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- PDB-3off: Structured Domain of Drosophila melanogaster Boca p65 2 2 Crystal form -

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Basic information

Entry
Database: PDB / ID: 3off
TitleStructured Domain of Drosophila melanogaster Boca p65 2 2 Crystal form
ComponentsLDLR chaperone boca
KeywordsCHAPERONE / mesd / molecular chaperone / protein folding / YWTD propeller / LRP
Function / homology
Function and homology information


protein targeting to membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / Wnt signaling pathway / apical part of cell / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum / identical protein binding / cytoplasm
Similarity search - Function
LRP chaperone MESD / Chaperone for wingless signalling and trafficking of LDL receptor / ACT domain / Endoplasmic reticulum targeting sequence. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / LDLR chaperone boca
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsCollins, M.N. / Hendrickson, W.A.
CitationJournal: Structure / Year: 2011
Title: Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta-Propeller Domains
Authors: Collins, M.N. / Hendrickson, W.A.
History
DepositionAug 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: LDLR chaperone boca
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0086
Polymers10,6371
Non-polymers3705
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.284, 62.284, 89.675
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1-

SO4

21A-174-

NA

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Components

#1: Protein LDLR chaperone boca


Mass: 10637.482 Da / Num. of mol.: 1 / Fragment: sequence database residues 88-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: boca, CG30498 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8T9B6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 48-52% saturated AmSO4, 100mM NaAc pH 5.6-5.8 at 298 C, one of four crystal morphologies, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2009 / Details: monochromator + mirror
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 11.1 % / Av σ(I) over netI: 20.64 / Number: 144983 / Rmerge(I) obs: 0.129 / Χ2: 0.82 / D res high: 2 Å / D res low: 40 Å / Num. obs: 13036 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.424092.110.0641.18710.3
4.315.4298.210.0631.2410.9
3.764.3198.510.0731.33611
3.423.7698.510.0831.12711.2
3.173.4299.110.0920.95411.5
2.993.1799.210.1030.8911.5
2.842.9999.210.1170.85511.7
2.712.8499.410.1580.81511.8
2.612.7199.210.2070.92711.6
2.522.6199.710.2730.84411.7
2.442.5299.710.2580.75911.6
2.372.4499.710.2810.75211.7
2.312.3799.710.2680.62111.6
2.252.3199.710.3690.70111.5
2.22.2599.710.3960.61811.1
2.152.299.810.3190.57310.8
2.112.1599.910.3890.53410.7
2.072.1199.810.4160.54310.4
2.032.0799.810.4330.52810.1
22.0310010.430.5679.8
ReflectionResolution: 2→40 Å / Num. all: 13168 / Num. obs: 13036 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.129 / Χ2: 0.82 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.039.80.436610.567100
2.03-2.0710.10.4336550.52899.8
2.07-2.1110.40.4166490.54399.8
2.11-2.1510.70.3896680.53499.9
2.15-2.210.80.3196420.57399.8
2.2-2.2511.10.3966580.61899.7
2.25-2.3111.50.3696530.70199.7
2.31-2.3711.60.2686700.62199.7
2.37-2.4411.70.2816330.75299.7
2.44-2.5211.60.2586600.75999.7
2.52-2.6111.70.2736640.84499.7
2.61-2.7111.60.2076560.92799.2
2.71-2.8411.80.1586500.81599.4
2.84-2.9911.70.1176450.85599.2
2.99-3.1711.50.1036570.8999.2
3.17-3.4211.50.0926470.95499.1
3.42-3.7611.20.0836501.12798.5
3.76-4.31110.0736421.33698.5
4.31-5.4210.90.0636571.2498.2
5.42-4010.30.0646191.18792.1

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.66 / FOM acentric: 0.65 / FOM centric: 0.68 / Reflection: 6551 / Reflection acentric: 5192 / Reflection centric: 1359
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-29.4190.890.930.85342174168
3.6-5.70.90.930.84980695285
2.9-3.60.820.850.741200934266
2.5-2.90.70.70.691055868187
2.1-2.50.550.550.5518061522284
2-2.10.340.340.371168999169

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MAR345softwaredata collection
RefinementMethod to determine structure: SAD / Resolution: 2.002→29.419 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.22 / σ(F): 0.06 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1198 9.95 %random
Rwork0.19 ---
obs0.1935 12039 91.67 %-
all-13133 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.308 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 74.08 Å2 / Biso mean: 24.4629 Å2 / Biso min: 9.29 Å2
Baniso -1Baniso -2Baniso -3
1-4.1982 Å2-0 Å2-0 Å2
2--4.1982 Å20 Å2
3----8.3964 Å2
Refinement stepCycle: LAST / Resolution: 2.002→29.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms668 0 20 76 764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003728
X-RAY DIFFRACTIONf_angle_d0.667985
X-RAY DIFFRACTIONf_chiral_restr0.046112
X-RAY DIFFRACTIONf_plane_restr0.002125
X-RAY DIFFRACTIONf_dihedral_angle_d15.563254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0016-2.08170.24981440.19911263140796
2.0817-2.17640.24521330.19021193132692
2.1764-2.29110.17331200.17791132125285
2.2911-2.43460.23561340.18591163129789
2.4346-2.62250.21051240.18571063118783
2.6225-2.88620.19751310.21111196132791
2.8862-3.30330.26731420.18281306144899
3.3033-4.160.18431340.17311261139595
4.16-29.42170.24041360.19761264140096

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