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Basic information

Entry
Database: PDB / ID: 4mud
TitleCrystal structure of a ring oxydation complex/ phenylacetic acid degradation-like protein (SSO1313) from Sulfolobus solfataricus P2 at 2.43 A resolution
ComponentsRing oxydation complex/ phenylacetic acid degradation related protein
KeywordsOXIDOREDUCTASE / Phenylacetic acid catabolic protein / PF05138 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


phenylacetate catabolic process / cytosol
Similarity search - Function
1,2-phenylacetyl-CoA epoxidase, subunit A/C / Phenylacetic acid catabolic protein / : / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ring oxydation complex/ phenylacetic acid degradation related protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a ring oxydation complex/ phenylacetic acid degradation-like protein (SSO1313) from Sulfolobus solfataricus P2 at 2.43 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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
Revision 1.4Oct 16, 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: Ring oxydation complex/ phenylacetic acid degradation related protein
B: Ring oxydation complex/ phenylacetic acid degradation related protein
C: Ring oxydation complex/ phenylacetic acid degradation related protein
D: Ring oxydation complex/ phenylacetic acid degradation related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,09912
Polymers110,6034
Non-polymers4978
Water3,063170
1
A: Ring oxydation complex/ phenylacetic acid degradation related protein
B: Ring oxydation complex/ phenylacetic acid degradation related protein


Theoretical massNumber of molelcules
Total (without water)55,3012
Polymers55,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-9 kcal/mol
Surface area20360 Å2
MethodPISA
2
C: Ring oxydation complex/ phenylacetic acid degradation related protein
D: Ring oxydation complex/ phenylacetic acid degradation related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,79810
Polymers55,3012
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint6 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.730, 64.250, 77.010
Angle α, β, γ (deg.)80.290, 70.080, 86.420
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ring oxydation complex/ phenylacetic acid degradation related protein


Mass: 27650.701 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: SSO1313 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97YL0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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 RESIDUES 1-234 OF 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20.00% polyethylene glycol 3350, 0.200M sodium formate, No Buffer pH 7.2, Additive: 0.003 M phenylacetate, 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: 0.91837,0.97941,0.97855
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.978551
ReflectionResolution: 2.43→29.229 Å / Num. obs: 31723 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 45.633 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.43-2.520.2241.97327644587.7
2.52-2.620.1842.26881609687.8
2.62-2.740.1642.66992619287.6
2.74-2.880.1293.46703592886.2
2.88-3.060.1164.26289558978.3
3.06-3.30.0945.27236645290.7
3.3-3.620.096.56804612890
3.62-4.150.0747.66938628287.1
4.15-5.210.0528.16502589183.9
5.210.0578.36965635488.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.43→29.229 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 1563 4.93 %RANDOM
Rwork0.1809 ---
obs0.1821 31723 89.91 %-
Displacement parametersBiso max: 141.93 Å2 / Biso mean: 46.8855 Å2 / Biso min: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1-4.6777 Å2-2.2715 Å22.4879 Å2
2---2.3954 Å21.1644 Å2
3----2.2824 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: LAST / Resolution: 2.43→29.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7252 0 32 170 7454
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3603SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes236HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1058HARMONIC5
X-RAY DIFFRACTIONt_it7551HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion964SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8924SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7551HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg10231HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion3.22
LS refinement shellResolution: 2.43→2.51 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.198 121 4.02 %
Rwork0.1871 2890 -
all0.1875 3011 -
obs--89.91 %
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)
12.4368-0.42310.27891.3671-0.38042.57780.05880.21480.0638-0.1367-0.02040.0083-0.1143-0.0232-0.0384-0.10380.0010.0115-0.0613-0.0268-0.147310.636526.2881-9.6103
21.82380.57850.22353.05620.21111.2184-0.0936-0.08580.17680.07820.0652-0.0301-0.0815-0.07060.0284-0.1050.0147-0.0284-0.0957-0.0195-0.121817.298336.02224.2958
32.33080.0334-0.01153.929-0.25851.3134-0.07420.2435-0.1311-0.16820.0921-0.13980.1545-0.0921-0.0178-0.1289-0.04710.0813-0.1247-0.0401-0.1621.541858.06590.4626
42.43980.4099-0.2421.8276-0.93742.7308-0.0554-0.2718-0.05970.14940.1228-0.0070.1117-0.1028-0.0674-0.11220.01310.0058-0.0938-0.0255-0.157514.614668.089834.0654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1-222 }
2X-RAY DIFFRACTION2{ B|3-223 }
3X-RAY DIFFRACTION3{ C|3-222 }
4X-RAY DIFFRACTION4{ D|1-223 }

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