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- PDB-4r21: Zebra fish cytochrome P450 17A2 with Progesterone -

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Basic information

Entry
Database: PDB / ID: 4r21
TitleZebra fish cytochrome P450 17A2 with Progesterone
ComponentsCytochrome P450 family 17 polypeptide 2
KeywordsOXIDOREDUCTASE / Cytochrome P450 17A2 / progesterone / P450 17A2 / 17 (alpha)-hydroxylation / steroid biosynthesis / enzyme kinetics
Function / homology
Function and homology information


steroid 17-alpha-monooxygenase activity / : / hormone biosynthetic process / progesterone metabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PROGESTERONE / Cytochrome P450 family 17 polypeptide 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Kinetic Basis of Steroid 17 alpha, 20-Lyase Activity in Teleost Fish Cytochrome P450 17A1 and Its Absence in Cytochrome P450 17A2.
Authors: Pallan, P.S. / Nagy, L.D. / Lei, L. / Gonzalez, E. / Kramlinger, V.M. / Azumaya, C.M. / Wawrzak, Z. / Waterman, M.R. / Guengerich, F.P. / Egli, M.
History
DepositionAug 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Cytochrome P450 family 17 polypeptide 2
B: Cytochrome P450 family 17 polypeptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1546
Polymers108,2922
Non-polymers1,8624
Water30617
1
A: Cytochrome P450 family 17 polypeptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0773
Polymers54,1461
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 family 17 polypeptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0773
Polymers54,1461
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.940, 78.630, 95.410
Angle α, β, γ (deg.)90.00, 92.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 family 17 polypeptide 2


Mass: 54146.156 Da / Num. of mol.: 2 / Fragment: UNP residues 26-495 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A7U483
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 50 mM sodium HEPES buffer, 25 mM MgCl2 and 15% (v/v) polyethylene glycol monomethyl ether 3550, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→17.08 Å / Num. obs: 22643 / % possible obs: 99 % / Observed criterion σ(I): 5 / Redundancy: 4.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.4
Reflection shellResolution: 2.73→2.81 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→17.08 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.883 / SU B: 41.57 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1159 5.1 %RANDOM
Rwork0.205 ---
obs0.209 21459 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å2-0 Å2-0.57 Å2
2---1.98 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→17.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 130 17 6752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196887
X-RAY DIFFRACTIONr_bond_other_d0.0020.026638
X-RAY DIFFRACTIONr_angle_refined_deg1.6152.0029397
X-RAY DIFFRACTIONr_angle_other_deg0.8693.00315268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9065838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77123.446296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.057151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6951554
X-RAY DIFFRACTIONr_chiral_restr0.0960.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217690
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021556
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9013.0373373
X-RAY DIFFRACTIONr_mcbond_other1.9013.0373372
X-RAY DIFFRACTIONr_mcangle_it3.2874.5484204
X-RAY DIFFRACTIONr_mcangle_other3.2874.5484205
X-RAY DIFFRACTIONr_scbond_it1.9413.1613514
X-RAY DIFFRACTIONr_scbond_other1.943.1613515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2244.6535194
X-RAY DIFFRACTIONr_long_range_B_refined5.88924.2528030
X-RAY DIFFRACTIONr_long_range_B_other5.88924.2548031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 85 -
Rwork0.285 1556 -
obs--97.45 %
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)
11.2834-0.51780.46021.4371-0.30471.4289-0.0328-0.0299-0.14090.07190.02840.0760.00980.02240.00440.057-0.0174-0.04720.45340.01390.071712.47160.43961.0003
20.92740.5818-0.05631.72980.652.42820.05850.2871-0.0417-0.1268-0.1594-0.0037-0.2878-0.69880.1010.05350.1454-0.01880.7688-0.04150.009-14.62625.224645.0225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 601
2X-RAY DIFFRACTION2B53 - 601

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