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- PDB-5vbu: Crystal Structure of Human Cytochrome P450 21A2 Hydroxyprogestero... -

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Basic information

Entry
Database: PDB / ID: 5vbu
TitleCrystal Structure of Human Cytochrome P450 21A2 Hydroxyprogesterone Complex
ComponentsCytochrome P450 21-hydroxylase
KeywordsOXIDOREDUCTASE / STEROID HYDROXYLATION / MONOOXYGENASES / ADRENAL STEROIDOGENESIS / CONGENITAL ADRENAL HYPERPLASIA / ADDISON'S DISEASE / KINETIC ISOTOPE EFFECTS / Hydroxyprogesterone
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 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
(9beta)-17-hydroxypregn-4-ene-3,20-dione / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 21-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.31 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103937 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Functional analysis of human cytochrome P450 21A2 variants involved in congenital adrenal hyperplasia.
Authors: Wang, C. / Pallan, P.S. / Zhang, W. / Lei, L. / Yoshimoto, F.K. / Waterman, M.R. / Egli, M. / Guengerich, F.P.
History
DepositionMar 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Advisory / Author supporting evidence / Database references
Category: database_2 / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 21-hydroxylase
B: Cytochrome P450 21-hydroxylase
C: Cytochrome P450 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9729
Polymers161,1313
Non-polymers2,8416
Water905
1
A: Cytochrome P450 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6573
Polymers53,7101
Non-polymers9472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6573
Polymers53,7101
Non-polymers9472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6573
Polymers53,7101
Non-polymers9472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-61 kcal/mol
Surface area54860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.431, 88.385, 111.417
Angle α, β, γ (deg.)90.00, 102.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytochrome P450 21-hydroxylase / Cytochrome P450 / family 21 / subfamily A / polypeptide 2 / isoform CRA_b / DJ34F7.3 (Cytochrome ...Cytochrome P450 / family 21 / subfamily A / polypeptide 2 / isoform CRA_b / DJ34F7.3 (Cytochrome P450 / subfamily XXIA (Steroid 21-hydroxylase / congenital adrenal hyperplasia) / polypeptide 2 (CYP21 / P450c21B)) / Steroid 21-hydroxylase / cDNA / FLJ95495 / Homo sapiens cytochrome P450 / polypeptide 2(CYP21A2) / mRNA


Mass: 53710.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P450-CYP21B, CYP21A2, CYP21B, hCG_1999926 / Plasmid: PET17B / Cell (production host): BL21-GOLD DE(3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q16874
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-3QZ / (9beta)-17-hydroxypregn-4-ene-3,20-dione / 17α-Hydroxyprogesterone


Mass: 330.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30O3 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7
Details: 0.2M Ammonium citrate tribasic pH 7.0, 20% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 10, 2014 / Details: Diamond (111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.31→108.83 Å / Num. obs: 19819 / % possible obs: 92.3 % / Observed criterion σ(I): 5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.06 / Net I/σ(I): 11.79
Reflection shellResolution: 3.31→3.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 1982 / Rpim(I) all: 0.456 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MD2MD2 diffractometer with LS-CAT software extensionsdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.31→108.83 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 71.111 / SU ML: 0.495 / Cross valid method: THROUGHOUT / ESU R Free: 0.65 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24106 1549 7.8 %RANDOM
Rwork0.19056 ---
obs0.1945 18270 91.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å2-0 Å21.54 Å2
2---1.98 Å2-0 Å2
3---3.47 Å2
Refinement stepCycle: 1 / Resolution: 3.31→108.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10589 0 201 5 10795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911090
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1942.00815157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52651316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76723.038474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.893151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8051590
X-RAY DIFFRACTIONr_chiral_restr0.120.21689
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0228366
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.8056.5655291
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.3439.8486598
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0986.8215799
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.42146648
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: 3.313→3.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 115 -
Rwork0.309 1148 -
obs--78.35 %
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)
11.2996-0.43780.01830.6497-0.10160.05340.0731-0.06060.0810.1288-0.03670.1441-0.0469-0.0847-0.03640.2907-0.04150.00610.3083-0.00730.0798-36.8922-26.505426.6798
20.01220.00080.11760.0010.00651.16550.00080.0014-0.01210.00170.0070.011-0.0033-0.0014-0.00780.0070.00990.06190.04360.0291.3253-36.9237-26.510329.5725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 485
2X-RAY DIFFRACTION1B29 - 484
3X-RAY DIFFRACTION1C29 - 485
4X-RAY DIFFRACTION2A501 - 502
5X-RAY DIFFRACTION2B501 - 502
6X-RAY DIFFRACTION2C501 - 502

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