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- PDB-9ft5: 25-hydroxy steroid kinase (25-HSK) + ADP + 25-phospho-cholest-1,4... -

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Basic information

Entry
Database: PDB / ID: 9ft5
Title25-hydroxy steroid kinase (25-HSK) + ADP + 25-phospho-cholest-1,4-diene-3-one
ComponentsAminoglycoside phosphotransferase-like protein
KeywordsTRANSFERASE / anaerobic cholesterol degradation / Kinase / ATP / substrate-induced dimerisation
Function / homologyAcyl-CoA dehydrogenase family member 10/11, N-terminal / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / : / ADENOSINE-5'-DIPHOSPHATE / Aminoglycoside phosphotransferase-like protein
Function and homology information
Biological speciesSterolibacterium denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsErmler, U. / Boll, M. / Demmer, U. / Warkentin, E. / Jacoby, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of 25-hydroxy steroid kinase (25-HSK)
Authors: Jacoby, C. / Demmer, U. / Warkentin, E. / Ermler, U. / Boll, M.
History
DepositionJun 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 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: Aminoglycoside phosphotransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2046
Polymers43,2091
Non-polymers9945
Water1,47782
1
A: Aminoglycoside phosphotransferase-like protein
hetero molecules

A: Aminoglycoside phosphotransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,40712
Polymers86,4182
Non-polymers1,98910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4540 Å2
ΔGint-89 kcal/mol
Surface area30890 Å2
Unit cell
Length a, b, c (Å)77.880, 154.870, 89.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminoglycoside phosphotransferase-like protein


Mass: 43209.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sterolibacterium denitrificans (bacteria)
Gene: SDENCHOL_21286
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A7Z7HU23

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Non-polymers , 5 types, 87 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1IFV / [(6~{R})-6-[(8~{S},9~{R},10~{R},13~{R},14~{R},17~{S})-10,13-dimethyl-3-oxidanylidene-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-17-yl]-2-methyl-heptan-2-yl] dihydrogen phosphate


Mass: 478.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H43O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, isopropanol, sodium acetate, calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 26672 / % possible obs: 95.7 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.117 / Net I/σ(I): 10.73
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.30.81224420.6491.0551
2.3-2.50.6751620.7560.8071
2.5-2.80.52554230.9430.5811
2.8-3.20.27444420.9840.3011
3.2-3.80.11636280.9950.1281
3.8-4.70.06225730.9970.0691
4.7-5.90.04814510.9970.0541
5.9-80.0459100.9980.051
8-120.0414390.9930.0461
12-500.0332020.9980.0361

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.03 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1354 5.09 %
Rwork0.2318 --
obs0.2334 26609 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 63 82 3112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.721
X-RAY DIFFRACTIONf_dihedral_angle_d27.0261164
X-RAY DIFFRACTIONf_chiral_restr0.083434
X-RAY DIFFRACTIONf_plane_restr0.004556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.42361090.43561728X-RAY DIFFRACTION67
2.28-2.370.41391330.37452380X-RAY DIFFRACTION92
2.37-2.480.37681440.35692570X-RAY DIFFRACTION99
2.48-2.610.34741280.29112610X-RAY DIFFRACTION100
2.61-2.770.28251490.26572611X-RAY DIFFRACTION100
2.77-2.990.3191490.26452622X-RAY DIFFRACTION100
2.99-3.290.31151180.24922636X-RAY DIFFRACTION100
3.29-3.760.26251410.21882654X-RAY DIFFRACTION100
3.76-4.740.20171420.17932671X-RAY DIFFRACTION100
4.74-43.030.22251410.20482773X-RAY DIFFRACTION99
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)
13.0113-0.581-1.53823.43681.93096.97190.1763-0.27150.35120.05760.1755-0.36290.07590.6898-0.33630.67140.0033-0.03110.4255-0.05820.465915.419833.326427.6542
21.3021-0.3156-0.2271.3493-0.10620.942-0.0284-0.08640.01830.19210.0437-0.08680.16640.10420.00140.69340.0212-0.04050.3503-0.01630.338825.869418.73847.5278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 379 )

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