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- PDB-6h1i: Crystal structure of human Pirin in complex with bisamide compound 2 -

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Basic information

Entry
Database: PDB / ID: 6h1i
TitleCrystal structure of human Pirin in complex with bisamide compound 2
ComponentsPirin
KeywordsTRANSCRIPTION / Transcriptional coregulator / Quercetin 2 / 3-dioxygenase / Inhibitor
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 / nucleus ...Digestion / quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / monocyte differentiation / digestion / transcription coregulator activity / transcription by RNA polymerase II / nuclear body / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
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-FJH / Pirin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsAli, S. / Le Bihan, Y.V. / van Montfort, R.L.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC309/A11566 United Kingdom
Cancer Research UKC2739/A22897 United Kingdom
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Privileged Structures and Polypharmacology within and between Protein Families.
Authors: Meyers, J. / Chessum, N.E.A. / Ali, S. / Mok, N.Y. / Wilding, B. / Pasqua, A.E. / Rowlands, M. / Tucker, M.J. / Evans, L.E. / Rye, C.S. / O'Fee, L. / Le Bihan, Y.V. / Burke, R. / Carter, M. ...Authors: Meyers, J. / Chessum, N.E.A. / Ali, S. / Mok, N.Y. / Wilding, B. / Pasqua, A.E. / Rowlands, M. / Tucker, M.J. / Evans, L.E. / Rye, C.S. / O'Fee, L. / Le Bihan, Y.V. / Burke, R. / Carter, M. / Workman, P. / Blagg, J. / Brown, N. / van Montfort, R.L.M. / Jones, K. / Cheeseman, M.D.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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

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Assembly

Deposited unit
A: Pirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2276
Polymers32,4421
Non-polymers7865
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-16 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.054, 67.152, 107.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32441.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00625, quercetin 2,3-dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FJH / ~{N}-[5-(2,3-dihydro-1,4-benzodioxin-6-ylcarbonylamino)-2-methyl-phenyl]-2-methyl-quinoline-6-carboxamide


Mass: 453.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H23N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.33 Å3/Da / Density % sol: 47.3 % / Description: Needle-shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 microliter of protein 50 mg/mL and 1 microliter of reservoir solution containing 0.1 M HEPES (pH 7.5), 8 % ethylene glycol, 20 % (w/v) PEG 8,000, placed over 200 microliters of reservoir solution

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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: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.69→41.9 Å / Num. obs: 33746 / % possible obs: 97.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 21.72 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.7
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.446 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1702 / CC1/2: 0.375 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JCT

5jct


Resolution: 1.69→41.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1722 5.11 %RANDOM
Rwork0.178 ---
obs0.18 33699 96.8 %-
Displacement parametersBiso mean: 25.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.3012 Å20 Å20 Å2
2--3.5587 Å20 Å2
3----3.2575 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.69→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 53 272 2505
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012373HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153229HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d821SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes442HARMONIC5
X-RAY DIFFRACTIONt_it2373HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion16.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion299SEMIHARMONIC5
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_contact3058SEMIHARMONIC4
LS refinement shellResolution: 1.69→1.7 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2183 -6.08 %
Rwork0.2439 633 -
all0.2423 674 -
obs--96.96 %
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)
11.20830.5982-0.31053.7020.98292.32390.02440.3631-0.0105-0.22110.0843-0.0826-0.0902-0.0941-0.1088-0.0898-0.00140.00140.1459-0.0053-0.1219-11.4907-3.18683.4716
25.6828-0.2150.29490.3909-0.40690.81-0.05740.41860.2975-0.0669-0.01350.01590.0969-0.03530.0709-0.0941-0.0060.00670.05850.0134-0.0748-11.5307-9.06026.9928
31.33130.4013-0.45150.63010.14350.5144-0.1282-0.0098-0.05080.02680.11280.13740.0728-0.05020.0154-0.07020.00790.01730.07610.0159-0.0096-18.1992-14.680115.6813
41.9107-1.0403-0.94271.59990.16640.8557-0.0488-0.1063-0.07780.15390.01840.0740.09570.0840.0305-0.02420.02560.02980.10570.0086-0.0531-9.8604-16.419223.6643
50.5225-0.6363-0.8452.30421.10690.4367-0.0849-0.09690.230.2280.0702-0.0299-0.11110.05340.0147-0.01560.03850.0090.0316-0.0302-0.0562-12.30640.307526.8827
61.2877-0.7587-0.13041.6406-0.66441.33430.0235-0.03880.27890.07110.07630.1143-0.2669-0.041-0.0998-0.02240.025-0.00020.0183-0.02970.0036-12.07277.657620.3706
72.7507-0.7490.06332.13720.06431.9604-0.00970.20680.3148-0.0970.0887-0.1394-0.43530.1549-0.079-0.0229-0.01560.0027-0.0073-0.0018-0.0393-8.46638.411912.9944
82.539-0.9998-1.11541.92620.01351.4227-0.17130.3452-0.22320.01840.14840.14050.3320.14830.0228-0.10760.01230.02560.0845-0.0135-0.0848-0.0037-21.602510.8318
90.32690.1453-1.55950.30480.41771.6142-0.037-0.005-0.3097-0.2036-0.00890.20780.5007-0.09750.0459-0.0433-0.0540.0662-0.07420.01360.1575-16.6306-30.75213.0751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|4 - 26}
2X-RAY DIFFRACTION2{A|27 - 55}
3X-RAY DIFFRACTION3{A|56 - 119}
4X-RAY DIFFRACTION4{A|120 - 138}
5X-RAY DIFFRACTION5{A|139 - 168}
6X-RAY DIFFRACTION6{A|169 - 185}
7X-RAY DIFFRACTION7{A|186 - 243}
8X-RAY DIFFRACTION8{A|244 - 272}
9X-RAY DIFFRACTION9{A|273 - 290}

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