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- PDB-3loi: Crystal structures of Cupin superfamily BbDUF985 from Branchiosto... -

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Basic information

Entry
Database: PDB / ID: 3loi
TitleCrystal structures of Cupin superfamily BbDUF985 from Branchiostoma belcheri tsingtauense in the apo and GDP-bound forms
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Beta barrel
Function / homology
Function and homology information


Cupin domain of unknown function DUF985 / Uncharacterized protein YML079W-like / Cupin superfamily (DUF985) / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF985 domain-containing protein
Similarity search - Component
Biological speciesBranchiostoma belcheri tsingtauense (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZou, C.Z. / Du, Y. / He, Y.-X. / Saren, G. / Zhang, X. / Chen, Y. / Zhang, S.-C.
CitationJournal: Proteins / Year: 2010
Title: Crystal structures of the apo and GDP-bound forms of a cupin-like protein BbDUF985 from Branchiostoma belcheri tsingtauense
Authors: Zou, C.Z. / Du, Y. / He, Y.-X. / Saren, G. / Zhang, X. / Chen, Y. / Zhang, S.-C.
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,5581
Polymers19,5581
Non-polymers00
Water3,117173
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,1162
Polymers39,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
Buried area3080 Å2
ΔGint-22 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.541, 91.541, 173.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

21A-242-

HOH

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Components

#1: Protein Putative uncharacterized protein / cupin superfamily hypothetical BbDUF985


Mass: 19558.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma belcheri tsingtauense (invertebrata)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WRH7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 4.64 Å3/Da / Density % sol: 73.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0M ammonium sulfate, 0.1M sodium acetate trihydate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 21913 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1071 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUD

1yud


Resolution: 2.1→33.396 Å / SU ML: 0.32 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 1123 5.13 %RANDOM
Rwork0.2198 ---
obs0.2212 21880 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.435 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.5425 Å20 Å20 Å2
2--2.5425 Å20 Å2
3----5.085 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 173 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091326
X-RAY DIFFRACTIONf_angle_d1.0781795
X-RAY DIFFRACTIONf_dihedral_angle_d16.661484
X-RAY DIFFRACTIONf_chiral_restr0.08187
X-RAY DIFFRACTIONf_plane_restr0.004235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.19580.31731450.26352531X-RAY DIFFRACTION99
2.1958-2.31150.25141390.2342558X-RAY DIFFRACTION100
2.3115-2.45630.30541370.23442548X-RAY DIFFRACTION100
2.4563-2.64580.28111490.24922553X-RAY DIFFRACTION100
2.6458-2.9120.31911570.24032559X-RAY DIFFRACTION100
2.912-3.3330.25831270.22952593X-RAY DIFFRACTION100
3.333-4.19790.22511440.19222633X-RAY DIFFRACTION100
4.1979-33.40010.18391250.19722782X-RAY DIFFRACTION100

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