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- PDB-3ofg: Structured Domain of Caenorhabditis elegans BMY-1 -

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Basic information

Entry
Database: PDB / ID: 3ofg
TitleStructured Domain of Caenorhabditis elegans BMY-1
ComponentsBoca/mesd chaperone for ywtd beta-propeller-egf protein 1
KeywordsCHAPERONE / molecular chaperone / protein folding / YWTD propeller / LDLR / LRP
Function / homology
Function and homology information


Wnt signaling pathway / protein folding / endoplasmic reticulum / identical protein binding
Similarity search - Function
LRP chaperone MESD / Chaperone for wingless signalling and trafficking of LDL receptor / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Boca/MESD chaperone for YWTD beta-propeller-EGF
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.367 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 1.3Oct 16, 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: Boca/mesd chaperone for ywtd beta-propeller-egf protein 1
B: Boca/mesd chaperone for ywtd beta-propeller-egf protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4486
Polymers22,3062
Non-polymers1424
Water4,125229
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-41 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.522, 38.148, 40.706
Angle α, β, γ (deg.)63.390, 85.740, 84.690
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Boca/mesd chaperone for ywtd beta-propeller-egf protein 1


Mass: 11153.080 Da / Num. of mol.: 2 / Fragment: sequence database residues 84-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: bmy-1, F09E5.17 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IG33
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.83 Å3/Da / Density % sol: 32.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15-18% PEG 3350, 300-500mM LiCl2, 100mM Mes pH 5.5, vapor diffusion, hanging drop, temperature 293K

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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: Apr 24, 2007 / Details: monochromator + mirror
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.37→36.37 Å / Num. all: 33460 / Num. obs: 33444 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.03 Å
Translation2.5 Å34.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MAR345softwaredata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.367→34.033 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.12 / σ(F): 2.05 / Phase error: 16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 1600 5.1 %random
Rwork0.1456 ---
obs0.1467 31382 93.79 %-
all-33444 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.974 Å2 / ksol: 0.422 e/Å3
Displacement parametersBiso max: 51.1 Å2 / Biso mean: 14.5199 Å2 / Biso min: 0.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.3203 Å20.494 Å20.2071 Å2
2---0.8605 Å20.0188 Å2
3----1.3115 Å2
Refinement stepCycle: LAST / Resolution: 1.367→34.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 4 229 1663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073188
X-RAY DIFFRACTIONf_angle_d1.0225755
X-RAY DIFFRACTIONf_chiral_restr0.086241
X-RAY DIFFRACTIONf_plane_restr0.005534
X-RAY DIFFRACTIONf_dihedral_angle_d16.701780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3667-1.41080.21461410.17042575271689
1.4108-1.46130.1871470.1682671281893
1.4613-1.51980.17341430.1522635277892
1.5198-1.58890.18021360.15042715285193
1.5889-1.67270.17221490.14882644279392
1.6727-1.77750.16041360.14592666280292
1.7775-1.91470.14891390.13782710284994
1.9147-2.10740.14421480.132820296897
2.1074-2.41230.15421500.13472797294798
2.4123-3.03890.17611550.14692823297898
3.0389-34.04320.16571560.14452726288295

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