95.678, 184.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 279
2114B1 - 279
3114C1 - 279
4114D1 - 279
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS POSSIBLE OLIGOMERIZATION STATES.

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Components

#1: Protein
Oxidoreductase, iron/ascorbate family /


Mass: 32159.189 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_2589 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8EE01
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND .
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.80M lithium chloride, 24.00% polyethylene glycol 6000, 0.1M HEPES pH 6.5, NANODROP, 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: 0.91837,0.97963,0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979631
30.979161
ReflectionResolution: 2.2→29.587 Å / Num. obs: 59238 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.859 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.98
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.280.5221.62038310943195.2
2.28-2.370.422034110834197.2
2.37-2.480.3322.52138011284197.8
2.48-2.610.2653.12112111053198.2
2.61-2.770.20442091910888198.4
2.77-2.980.1525.32147011070198.8
2.98-3.280.0988.12189411245198.9
3.28-3.760.05613.12212411354198.8
3.76-4.720.03818.42175511125199
4.72-29.5870.03121.22214611236198

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.587 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.31 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.217
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. CHLORIDE (CL) AND POLYETHYLENE GLYCROL (PEG) FROM THE CRYSTALLIZATION AND GLYCEROL(GOL) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 2982 5 %RANDOM
Rwork0.1847 ---
obs0.1873 59183 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.89 Å2 / Biso mean: 28.0169 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---1.01 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8694 0 32 687 9413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229075
X-RAY DIFFRACTIONr_bond_other_d0.0010.026181
X-RAY DIFFRACTIONr_angle_refined_deg1.311.96512363
X-RAY DIFFRACTIONr_angle_other_deg0.868315065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83551126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97623.756426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.058151506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8131559
X-RAY DIFFRACTIONr_chiral_restr0.0760.21357
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021854
X-RAY DIFFRACTIONr_mcbond_it1.28635534
X-RAY DIFFRACTIONr_mcbond_other0.50332184
X-RAY DIFFRACTIONr_mcangle_it2.34158993
X-RAY DIFFRACTIONr_scbond_it4.03783541
X-RAY DIFFRACTIONr_scangle_it5.758113350
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3411 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.230.5
BMEDIUM POSITIONAL0.30.5
CMEDIUM POSITIONAL0.250.5
DMEDIUM POSITIONAL0.220.5
AMEDIUM THERMAL0.872
BMEDIUM THERMAL0.922
CMEDIUM THERMAL0.912
DMEDIUM THERMAL0.792
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 194 -
Rwork0.266 4041 -
all-4235 -
obs--97.6 %
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)
10.8087-0.1456-0.20391.07030.16440.91340.0363-0.1706-0.02740.3264-0.0283-0.14580.00470.1267-0.0080.1289-0.0448-0.03880.07870.01910.052747.421141.206592.451
20.84930.05650.06430.60540.16970.64810.02030.083-0.11090.011-0.01270.02690.041-0.0338-0.00760.0068-0.00660.00020.0275-0.01090.087936.672123.852860.2103
30.73010.04740.0980.53240.22390.79530.03340.0275-0.1314-0.01130.0182-0.09420.0680.0949-0.05150.00940.011-0.00110.0284-0.01810.072260.432537.145947.8925
40.67660.14490.26221.1251-0.07780.87570.0082-0.09580.01560.19560.01730.0679-0.1644-0.0786-0.02540.06620.00470.02440.0306-0.01350.020352.930964.423474.0207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 279
2X-RAY DIFFRACTION2B1 - 279
3X-RAY DIFFRACTION3C1 - 279
4X-RAY DIFFRACTION4D1 - 279

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