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- PDB-1x8k: Crystal structure of retinol dehydratase in complex with anhydror... -

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Basic information

Entry
Database: PDB / ID: 1x8k
TitleCrystal structure of retinol dehydratase in complex with anhydroretinol and inactive cofactor PAP
Componentsretinol dehydratase
KeywordsTRANSFERASE / sulfotransferase / dehydratase / anhydroretinol
Function / homology
Function and homology information


sulfotransferase activity / metal ion binding
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / ANHYDRORETINOL / ETHYL MERCURY ION / Retinol dehydratase
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPakhomova, S. / Buck, J. / Newcomer, M.E.
CitationJournal: Protein Sci. / Year: 2005
Title: The structures of the unique sulfotransferase retinol dehydratase with product and inhibitors provide insight into enzyme mechanism and inhibition.
Authors: Pakhomova, S. / Buck, J. / Newcomer, M.E.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Atomic model
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_struct_conn_angle / 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 / _pdbx_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE Author states that there is an error in the sequence database. PHE142 is actually SER142.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: retinol dehydratase
B: retinol dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,97710
Polymers83,0472
Non-polymers1,9318
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.286, 66.661, 84.464
Angle α, β, γ (deg.)90.00, 110.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 4 / Auth seq-ID: 6 - 349 / Label seq-ID: 6 - 349

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a dimer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein retinol dehydratase


Mass: 41523.355 Da / Num. of mol.: 2 / Mutation: C258S,C279S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Plasmid: PET-19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q26490

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Non-polymers , 5 types, 82 molecules

#2: Chemical ChemComp-EMC / ETHYL MERCURY ION / Ethylmercury


Mass: 229.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ANR / ANHYDRORETINOL / (6E)-6-[(2E,4E,6E)-3,7-DIMETHYLNONA-2,4,6,8-TETRAENYLIDENE]-1,5,5-TRIMETHYLCYCLOHEXENE


Mass: 268.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28
#5: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 7.5% PEG4000, 0.1M Na Hepes, 0.05M calcium chloride, 4% glycerol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2000 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→100 Å / Num. obs: 20545 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.113 / Net I/σ(I): 7.8
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1612 / Rsym value: 0.404 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1FMJ

1fmj


Resolution: 2.75→15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.87 / SU B: 15.677 / SU ML: 0.303 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25506 1822 8.6 %RANDOM
Rwork0.19363 ---
all0.199 19249 --
obs0.19905 19249 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-1.04 Å2
2---0.86 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5696 0 102 74 5872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225962
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9828081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895686
X-RAY DIFFRACTIONr_chiral_restr0.1030.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024638
X-RAY DIFFRACTIONr_nbd_refined0.220.22781
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2206
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.210
X-RAY DIFFRACTIONr_mcbond_it0.3981.53454
X-RAY DIFFRACTIONr_mcangle_it0.80925573
X-RAY DIFFRACTIONr_scbond_it1.3132508
X-RAY DIFFRACTIONr_scangle_it2.1684.52508
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2842 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.190.5
medium thermal0.412
LS refinement shellResolution: 2.75→2.819 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.343 82
Rwork0.315 1000
obs-1082
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)
11.79220.2496-0.19561.8159-0.76471.9204-0.10950.01920.0481-0.03470.0808-0.06940.0265-0.00550.02870.0632-0.0059-0.01620.0431-0.03870.042210.6456-3.041435.6256
21.5053-0.01890.19921.85320.25131.78850.01230.0134-0.0854-0.11950.0736-0.0031-0.06540.0083-0.08590.0544-0.032400.03750.01260.05354.55144.08616.9673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 3496 - 349
2X-RAY DIFFRACTION2BB6 - 3496 - 349

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