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- PDB-4hlt: Crystal structure of ferric E32V Pirin -

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Basic information

Entry
Database: PDB / ID: 4hlt
TitleCrystal structure of ferric E32V Pirin
ComponentsPirin
KeywordsSIGNALING PROTEIN / beta sandwich / cupin / iron / metal binding protein / transcription cofactor activity / protein binding / nucleus
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, F. / Rehmani, I. / Esaki, S. / Fu, R. / Chen, L. / Serrano, V. / Liu, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Pirin is an iron-dependent redox regulator of NF-kappa B.
Authors: Liu, F. / Rehmani, I. / Esaki, S. / Fu, R. / Chen, L. / de Serrano, V. / Liu, A.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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: Pirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9972
Polymers31,9411
Non-polymers561
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.414, 66.635, 107.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 31941.166 Da / Num. of mol.: 1 / Mutation: E32V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human, PIR / Plasmid: PET 27A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O00625, quercetin 2,3-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20000, 0.1 MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→31.84 Å / Num. all: 34022 / Num. obs: 33036 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Redundancy: 12.2 % / Rsym value: 0.074 / Net I/σ(I): 55.14
Reflection shellResolution: 1.7→1.73 Å / % possible all: 79.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GUL

4gul


Resolution: 1.7→31.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.124 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1677 5.1 %RANDOM
Rwork0.1842 ---
all0.1868 34160 --
obs0.1868 32975 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.41 Å2 / Biso mean: 25.0338 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2--1.14 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 1 230 2480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192306
X-RAY DIFFRACTIONr_bond_other_d0.0050.022187
X-RAY DIFFRACTIONr_angle_refined_deg2.3531.9643118
X-RAY DIFFRACTIONr_angle_other_deg1.03735069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0975287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64224.135104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74415398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7851514
X-RAY DIFFRACTIONr_chiral_restr0.180.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
LS refinement shellResolution: 1.702→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 92 -
Rwork0.243 1795 -
all-1887 -
obs--75.69 %

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