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- PDB-1gqb: HUMAN MIR-RECEPTOR, REPEAT 11 -

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Basic information

Entry
Database: PDB / ID: 1gqb
TitleHUMAN MIR-RECEPTOR, REPEAT 11
ComponentsCATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
KeywordsRECEPTOR / MIR-RECEPTOR / IGF-II RECEPTOR / TRANSPORT / GLYCOPROTEIN
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / insulin-like growth factor receptor activity / response to tetrachloromethane / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / insulin-like growth factor receptor activity / response to tetrachloromethane / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / post-embryonic development / receptor-mediated endocytosis / liver development / secretory granule membrane / trans-Golgi network membrane / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / signaling receptor activity / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily ...Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVon Buelow, R. / Dauter, M. / Dauter, Z. / Rajashankar, K.R. / Grimme, S. / Schmidt, B. / Von Figura, K. / Uson, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Locating the Anomalous Scatterer Substructures in Halide and Sulfur Phasing
Authors: Uson, I. / Schmidt, B. / Von Buelow, R. / Grimme, S. / Von Figura, K. / Dauter, M. / Rajashankar, K.R. / Dauter, Z. / Sheldrick, G.M.
History
DepositionNov 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection / Experimental preparation
Category: atom_site / exptl_crystal_grow / Item: _atom_site.occupancy / _exptl_crystal_grow.method
Revision 2.1May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
B: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,92812
Polymers31,1292
Non-polymers79910
Water2,612145
1
A: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8845
Polymers15,5651
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0447
Polymers15,5651
Non-polymers4796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.426, 49.060, 74.380
Angle α, β, γ (deg.)90.00, 129.01, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.02057, -0.99979, -0.00014), (-0.95456, -0.0196, -0.29736), (0.2973, 0.00625, -0.95476)
Vector: 7.67511, 20.07979, 21.65717)

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Components

#1: Protein CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR / MANNOSE-6-PHOSPHATE RECEPTOR / INSULIN-LIKE GROWTH-FACTOR II RECEPTOR / CI MAN-6-P RECEPTOR / CI- ...MANNOSE-6-PHOSPHATE RECEPTOR / INSULIN-LIKE GROWTH-FACTOR II RECEPTOR / CI MAN-6-P RECEPTOR / CI-MPR / 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR / MPR 300


Mass: 15564.672 Da / Num. of mol.: 2
Fragment: IGF-II-BINDING DOMAIN, REPEAT 11, RESIDUES 1508-1650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: FIBROBLAST / Cell line: BHK-21 / Organ: KIDNEY / Production host: CRICETINAE GEN. SP. (mammal) / References: UniProt: P11717
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREPONSIBLE FOR THE TRANSPORT OF PHOSPHORYLATED LYSOSOMAL FROM CELL SURFACE AND GOLGI COMPLEX TO ...REPONSIBLE FOR THE TRANSPORT OF PHOSPHORYLATED LYSOSOMAL FROM CELL SURFACE AND GOLGI COMPLEX TO LYSOSOMES. THIS ENTRY CONTAINS THE SAME COMPOUND AS 1E6F IN A DIFFERENT CRYSTAL FORM. BOTH CRYSTALS GROW UNDER THE SAME CONDITIONS.

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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: 2.17 Å3/Da / Density % sol: 35 % / Description: ALSO SOLVED THROUGH BR-SAD WITH THESE DATA
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: PRECIPITANT: 0.2 M AMMONIUM ACETATE, 0.1 M CACODYLATE PH 5, 28% PEG 4000. PROTEIN SOLUTION: 8 MG/ML IN 10 MM TRIS-HCL PH7.5, 150 MM VAPOUR DIFFUSION, HANGING DROPS,1:1 RATIO.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.919
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999 / Details: FLAT BENT MIRROR
RadiationMonochromator: SI 111 DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 29383 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 97.5

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→15 Å / Num. parameters: 8659 / Num. restraintsaints: 10445 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: REFINED OCCUPANCY FOR ALTERNATIVE DISORDERED SITES
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 1340 5 %RANDOM
all0.209 26877 --
obs0.2084 -99.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2132.3
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 10 145 2147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.042
X-RAY DIFFRACTIONs_from_restr_planes0.0281
X-RAY DIFFRACTIONs_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0

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