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- PDB-2e46: Crystal Structure Analysis of the clock protein EA4 -

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Basic information

Entry
Database: PDB / ID: 2.0E+46
TitleCrystal Structure Analysis of the clock protein EA4
ComponentsTime interval measuring enzyme TIME
KeywordsMETAL BINDING PROTEIN / metalloprotein
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPark, S.-Y. / Hiraki, T.
CitationJournal: To be Published
Title: the clock protein EA4 ticks away with movement of a mobile copper ion
Authors: Hiraki, T. / Shibayama, N. / Tame, J.R.M. / Akashi, S. / Park, S.-Y.
History
DepositionDec 5, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: Time interval measuring enzyme TIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9594
Polymers16,7661
Non-polymers1933
Water1,00956
1
A: Time interval measuring enzyme TIME
hetero molecules

A: Time interval measuring enzyme TIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9188
Polymers33,5332
Non-polymers3856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)59.500, 59.500, 112.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Time interval measuring enzyme TIME / EA4


Mass: 16766.496 Da / Num. of mol.: 1 / Fragment: residues 0-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Plasmid: pET3b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08J22
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 9% ethlene glycol, 1M ammonium fluoride, 100mM Bis-Tris, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 9519 / % possible obs: 99.9 % / Redundancy: 6.9 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E9P

1e9p


Resolution: 2.3→19.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.89 / SU B: 8.345 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28522 493 5.4 %RANDOM
Rwork0.20795 ---
obs0.21229 8710 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 3 56 1240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0211223
X-RAY DIFFRACTIONr_angle_refined_deg2.9021.9241640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.65156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90723.89859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.54615183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.345157
X-RAY DIFFRACTIONr_chiral_restr0.3560.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02954
X-RAY DIFFRACTIONr_nbd_refined0.2770.2540
X-RAY DIFFRACTIONr_nbtor_refined0.330.2764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4510.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3220.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.050.23
X-RAY DIFFRACTIONr_mcbond_it1.6841.5801
X-RAY DIFFRACTIONr_mcangle_it2.65521231
X-RAY DIFFRACTIONr_scbond_it4.5353475
X-RAY DIFFRACTIONr_scangle_it6.3184.5409
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 24 -
Rwork0.264 585 -
obs--100 %

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