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- PDB-3k43: Crystal structure of sCD-MPR mutant E19Q/K137M pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 3k43
TitleCrystal structure of sCD-MPR mutant E19Q/K137M pH 6.5
ComponentsCation-dependent mannose-6-phosphate receptor
Keywordsprotein transport / sugar binding protein / transport / lysosome / mannose / receptor / sugar binding / Glycoprotein / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / Glycosphingolipid catabolism / Lysosome Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / protein targeting to lysosome / Clathrin-mediated endocytosis / lysosomal transport / trans-Golgi network / endosome / lysosomal membrane ...Retrograde transport at the Trans-Golgi-Network / Glycosphingolipid catabolism / Lysosome Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / protein targeting to lysosome / Clathrin-mediated endocytosis / lysosomal transport / trans-Golgi network / endosome / lysosomal membrane / protein domain specific binding / Golgi apparatus
Similarity search - Function
Cation-dependent mannose-6-phosphate receptor / Mannose-6-phosphate receptor / Mannose-6-phosphate receptor / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Cation-dependent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / difference fourier / Resolution: 2 Å
AuthorsOlson, L.J. / Sun, G. / Bohnsack, R.N. / Peterson, F.C. / Dahms, N.M. / Kim, J.J.P.
CitationJournal: Biochemistry / Year: 2010
Title: Intermonomer interactions are essential for lysosomal enzyme binding by the cation-dependent mannose 6-phosphate receptor.
Authors: Olson, L.J. / Sun, G. / Bohnsack, R.N. / Peterson, F.C. / Dahms, N.M. / Kim, J.J.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cation-dependent mannose-6-phosphate receptor
B: Cation-dependent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7489
Polymers34,8892
Non-polymers8597
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-39 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.978, 102.978, 99.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Cation-dependent mannose-6-phosphate receptor / / CD Man-6-P receptor / CD-MPR / 46 kDa mannose 6-phosphate receptor / MPR 46


Mass: 17444.611 Da / Num. of mol.: 2 / Fragment: UNP residues 29-182 / Mutation: E19Q, K137M,N31Q, N57Q, N68Q, N87Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: M6PR / Plasmid: pPICZalphaA / Production host: Pichia Pastoris (fungus) / Strain (production host): x-33 / References: UniProt: P11456
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 200 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 3M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.284
ReflectionResolution: 2→50 Å / Num. obs: 35223 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.068 / Χ2: 1.262 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.075.60.41334931.2191100
2.07-2.155.60.31835481.271100
2.15-2.255.60.2535031.2961100
2.25-2.375.70.19535091.3271100
2.37-2.525.70.15935531.3791100
2.52-2.715.70.11935051.3941100
2.71-2.995.80.08635301.409199.9
2.99-3.425.80.05635331.377199.9
3.42-4.315.90.0435171.032199.6
4.31-505.90.03535320.93197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
CNSphasing
RefinementMethod to determine structure: difference fourier
Starting model: PDB entry 3K42

3k42


Resolution: 2→27.46 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 271
RfactorNum. reflection% reflection
Rfree0.199 3278 9.3 %
Rwork0.165 --
obs-34481 98 %
Solvent computationBsol: 57.299 Å2
Displacement parametersBiso max: 74.73 Å2 / Biso mean: 30.533 Å2 / Biso min: 12.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.104 Å20 Å20 Å2
2--0.104 Å20 Å2
3----0.209 Å2
Refinement stepCycle: LAST / Resolution: 2→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 52 195 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4051.5
X-RAY DIFFRACTIONc_scbond_it1.9272
X-RAY DIFFRACTIONc_mcangle_it2.4562
X-RAY DIFFRACTIONc_scangle_it2.9542.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5imd.par

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