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- PDB-3acl: Crystal Structure of Human Pirin in complex with Triphenyl Compound -

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Basic information

Entry
Database: PDB / ID: 3acl
TitleCrystal Structure of Human Pirin in complex with Triphenyl Compound
ComponentsPirin
KeywordsMETAL BINDING PROTEIN / cupin / inhibitor / complex / Iron
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 / 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-3F1 / : / Pirin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsOkumura, H. / Miyazaki, I. / Simizu, S. / Osada, H.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: A small-molecule inhibitor shows that pirin regulates migration of melanoma cells
Authors: Miyazaki, I. / Simizu, S. / Okumura, H. / Takagi, S. / Osada, H.
History
DepositionJan 5, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Pirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4443
Polymers32,9881
Non-polymers4552
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.343, 67.415, 107.785
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


Mass: 32988.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIR / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O00625
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-3F1 / N-{[4-(benzyloxy)phenyl](methyl)-lambda~4~-sulfanylidene}-4-methylbenzenesulfonamide / N-{[4-(benzyloxy)phenyl](methyl)-lambda}-4-methylbenzenesulfonamide


Mass: 399.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21NO3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 34% PEG 3350, 0.1M PIPES, 0.1M MGCL2, 1.4mM INHIBITOR, PH 6.5, VAPOR DIFFUSION, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 19, 2009
Diffraction measurementDetails: 1.00 degrees, 31.2 sec, detector distance 200.00mm
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.127 / Number: 13541
ReflectionResolution: 2.35→50 Å / Num. all: 13554 / Num. obs: 13541 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 16
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.803 / Rsym value: 0.34 / % possible all: 100
Cell measurementReflection used: 13541

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.39 Å34.02 Å
Translation2.39 Å34.02 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
CNS1.2refinement
PDB_EXTRACT3.005data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J1L

1j1l


Resolution: 2.35→35.86 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1297395 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 662 4.9 %RANDOM
Rwork0.203 ---
obs0.203 13378 99.8 %-
all-13409 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.223 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 50.33 Å2 / Biso mean: 19.79 Å2 / Biso min: 1.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.35→35.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 28 131 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.912.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 -5.3 %
Rwork0.257 2071 -
all-2186 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_pirin.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4DRGCNS_mod.paramDRGCNS_mod.top

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