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- PDB-1uoy: The bubble protein from Penicillium brevicompactum Dierckx exudate. -

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Basic information

Entry
Database: PDB / ID: 1uoy
TitleThe bubble protein from Penicillium brevicompactum Dierckx exudate.
ComponentsBUBBLE PROTEIN
KeywordsEXUDATE PROTEIN / SULFUR PHASING / POTENTIAL KILLER TOXIN
Function / homologyArchaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #50 / Bubble protein / Bubble superfamily / Bubble protein / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Roll / extracellular region / Mainly Beta / Bubble protein
Function and homology information
Biological speciesPENICILLIUM BREVICOMPACTUM (fungus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.5 Å
AuthorsOlsen, J.G. / Flensburg, C. / Olsen, O. / Seibold, M. / Bricogne, G. / Henriksen, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Solving the Structure of the Bubble Protein Using the Anomalous Sulfur Signal from Single-Crystal in-House Cu Kalpha Diffraction Data Only
Authors: Olsen, J.G. / Flensburg, C. / Olsen, O. / Bricogne, G. / Henriksen, A.
History
DepositionSep 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BUBBLE PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,5791
Polymers6,5791
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.615, 58.436, 53.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BUBBLE PROTEIN


Mass: 6579.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PENICILLIUM BREVICOMPACTUM (fungus) / Variant: DIERCKX / References: UniProt: P83799*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE YET TO BE DEPOSITED IN PUBLIC DATABASE

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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: 2.6 Å3/Da / Density % sol: 52 %
Description: PHASING USING THE ANOMALOUS SIGNAL FROM 8 CYSTEINE SULFURS (4 DISULFIDE BRIDGES). THE IMAGE PLATE MODEL USED WAS RAXIS IV++
Crystal growTemperature: 277 K / pH: 5
Details: 16 MG/ML PROTEIN IN 30 MM NA-ACETATE BUFFER, PH 5.0 AT 4 DEG.
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
217 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 15, 2002 / Details: MAX-FLUX OPTICAL SYSTEM
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→15.2 Å / Num. obs: 11250 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 8.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.6 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Redundancy: 13.5 % / Num. measured all: 151997 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→15.21 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 834780.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.185 908 8.1 %RANDOM
Rwork0.164 ---
obs0.164 11234 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1916 Å2 / ksol: 0.340968 e/Å3
Displacement parametersBiso mean: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2--0.68 Å20 Å2
3---0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.12 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.5→15.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 0 129 581
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it2.662
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 134 7.3 %
Rwork0.164 1707 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33

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