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- PDB-5jct: Crystal Structure of Human Pirin in complex with a Chemical Probe... -

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Basic information

Entry
Database: PDB / ID: 5jct
TitleCrystal Structure of Human Pirin in complex with a Chemical Probe pyrrolidine 24
ComponentsPirin
KeywordsOXIDOREDUCTASE / Cupin / Beta-barrel fold / Inhibitor / Complex
Function / homology
Function and homology information


Digestion / quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / monocyte differentiation / digestion / transcription coregulator activity / transcription by RNA polymerase II / nuclear body / nucleoplasm / metal ion binding ...Digestion / quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / monocyte differentiation / digestion / transcription coregulator activity / transcription by RNA polymerase II / nuclear body / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pirin, C-terminal domain / Pirin C-terminal cupin domain / Pirin, N-terminal domain / Pirin / Pirin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6JQ / : / Pirin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsAli, S. / van Montfort, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC309/A8274 United Kingdom
Cancer Research UKC309/A11566 United Kingdom
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of a Chemical Probe Bisamide (CCT251236): An Orally Bioavailable Efficacious Pirin Ligand from a Heat Shock Transcription Factor 1 (HSF1) Phenotypic Screen.
Authors: Cheeseman, M.D. / Chessum, N.E. / Rye, C.S. / Pasqua, A.E. / Tucker, M.J. / Wilding, B. / Evans, L.E. / Lepri, S. / Richards, M. / Sharp, S.Y. / Ali, S. / Rowlands, M. / O'Fee, L. / Miah, A. ...Authors: Cheeseman, M.D. / Chessum, N.E. / Rye, C.S. / Pasqua, A.E. / Tucker, M.J. / Wilding, B. / Evans, L.E. / Lepri, S. / Richards, M. / Sharp, S.Y. / Ali, S. / Rowlands, M. / O'Fee, L. / Miah, A. / Hayes, A. / Henley, A.T. / Powers, M. / Te Poele, R. / De Billy, E. / Pellegrino, L. / Raynaud, F. / Burke, R. / van Montfort, R.L. / Eccles, S.A. / Workman, P. / Jones, K.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1866
Polymers34,3311
Non-polymers8555
Water5,837324
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-13 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.148, 67.415, 107.062
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pirin / / Probable quercetin 2 / 3-dioxygenase PIR / Probable quercetinase


Mass: 34330.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIR / Plasmid: pET28a / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: O00625, quercetin 2,3-dioxygenase

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Non-polymers , 5 types, 329 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-6JQ / N-{5-[(2,3-dihydro-1,4-benzodioxine-6-carbonyl)amino]-2-methylphenyl}-2-[3-(pyrrolidin-1-yl)propyl]quinoline-6-carboxamide


Mass: 550.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH7.5), 8% (v/v) Eythylene Glycol, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.73→42.15 Å / Num. obs: 32524 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 27.81 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.7
Reflection shellHighest resolution: 1.73 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EWA

4ewa


Resolution: 1.73→41.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.101
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1631 5.02 %RANDOM
Rwork0.171 ---
obs0.173 32467 99.5 %-
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.6823 Å20 Å20 Å2
2---1.9026 Å20 Å2
3----0.7798 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.73→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 48 325 2570
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012402HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083275HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d840SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes396HARMONIC5
X-RAY DIFFRACTIONt_it2402HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion17.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion300SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies23HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3153SEMIHARMONIC4
LS refinement shellHighest resolution: 1.73 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.257 134 4.58 %
Rwork0.251 2793 -
obs--99.59 %
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)
12.73820.40851.03972.9517-1.1953.53390.07950.5246-0.0283-0.28170.03450.03370.24650.3529-0.114-0.00780.00330.00760.0399-0.0335-0.092653.511469.93653.3654
22.46380.09690.45941.0170.30870.8805-0.13890.12390.0188-0.0320.1206-0.1478-0.06680.07250.0183-0.047-0.0102-0.0161-0.0258-0.0014-0.024758.92880.506813.0123
31.5778-0.57971.91651.7425-0.73561.2396-0.0321-0.10690.00130.2008-0.035-0.0661-0.1003-0.15170.0670.03430.0301-0.04420.0223-0.0159-0.023752.865483.894923.9815
40.8802-0.99861.13673.4392-0.86880.4675-0.0514-0.146-0.27680.33780.08450.03250.1452-0.0891-0.03310.03210.0196-0.0112-0.05060.0358-0.054654.205668.138226.7185
52.0271-0.6808-0.00573.0005-0.02792.41160.03560.1314-0.3602-0.09050.0920.13260.4517-0.1586-0.12760.0214-0.0366-0.0208-0.09610.0044-0.010151.459259.200714.586
62.9894-0.56741.34162.2304-0.30392.4189-0.21220.31420.32530.02920.139-0.0129-0.3275-0.12770.0733-0.08950.013-0.0313-0.00230.0166-0.057742.235489.297410.8609
70.0171-0.938-0.46621.12110.07521.0798-0.05520.00190.2212-0.1533-0.0217-0.2108-0.43230.05440.0769-0.0302-0.0535-0.1169-0.09860.00280.214658.670398.418613.3595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|3 - 26}
2X-RAY DIFFRACTION2{A|27 - 119}
3X-RAY DIFFRACTION3{A|120 - 138}
4X-RAY DIFFRACTION4{A|139 - 168}
5X-RAY DIFFRACTION5{A|169 - 243}
6X-RAY DIFFRACTION6{A|244 - 272}
7X-RAY DIFFRACTION7{A|273 - 290}

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