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- PDB-1keo: TWISTS AND TURNS OF THE CD-MPR: LIGAND-BOUND VERSUS LIGAND-FREE R... -

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Basic information

Entry
Database: PDB / ID: 1keo
TitleTWISTS AND TURNS OF THE CD-MPR: LIGAND-BOUND VERSUS LIGAND-FREE RECEPTOR
Componentscation-dependent mannose-6-phosphate receptor
KeywordsSUGAR BINDING PROTEIN / p lectin / receptor / mannose 6-phosphate
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
Cation-dependent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOlson, L.J. / Zhang, J. / Dahms, N.M. / Kim, J.J.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Twists and turns of the cation-dependent mannose 6-phosphate receptor. Ligand-bound versus ligand-free receptor
Authors: Olson, L.J. / Zhang, J. / Dahms, N.M. / Kim, J.J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: MOLECULAR BASIS OF LYSOSOMAL ENZYME RECOGNITION: THREE-DIMENSIONAL STRUCTURE OF THE CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR
Authors: Roberts, D.L. / Weix, D.J. / Dahms, N.M. / Kim, J.-J.P.
#2: Journal: J.Biol.Chem. / Year: 1999
Title: STRUCTURAL BASIS FOR RECOGNITION OF PHOSPHORYLATED HIGH-MANNOSE OLIGOSACCHARIDES BY THE CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR
Authors: Olson, L.J. / Zhang, J. / Lee, Y.C. / Dahms, N.M. / Kim, J.-J.P.
History
DepositionNov 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 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

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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)35,3304
Polymers34,8872
Non-polymers4422
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-0 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.772, 108.772, 72.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein cation-dependent mannose-6-phosphate receptor / / CD MAN-6-P RECEPTOR / CD-MPR / 46 KDA MANNOSE 6-PHOSPHATE RECEPTOR / MPR 46


Mass: 17443.580 Da / Num. of mol.: 2 / Fragment: (Residues 29-182) / Mutation: N31Q, N57Q, N68Q, N87Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper)
Keywords: truncated at residue 154, glycosylation deficient mutant
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 5000 monomethyl ether, 0.2M ammonium acetate, 0.1M cacodoylate, 150 mM Nacl, 50 mM imidazole (pH=6.5), 10 mM Manganese chloride, 5 mM beta-glycerophosphate, VAPOR DIFFUSION, SITTING ...Details: 25% PEG 5000 monomethyl ether, 0.2M ammonium acetate, 0.1M cacodoylate, 150 mM Nacl, 50 mM imidazole (pH=6.5), 10 mM Manganese chloride, 5 mM beta-glycerophosphate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 %(w/v)PEG5000 MME1reservoir
30.2 Mammonium acetate1reservoir
40.1 Mcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 18385 / Num. obs: 18385 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.49 / Num. unique all: 138 / % possible all: 70.5
Reflection
*PLUS
Num. obs: 11338 / Num. measured all: 83198
Reflection shell
*PLUS
% possible obs: 70.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 116851.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1580 8 %RANDOM
Rwork0.215 ---
all-19965 --
obs-18385 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.6488 Å2 / ksol: 0.353773 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 29 75 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.991.5
X-RAY DIFFRACTIONc_mcangle_it4.592
X-RAY DIFFRACTIONc_scbond_it5.312
X-RAY DIFFRACTIONc_scangle_it7.252.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4583 1208 8.9 %
Rwork0.3981 1519 -
obs--56.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it2.991.5
X-RAY DIFFRACTIONc_scbond_it5.312
X-RAY DIFFRACTIONc_mcangle_it4.592
X-RAY DIFFRACTIONc_scangle_it7.252.5
LS refinement shell
*PLUS
% reflection Rfree: 8.9 %

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