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- PDB-4ero: Study on structure and function relationships in human Pirin with... -

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Basic information

Entry
Database: PDB / ID: 4ero
TitleStudy on structure and function relationships in human Pirin with Cobalt ion
ComponentsPirin
KeywordsOXIDOREDUCTASE / beta sandwich / cupin / metatl binding protein / transcription 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 / Resolution: 2.65 Å
AuthorsLiu, F. / Rehmani, I. / Fu, R. / Esaka, S. / 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
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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

Downloads & links

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Assembly

Deposited unit
A: Pirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4676
Polymers32,1591
Non-polymers3075
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.127, 66.254, 106.127
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: 32159.393 Da / Num. of mol.: 1
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 (DH5 alpha) / References: UniProt: O00625, quercetin 2,3-dioxygenase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 200000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 11040 / Num. obs: 9285 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.6 / Num. unique all: 345 / % possible all: 66

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.65→25.08 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 0.68 / SU B: 7.88 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 369 5 %RANDOM
Rwork0.1924 7030 --
obs0.1946 7399 81.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.79 Å2 / Biso mean: 14.6705 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0 Å2
2--4.64 Å20 Å2
3----4.79 Å2
Refinement stepCycle: LAST / Resolution: 2.65→25.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 17 56 2314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192310
X-RAY DIFFRACTIONr_bond_other_d0.0020.022186
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9673115
X-RAY DIFFRACTIONr_angle_other_deg0.92735067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7015287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.56624.272103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91415394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1451513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212603
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02508
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 7 -
Rwork0.21 262 -
all-269 -
obs--42.16 %

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