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- PDB-3ofe: Structured Domain of Drosophila melanogaster Boca p41 2 2 Crystal form -

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Basic information

Entry
Database: PDB / ID: 3ofe
TitleStructured Domain of Drosophila melanogaster Boca p41 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 / protein folding / apical part of cell / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.288 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 1.2Oct 30, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LDLR chaperone boca
B: LDLR chaperone boca


Theoretical massNumber of molelcules
Total (without water)21,4492
Polymers21,4492
Non-polymers00
Water2,180121
1
A: LDLR chaperone boca


Theoretical massNumber of molelcules
Total (without water)10,7251
Polymers10,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LDLR chaperone boca


Theoretical massNumber of molelcules
Total (without water)10,7251
Polymers10,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.106, 34.106, 311.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-44-

HOH

21A-57-

HOH

31A-183-

HOH

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Components

#1: Protein LDLR chaperone boca


Mass: 10724.560 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 18-21% PEG 3350, 100-200mM Na citrate, 100mM CHES pH9.0, and 10mM DTT with macroseeding, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9795 0.9802 0.9645
SYNCHROTRONNSLS X2520.9794
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDSep 14, 2005DCM + mirrors
ADSC QUANTUM 3152CCDSep 14, 2005DCM + mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SILICONMADMx-ray1
2SILICONSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.98021
30.96451
40.97941
ReflectionRedundancy: 14.6 % / Av σ(I) over netI: 27.96 / Number: 155098 / Rmerge(I) obs: 0.067 / Χ2: 1 / D res high: 2.5 Å / D res low: 20 Å / Num. obs: 10635 / % possible obs: 85.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.352095.410.0381.00413.9
4.265.3598.710.0391.00414.9
3.734.2699.210.0450.99915.2
3.393.7399.210.0610.99815.4
3.153.3998.910.0870.99915.5
2.963.159910.1191.00315.3
2.812.968910.1571.00415.1
2.692.8171.710.1721.00513.3
2.592.6959.210.2311.00412.6
2.52.5947.310.2821.00212.4
ReflectionResolution: 2.3→20 Å / Num. all: 15868 / Num. obs: 15757 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Χ2: 1 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.386.50.28215260.99799.3
2.38-2.486.60.22716030.99999.4
2.48-2.596.50.19915510.99799.6
2.59-2.736.50.1581587199.6
2.73-2.96.60.11715871.00299.6
2.9-3.126.50.08615921.00399.4
3.12-3.436.50.06315931.00399.4
3.43-3.936.40.04715401.00199.6
3.93-4.936.20.0416071.00199.6
4.93-206.10.03515711.00197.6

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97956.71-8.16
3 wavelength120.98023.04-11.68
3 wavelength130.96455.26-4.36
Phasing dmFOM : 0.78 / FOM acentric: 0.79 / FOM centric: 0.76 / Reflection: 5109 / Reflection acentric: 3414 / Reflection centric: 1695
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-19.7810.90.950.8725888170
5-80.890.920.86734408326
4-50.890.920.83877559318
3.5-40.850.870.81861599262
3-3.50.730.750.6614931081412
2.8-30.570.590.53886679207

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.288→19.781 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.25 / σ(F): 0.08 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 750 4.85 %Random
Rwork0.1892 ---
obs0.1911 15471 97.97 %-
all-15792 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.335 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 130.75 Å2 / Biso mean: 27.323 Å2 / Biso min: 9.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.7694 Å20 Å2-0 Å2
2--0.7694 Å20 Å2
3----3.8839 Å2
Refinement stepCycle: LAST / Resolution: 2.288→19.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 0 121 1405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031328
X-RAY DIFFRACTIONf_angle_d0.6011803
X-RAY DIFFRACTIONf_chiral_restr0.046198
X-RAY DIFFRACTIONf_plane_restr0.002234
X-RAY DIFFRACTIONf_dihedral_angle_d16.268479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.288-2.46440.25081340.19552858299295
2.4644-2.71180.25531660.19782911307798
2.7118-3.10290.27031390.18673009314899
3.1029-3.90440.2271600.16632964312499
3.9044-19.78220.19141510.192979313098

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