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- PDB-4at0: The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 4at0
TitleThe crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1
Components3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDOGENASE / STEROID CATABOLISM
Function / homology
Function and homology information


3-oxo-5alpha-steroid 4-dehydrogenase (acceptor) / steroid dehydrogenase activity, acting on the CH-CH group of donors / steroid metabolic process / nucleotide binding
Similarity search - Function
: / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...: / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / 3-oxo-5-alpha-steroid 4-dehydrogenase
Similarity search - Component
Biological speciesRHODOCOCCUS JOSTII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Authorsvan Oosterwijk, N. / Knol, J. / Dijkhuizen, L. / van der Geize, R. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure and Catalytic Mechanism of 3-Ketosteroid-{Delta}4-(5Alpha)-Dehydrogenase from Rhodococcus Jostii Rha1 Genome.
Authors: Van Oosterwijk, N. / Knol, J. / Dijkhuizen, L. / Van Der Geize, R. / Dijkstra, B.W.
History
DepositionMay 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1156
Polymers54,0841
Non-polymers1,0315
Water10,953608
1
A: 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE
hetero molecules

A: 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,23012
Polymers108,1672
Non-polymers2,06210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8650 Å2
ΔGint-56.6 kcal/mol
Surface area31270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.233, 114.308, 110.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

21A-2387-

HOH

31A-2393-

HOH

41A-2407-

HOH

DetailsTHE BIOLOGICAL UNIT IS UNDETERMINED BY THE AUTHOR

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE


Mass: 54083.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS JOSTII (bacteria) / Strain: RHA1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0S4Q9, 3-oxo-5alpha-steroid 4-dehydrogenase (acceptor)

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Non-polymers , 5 types, 613 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTWO POINT MUTATIONS, COMPARED TO THE DATABASE SEQUENCE, WERE FOUND IN THE STRUCTURE. A60T AND ...TWO POINT MUTATIONS, COMPARED TO THE DATABASE SEQUENCE, WERE FOUND IN THE STRUCTURE. A60T AND T160A, AND CONFIRMED BY SEQUENCING OF THE CONSTRUCT. A HIS6-TAG AND LINKER, MGSSHHHHHHSSGLVPRGSH, WAS ADDED TO THE PROTEIN. GI111022663

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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: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE
Crystal growpH: 5.6
Details: CRYSTALS WERE OBTAINED FROM 200 MM AMMONIUM ACETATE, 100 MM SODIUM CITRATE PH 5.6 AND 30%(W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 18, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→49.6 Å / Num. obs: 80282 / % possible obs: 97 % / Redundancy: 11.1 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.7 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY

1d4c

1e39

1kf6

1nek

1zoy


Resolution: 1.6→39.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.117 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17539 4019 5 %RANDOM
Rwork0.15786 ---
obs0.15875 75998 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.802 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 68 608 4274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023842
X-RAY DIFFRACTIONr_bond_other_d0.0020.02911
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9785243
X-RAY DIFFRACTIONr_angle_other_deg0.8693.53429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6123.72164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2615589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.351527
X-RAY DIFFRACTIONr_chiral_restr0.1020.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024
X-RAY DIFFRACTIONr_nbd_refined0.2250.22542
X-RAY DIFFRACTIONr_nbd_other0.30.2120
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22616
X-RAY DIFFRACTIONr_nbtor_other0.1420.28
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 197 -
Rwork0.231 4278 -
obs--75.5 %
Refinement TLS params.Method: refined / Origin x: 39.57 Å / Origin y: 22.733 Å / Origin z: 41.721 Å
111213212223313233
T0.0179 Å2-0.0009 Å2-0.0107 Å2-0.0308 Å2-0.0037 Å2--0.009 Å2
L0.0575 °2-0.0694 °2-0.0297 °2-0.3429 °20.0085 °2--0.0584 °2
S-0.0283 Å °0.0154 Å °0.0146 Å °0.0309 Å °0.0227 Å °-0.006 Å °0.0053 Å °-0.0407 Å °0.0055 Å °

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