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- PDB-2rfq: Crystal structure of 3-HSA hydroxylase from Rhodococcus sp. RHA1 -

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Basic information

Entry
Database: PDB / ID: 2rfq
TitleCrystal structure of 3-HSA hydroxylase from Rhodococcus sp. RHA1
Components3-HSA hydroxylase, oxygenase
KeywordsOXIDOREDUCTASE / 3-HSA hydroxylase / Rhodococcus sp. RHA1 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase / 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase activity / oxidoreductase activity, acting on the CH-CH group of donors / steroid biosynthetic process / : / lipid catabolic process / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / Flavin-dependent monooxygenase, oxygenase subunit HsaA
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChang, C. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of 3-HSA hydroxylase, oxygenase from Rhodococcus sp. RHA1.
Authors: Chang, C. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionOct 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-HSA hydroxylase, oxygenase
B: 3-HSA hydroxylase, oxygenase
C: 3-HSA hydroxylase, oxygenase
D: 3-HSA hydroxylase, oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,98217
Polymers174,3664
Non-polymers2,61613
Water32,3911798
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.283, 76.137, 80.881
Angle α, β, γ (deg.)83.78, 75.95, 89.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3-HSA hydroxylase, oxygenase


Mass: 43591.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: hsaA, RHA1_ro04539 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q0S811
#2: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM, PPS


Mass: 201.243 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C8H11NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1798 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaCl, 0.1M Hepes pH 7.5, 25% PEG 3350, 0.3M PPS, 2mM L-Cysteine, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 202431 / Num. obs: 196906 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 15.852 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 24.75
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.31 / Num. unique all: 19163 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.547 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17127 9923 5 %RANDOM
Rwork0.14615 ---
all0.14741 186903 --
obs0.14741 186903 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0.13 Å20.24 Å2
2---0.38 Å20.09 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11824 0 156 1798 13778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02112451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.93717007
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96351591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46223.221596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18151873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.55215109
X-RAY DIFFRACTIONr_chiral_restr0.0850.21837
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.26825
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.28676
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.21438
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.57862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06212409
X-RAY DIFFRACTIONr_scbond_it2.0135235
X-RAY DIFFRACTIONr_scangle_it3.0374.54567
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 656 -
Rwork0.187 13394 -
obs--94.51 %
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)
11.0773-0.05630.35890.5801-0.1420.5283-0.0161-0.02190.05250.0461-0.0354-0.0384-0.00870.09160.0514-0.03740.0012-0.0017-0.0217-0.0075-0.046534.65717.071668.2523
20.38550.00570.12650.3609-0.07130.4323-0.05-0.0347-0.00520.02980.0099-0.0105-0.01070.02290.0402-0.01520.00570.0089-0.0356-0.0016-0.023519.18511.624561.3323
31.00690.07530.27770.58160.22280.5897-0.00110.03270.0548-0.0552-0.02070.0629-0.0328-0.13390.0218-0.0280.003-0.0158-0.01240.0194-0.0391-6.462618.816931.5133
40.54830.09220.07110.38330.04520.4421-0.05210.0408-0.0013-0.02590.01770.0474-0.0267-0.02980.0344-0.0182-0.0124-0.001-0.0349-0.0006-0.03278.42872.673436.9669
50.6283-0.1653-0.46290.660.05180.8923-0.02070.02470.0104-0.08090.0018-0.00640.07070.04920.019-0.01140.00030.0002-0.0327-0.0102-0.046622.9579-30.66522.0993
60.24210.0039-0.10420.47690.01630.5497-0.01720.02290.0056-0.0253-0.0044-0.02870.06060.03670.0216-0.0188-0.007-0.0074-0.03480.0022-0.022214.068-14.916834.5294
70.6204-0.1393-0.48240.90040.24520.791-0.0581-0.0499-0.0350.06960.02710.09360.0657-0.05220.0309-0.02170.0120.0134-0.03850.0168-0.03764.4652-32.321273.9501
80.22910.0064-0.00910.3661-0.02850.4493-0.0394-0.03830.02510.03240.02060.00510.0774-0.02760.0188-0.01530.00360.0094-0.0371-0.0041-0.008113.7048-15.965962.6401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2277 - 230
2X-RAY DIFFRACTION2AA228 - 391231 - 394
3X-RAY DIFFRACTION3BB3 - 2276 - 230
4X-RAY DIFFRACTION4BB228 - 391231 - 394
5X-RAY DIFFRACTION5CC4 - 2277 - 230
6X-RAY DIFFRACTION6CC228 - 391231 - 394
7X-RAY DIFFRACTION7DD4 - 2277 - 230
8X-RAY DIFFRACTION8DD228 - 391231 - 394

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