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- PDB-1fml: CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN A COMPLEX WITH RETINO... -

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Basic information

Entry
Database: PDB / ID: 1fml
TitleCRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN A COMPLEX WITH RETINOL AND PAP
ComponentsRETINOL DEHYDRATASE
KeywordsTRANSFERASE / sulfotransferase / dehydratase / retinol / adenosine 3' / 5'-diphosphate
Function / homology
Function and homology information


sulfation / sulfotransferase activity / metal ion binding / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / RETINOL / Retinol dehydratase
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SIRAS Phasing / Resolution: 2.75 Å
AuthorsPakhomova, S. / Kobayashi, M. / Buck, J. / Newcomer, M.E.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: A helical lid converts a sulfotransferase to a dehydratase.
Authors: Pakhomova, S. / Kobayashi, M. / Buck, J. / Newcomer, M.E.
History
DepositionAug 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RETINOL DEHYDRATASE
B: RETINOL DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6188
Polymers83,1112
Non-polymers1,5076
Water1,63991
1
A: RETINOL DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3094
Polymers41,5551
Non-polymers7543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RETINOL DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3094
Polymers41,5551
Non-polymers7543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.053, 66.612, 84.904
Angle α, β, γ (deg.)90.00, 111.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RETINOL DEHYDRATASE


Mass: 41555.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q26490
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 3350, calcium chloride, Hepes, glycerol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal grow
*PLUS
Details: Pakhomova, S., (2000) Acta Crystallogr.D56, 1641. / PH range low: 6.8 / PH range high: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
28 %PEG33501reservoir
350 mM1reservoirCaCl2
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. all: 64864 / Num. obs: 20388 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.104 / Net I/σ(I): 12.7
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2136 / Rsym value: 0.371 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.371

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS Phasing / Resolution: 2.75→38.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 151607.03 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1851 9.5 %random
Rwork0.222 ---
all-20548 --
obs-19506 87.8 %-
Solvent computationSolvent model: flat model / Bsol: 28.24 Å2 / ksol: 0.315288 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.4 Å20 Å26.69 Å2
2---0.01 Å20 Å2
3----7.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.75→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 98 91 5859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.75→2.85 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.397 127 7.9 %
Rwork0.344 1484 -
obs--72.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2A3P_XPLOR_PAR.TXTA3P_XPLOR_TOP.TXT
X-RAY DIFFRACTION3LIGANDS1.PARRTL_XPLOR_TOP.TXT
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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