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- PDB-4acj: Crystal structure of the TLDC domain of Oxidation resistance prot... -

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Basic information

Entry
Database: PDB / ID: 4acj
TitleCrystal structure of the TLDC domain of Oxidation resistance protein 2 from zebrafish
ComponentsWU\:FB25H12 PROTEIN,
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


regulation of oocyte maturation / regulation of response to oxidative stress / mitochondrion
Similarity search - Function
TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Oxidation resistance protein 1
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.97 Å
AuthorsBlaise, M. / B Alsarraf, H.M.A. / Wong, J.E.M.M. / Midtgaard, S.R. / Laroche, F. / Schack, L. / Spaink, H. / Stougaard, J. / Thirup, S.
CitationJournal: Proteins / Year: 2012
Title: Crystal Structure of the Tldc Domain of Oxidation Resistance Protein 2 from Zebrafish.
Authors: Blaise, M. / Alsarraf, H.M. / Wong, J.E. / Midtgaard, S.R. / Laroche, F. / Schack, L. / Spaink, H. / Stougaard, J. / Thirup, S.
History
DepositionDec 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WU\:FB25H12 PROTEIN,


Theoretical massNumber of molelcules
Total (without water)18,9001
Polymers18,9001
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.620, 69.110, 36.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein WU\:FB25H12 PROTEIN,


Mass: 18900.162 Da / Num. of mol.: 1 / Fragment: TLDC DOMAIN, RESIDUES 528-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS / References: UniProt: A9JTH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL GLYCINE IS AN EXTRA AMINO ACID COMING FROM THE TEV CLEAVGE SITE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 % / Description: NONE
Crystal growDetails: 100 MM HEPES PH8, 1.8 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: BRUKER / Detector: CCD / Date: Mar 11, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.97→19 Å / Num. obs: 98111 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.6
Reflection shellResolution: 0.97→0.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.9 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 0.97→19.446 Å / SU ML: 0.12 / σ(F): 2 / Phase error: 9.13 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1382 1999 2 %
Rwork0.1186 --
obs0.119 98078 99.8 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.969 Å2 / ksol: 0.403 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2--0.4235 Å20 Å2
3---0.0431 Å2
Refinement stepCycle: LAST / Resolution: 0.97→19.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 0 266 1597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011509
X-RAY DIFFRACTIONf_angle_d1.3932054
X-RAY DIFFRACTIONf_dihedral_angle_d14.017558
X-RAY DIFFRACTIONf_chiral_restr0.088199
X-RAY DIFFRACTIONf_plane_restr0.009275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.99430.16511480.14196689X-RAY DIFFRACTION99
0.9943-1.02110.12331270.11056814X-RAY DIFFRACTION100
1.0211-1.05120.11641470.10026781X-RAY DIFFRACTION100
1.0512-1.08510.10641450.09346810X-RAY DIFFRACTION100
1.0851-1.12390.09821380.08686806X-RAY DIFFRACTION100
1.1239-1.16890.1081420.08546826X-RAY DIFFRACTION100
1.1689-1.22210.1021390.09196834X-RAY DIFFRACTION100
1.2221-1.28650.11191460.0996845X-RAY DIFFRACTION100
1.2865-1.36710.12131400.09976827X-RAY DIFFRACTION100
1.3671-1.47260.1071480.0986875X-RAY DIFFRACTION100
1.4726-1.62070.10351390.10016883X-RAY DIFFRACTION100
1.6207-1.85510.12011440.11056930X-RAY DIFFRACTION100
1.8551-2.33660.13951450.11676981X-RAY DIFFRACTION100
2.3366-19.44980.19691510.16027178X-RAY DIFFRACTION99

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