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- PDB-21gu: OleP in complex with lithocholic acid -

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Basic information

Entry
Database: PDB / ID: 21gu
TitleOleP in complex with lithocholic acid
ComponentsCytochrome P-450
KeywordsBIOSYNTHETIC PROTEIN / P450 OleP / lithocholic acid / murideoxycholic acid / ursodeoxycholic acid
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsZhou, J.H. / Pang, C.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: OleP in complex with lithocholic acid
Authors: Zhou, J.H. / Pang, C.P.
History
DepositionDec 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cytochrome P-450
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4629
Polymers91,6822
Non-polymers1,7807
Water2,126118
1
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5424
Polymers45,8411
Non-polymers7023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-25 kcal/mol
Surface area16800 Å2
MethodPISA
2
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9195
Polymers45,8411
Non-polymers1,0784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.619, 59.575, 162.867
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Cytochrome P-450


Mass: 45840.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Production host: Escherichia coli B (bacteria) / References: UniProt: Q59819

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Non-polymers , 5 types, 125 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-4OA / (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid / Lithocholic acid


Mass: 376.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O3 / Comment: detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.55 Å3/Da / Density % sol: 51.77 % / Description: Regular rectangular prism
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 40 mM Potassium phosphate monobasic; 16% Glycerol; 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.79→48.68 Å / Num. obs: 22933 / % possible obs: 98.3 % / Redundancy: 4.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.086 / Rrim(I) all: 0.194 / Χ2: 1.05 / Net I/σ(I): 8.2
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3361 / CC1/2: 0.751 / Rpim(I) all: 0.419 / Rrim(I) all: 0.712 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→48.68 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 1123 4.94 %
Rwork0.2016 --
obs0.2045 22750 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6189 0 10 118 6317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096346
X-RAY DIFFRACTIONf_angle_d1.0438690
X-RAY DIFFRACTIONf_dihedral_angle_d14.8862301
X-RAY DIFFRACTIONf_chiral_restr0.051993
X-RAY DIFFRACTIONf_plane_restr0.0111136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.920.351540.28022737X-RAY DIFFRACTION99
2.92-3.070.29541440.25732714X-RAY DIFFRACTION99
3.07-3.260.3141480.24152729X-RAY DIFFRACTION100
3.26-3.510.26561520.20492724X-RAY DIFFRACTION99
3.52-3.870.23271370.19372744X-RAY DIFFRACTION99
3.87-4.430.25261190.17192742X-RAY DIFFRACTION98
4.43-5.580.23151510.18122635X-RAY DIFFRACTION95
5.58-48.680.21411180.17342602X-RAY DIFFRACTION90

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