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- PDB-3qz1: Crystal Structure of Bovine Steroid of 21-hydroxylase (P450c21) -

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Basic information

Entry
Database: PDB / ID: 3qz1
TitleCrystal Structure of Bovine Steroid of 21-hydroxylase (P450c21)
ComponentsSteroid 21-hydroxylase
KeywordsOXIDOREDUCTASE / P450 monooxygenase / 21-hydroxylase
Function / homology
Function and homology information


Glucocorticoid biosynthesis / Mineralocorticoid biosynthesis / steroid 21-monooxygenase / steroid 21-monooxygenase activity / 17-hydroxyprogesterone 21-hydroxylase activity / progesterone 21-hydroxylase activity / Endogenous sterols / glucocorticoid biosynthetic process / steroid biosynthetic process / steroid hydroxylase activity ...Glucocorticoid biosynthesis / Mineralocorticoid biosynthesis / steroid 21-monooxygenase / steroid 21-monooxygenase activity / 17-hydroxyprogesterone 21-hydroxylase activity / progesterone 21-hydroxylase activity / Endogenous sterols / glucocorticoid biosynthetic process / steroid biosynthetic process / steroid hydroxylase activity / steroid metabolic process / steroid binding / iron ion binding / heme binding / endoplasmic reticulum membrane
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 / Steroid 21-hydroxylase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsZhao, B. / Waterman, M.R.
CitationJournal: To be Published
Title: Crystal Structure of Bovine Steroid of 21-hydroxylase (P450c21)
Authors: Zhao, B. / Lei, L. / Sundaramoorthy, M. / Kagawa, N. / Waterman, M.R.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Data collection
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Steroid 21-hydroxylase
B: Steroid 21-hydroxylase
C: Steroid 21-hydroxylase
D: Steroid 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,75116
Polymers224,6414
Non-polymers5,11012
Water1,74797
1
A: Steroid 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4384
Polymers56,1601
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Steroid 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4384
Polymers56,1601
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Steroid 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4384
Polymers56,1601
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Steroid 21-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4384
Polymers56,1601
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.871, 167.998, 111.843
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Steroid 21-hydroxylase / 21-OHase / Cytochrome P-450c21 / Cytochrome P450 21 / Cytochrome P450 XXI / Cytochrome P450-C21


Mass: 56160.270 Da / Num. of mol.: 4 / Mutation: T241R, L442A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CYP21, CYP21A1 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha] / References: UniProt: P00191, EC: 1.14.99.10
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 330.461 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30O3 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND 3QZ IN THE STRUCTURE IS 17-HYDROXYPROGESTERONE, WHICH IS VERY HYDROPHOBIC AND ITS ...THE LIGAND 3QZ IN THE STRUCTURE IS 17-HYDROXYPROGESTERONE, WHICH IS VERY HYDROPHOBIC AND ITS SOLUBILITY IS POOR. THE AUTHORS COULD NOT ADD MORE LIGAND DURING CRYSTALLIZATION DUE TO THE POOR SOLUBILITY. THIS IS PROBABLY WHY THE LIGANDS (ESPECIALLY B502) SHOWED RELATIVELY HIGH REAL SPACE R VALUES. THE DISORDER IS ALSO ONE OF THE REASON TO BE CONSIDERED. THERE ARE FOUR MOLECULES IN ASYMMETRIC UNIT. THREE OF FOUR MOLECULES A, C, AND D CLEARLY SHOWED TWO MOLECULES IN THE ENZYME. MOLECULE B SHOWED TWO MOLECULES AS WELL EVEN THOUGH B502 IS MORE DISORDERED SOMEHOW. IN ADDITION, THE BIOCHEMICAL TITRATION DATA PROVIDE ADDITIONAL EVIDENCE TO SUPPORT TWO LIGANDS BOUND IN THE ENZYME AT SAME TIME

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, Tacsimate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97
SYNCHROTRONAPS 22-ID21.5
Detector
TypeIDDetectorDate
MAR scanner 300 mm plate1IMAGE PLATEFeb 6, 2011
MAR scanner 300 mm plate2IMAGE PLATENov 10, 2010
1,2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.51
Reflection twinOperator: -h,k,-l / Fraction: 0.5
ReflectionResolution: 3→50 Å / Num. all: 49955 / Num. obs: 47687 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.092 / Rsym value: 0.065 / Net I/σ(I): 4.5
Reflection shellResolution: 3→3.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.21 / Rsym value: 0.672 / % possible all: 91.9

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 3→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 1541
RfactorNum. reflection% reflection
Rfree0.2973 4666 9.3 %
Rwork0.2819 41569 -
obs-46235 92.4 %
Solvent computationBsol: 139.685 Å2
Displacement parametersBiso max: 323.81 Å2 / Biso mean: 119.1571 Å2 / Biso min: 51.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.352 Å20 Å2-0.008 Å2
2---0.514 Å20 Å2
3---0.162 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14064 0 364 97 14525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.110.47023700.40243697406781.3
3.11-3.230.42794330.38363775420884.3
3.23-3.380.41044220.35813919434186.8
3.38-3.560.37484640.33413958442289.2
3.56-3.780.33134420.3014166460892.6
3.78-4.070.31924790.28144257473694.6
4.07-4.480.2824970.26124355485297
4.48-5.120.27385080.25574432494098.8
5.12-6.440.27845070.26614492499999.2
6.44-300.26625440.2774518506299.6

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