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- PDB-30tw: Crystal structure of Sphingobium lactosutens styrene-oxide isomer... -

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Basic information

Entry
Database: PDB / ID: 30tw
TitleCrystal structure of Sphingobium lactosutens styrene-oxide isomerase with unknown ligand
ComponentsStyrene-oxide isomerase
KeywordsMEMBRANE PROTEIN / integral membrane protein / heme / LCP
Function / homology
Function and homology information


styrene-oxide isomerase activity / styrene catabolic process
Similarity search - Function
: / : / Styrene oxide isomerase
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / EICOSANE / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Styrene-oxide isomerase
Similarity search - Component
Biological speciesSphingobium lactosutens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.696 Å
AuthorsBloch, Y. / Kovalev, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission945405European Union
CitationJournal: To Be Published
Title: Crystal structure of Sphingobium lactosutens styrene-oxide isomerase
Authors: Bloch, Y. / Kovalev, K.
History
DepositionMay 13, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Styrene-oxide isomerase
B: Styrene-oxide isomerase
C: Styrene-oxide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,28749
Polymers62,2423
Non-polymers14,04546
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-60 kcal/mol
Surface area21980 Å2
Unit cell
Length a, b, c (Å)95.81, 99.323, 60.33
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Styrene-oxide isomerase


Mass: 20747.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: residues [1-17] cloning and purification tags residues [3-8] 6His tag residues [10-17] HRV 3C site first aligned residue
Source: (gene. exp.) Sphingobium lactosutens (bacteria) / Gene: RLDS_09420 / Details (production host): pET derived / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: T0HHY7

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Non-polymers , 7 types, 327 molecules

#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 0.2M (NH4)2SO4, 0.1M TRIS pH 8, 30% PEG500MME, monoolein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→99.323 Å / Num. obs: 64313 / % possible obs: 99.7 % / Redundancy: 13.677 % / Biso Wilson estimate: 31.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.135 / Net I/σ(I): 15.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
5.08-99.32312.4565.93259810.0399.3
1.7-1.813.851.28102830.6132.17399.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDS20230630data reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.696→24.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 3279 -RANDOM
Rwork0.1842 ---
obs0.1852 64263 99.7 %-
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.0505 Å20 Å20 Å2
2--0.0472 Å20 Å2
3----3.0976 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.696→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 573 281 4763
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099541HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.4917295HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d2746SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1421HARMONIC5
X-RAY DIFFRACTIONt_it5270HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion518SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact8507SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion14.84
LS refinement shellResolution: 1.7→1.71 Å
RfactorNum. reflection% reflection
Rfree0.3516 69 -
Rwork0.3418 --
obs0.3423 1286 97.59 %
Refinement TLS params.

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)
11.04490.1501-0.38992.3309-2.0354.5282-0.03210.2833-0.10090.2833-0.06220.0905-0.10090.09050.0943-0.0598-0.0016-0.012-0.092-0.0174-0.013120.771326.804410.0025
20.4804-0.0705-0.00640.82040.18620.3218-0.0161-0.050.0017-0.050.0173-0.00480.0017-0.0048-0.0012-0.07270.0026-0.001-0.0865-0.0004-0.021119.911922.687-1.9492
34.3343-0.1899-3.67291.2017-0.48285.5827-0.17910.14840.19440.14840.0613-0.05090.1944-0.05090.1178-0.042-0.005-0.0044-0.09510.0008-0.018713.96811.06895.7868
46.087-0.2355-2.64874.97633.84475.48690.0587-0.1638-0.0848-0.1638-0.0233-0.0195-0.0848-0.0195-0.0354-0.11020.00090.0017-0.0956-0.0137-0.028813.17918.1328-4.4098
51.19560.26960.06660.58490.00230.1519-0.01740.0268-0.03730.0268-0.0227-0.0371-0.0373-0.03710.0402-0.05470.01430.0058-0.0833-0.00580.01346.495638.41411.7147
62.3525-1.29942.84073.8985-4.28988.81840.03950.1883-0.05410.1883-0.16570.3646-0.05410.36460.1262-0.0511-0.0086-0.0033-0.0786-0.03870.047220.613839.64955.7714
74.07210.5727-1.90053.6585-3.46045.8808-0.0436-0.14620.1232-0.14620.13570.02420.12320.0242-0.0921-0.07170.0075-0.0043-0.09880.0228-0.008414.963235.2977-4.5356
81.0756-0.3705-0.0510.65270.05070.4852-0.02760.0570.03880.0570.0011-0.07480.0388-0.07480.0264-0.0736-0.00390.0112-0.07270.00990.00070.795619.17571.6219
93.25522.0432.63085.21024.99796.999-0.0729-0.0429-0.1764-0.0429-0.0656-0.3408-0.1764-0.34080.1385-0.06690.01730.0371-0.01550.03430.0336-7.35131.15015.6728
104.64941.19833.45553.6152.71335.1520.0062-0.0619-0.0964-0.06190.0307-0.0556-0.0964-0.0556-0.0369-0.08910.00890.0049-0.0872-0.0034-0.0271-0.794828.2594-4.516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|15 - 53}A15 - 53
2X-RAY DIFFRACTION2{A|54 - 147}A54 - 147
3X-RAY DIFFRACTION3{A|148 - 181}A148 - 181
4X-RAY DIFFRACTION4{A|201}A201
5X-RAY DIFFRACTION5{B|15 - 147}B15 - 147
6X-RAY DIFFRACTION6{B|148 - 181}B148 - 181
7X-RAY DIFFRACTION7{B|201}B201
8X-RAY DIFFRACTION8{C|15 - 147}C15 - 147
9X-RAY DIFFRACTION9{C|148 - 181}C148 - 181
10X-RAY DIFFRACTION10{C|201}C201

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