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- PDB-3ofh: Structured Domain of Mus musculus Mesd -

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Basic information

Entry
Database: PDB / ID: 3ofh
TitleStructured Domain of Mus musculus Mesd
ComponentsLDLR chaperone MESD
KeywordsCHAPERONE / mesd / molecular chaperone / protein folding / YWTD propeller / LRP
Function / homology
Function and homology information


positive regulation of skeletal muscle acetylcholine-gated channel clustering / protein localization to cell surface / low-density lipoprotein particle receptor binding / mesoderm development / phagocytosis / ossification / Wnt signaling pathway / protein folding / endoplasmic reticulum / identical protein binding / plasma membrane
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.013 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 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LDLR chaperone MESD
B: LDLR chaperone MESD


Theoretical massNumber of molelcules
Total (without water)20,2012
Polymers20,2012
Non-polymers00
Water1,946108
1
A: LDLR chaperone MESD


Theoretical massNumber of molelcules
Total (without water)10,1001
Polymers10,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LDLR chaperone MESD


Theoretical massNumber of molelcules
Total (without water)10,1001
Polymers10,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-11 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.651, 71.651, 37.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein LDLR chaperone MESD / Mesoderm development protein / Mesoderm development candidate 2


Mass: 10100.413 Da / Num. of mol.: 2 / Fragment: Structured core residues 98-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mesd, Mesdc2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ERE7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.7-0.9M AmPO4 and 100mM Hepes pH7.5, streak seeded with micro-crystals, vapor diffusion, hanging drop, temperature 277K

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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
Reflection twinOperator: h,-k,-l / Fraction: 0.246
ReflectionResolution: 2.01→30 Å / Num. all: 12762 / Num. obs: 12634 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.038 / Χ2: 1.035 / Net I/σ(I): 23.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.01-2.083.30.14812231.05196.4
2.08-2.173.90.11212771.08100
2.17-2.263.90.09612381.022100
2.26-2.383.90.08812831.019100
2.38-2.533.90.07112511.05699.8
2.53-2.733.90.05712621.01799.9
2.73-33.90.04612771.00999.8
3-3.443.70.03412591.02299.4
3.44-4.333.60.02612781.04798.8
4.33-303.50.02312861.02896.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.93 Å
Translation2.5 Å29.93 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: 2.013→29.934 Å / Occupancy max: 1 / Occupancy min: 0.34 / σ(F): 0.18 / Phase error: 21.37 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 1273 10.1 %random, free and work reflections are not related by a twin law
Rwork0.1474 ---
obs0.1502 12606 98.92 %-
all-12744 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.819 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 174.67 Å2 / Biso mean: 31.7918 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.1182 Å2-0 Å20 Å2
2---2.1182 Å2-0 Å2
3---1.3349 Å2
Refinement stepCycle: LAST / Resolution: 2.013→29.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 0 108 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031320
X-RAY DIFFRACTIONf_angle_d0.5631788
X-RAY DIFFRACTIONf_chiral_restr0.035198
X-RAY DIFFRACTIONf_plane_restr0.002229
X-RAY DIFFRACTIONf_dihedral_angle_d13.767465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0127-2.13880.21172070.188718492056
2.1388-2.30390.18732150.178318942109
2.3039-2.53560.22882060.183118832089
2.5356-2.90230.22172120.162418972109
2.9023-3.65550.15382140.132419062120
3.6555-29.93730.14252120.121619112123
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02080.3211-0.1390.567-0.79391.68460.0158-0.1290.0154-0.0889-0.0378-0.07730.13040.05250.01560.02970.00550.01240.0731-0.04190.066522.42776.0224-2.7908
20.76550.60750.43330.9172-0.11990.40130.12320.20370.00910.0879-0.138-0.0212-0.02330.13680.02350.0475-0.0534-0.00190.1056-0.00430.050324.8114-8.739911.6679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA98 - 183
2X-RAY DIFFRACTION2chain BB103 - 181

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