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- PDB-1edy: CRYSTAL STRUCTURE OF RAT ALPHA 1-MACROGLOBULIN RECEPTOR BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1edy
TitleCRYSTAL STRUCTURE OF RAT ALPHA 1-MACROGLOBULIN RECEPTOR BINDING DOMAIN
ComponentsALPHA 1-MACROGLOBULIN
KeywordsPROTEIN BINDING / beta sandwich / pseudo-symmetric dimer
Function / homology
Function and homology information


brain-derived neurotrophic factor binding / nerve growth factor binding / endopeptidase inhibitor activity / embryo implantation / serine-type endopeptidase inhibitor activity / protease binding / protein-containing complex binding / extracellular space
Similarity search - Function
Alpha-macroglobulin, receptor-binding domain / Alpha-2-macroglobulin, TED domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 ...Alpha-macroglobulin, receptor-binding domain / Alpha-2-macroglobulin, TED domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-1-macroglobulin / Alpha-1-macroglobulin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsXiao, T. / DeCamp, D.L. / Sprang, S.R.
CitationJournal: Protein Sci. / Year: 2000
Title: Structure of a rat alpha 1-macroglobulin receptor-binding domain dimer.
Authors: Xiao, T. / DeCamp, D.L. / Spran, S.R.
History
DepositionJan 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA 1-MACROGLOBULIN
B: ALPHA 1-MACROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)30,7632
Polymers30,7632
Non-polymers00
Water1,69394
1
A: ALPHA 1-MACROGLOBULIN
B: ALPHA 1-MACROGLOBULIN

A: ALPHA 1-MACROGLOBULIN
B: ALPHA 1-MACROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)61,5264
Polymers61,5264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
Unit cell
Length a, b, c (Å)64.377, 36.151, 77.978
Angle α, β, γ (deg.)90.00, 105.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALPHA 1-MACROGLOBULIN


Mass: 15381.416 Da / Num. of mol.: 2 / Fragment: RECEPTOR BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: PLASMA / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63332, UniProt: Q63041*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG6000, calcium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
122 %PEG60001reservoir
2100 mMNa-HEPES1reservoir
325 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 20, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 48604 / Num. obs: 14814 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.28 % / Biso Wilson estimate: 40.47 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.19 / Num. unique all: 1121 / % possible all: 72.5
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 72.5 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→14.88 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1434 -random
Rwork0.2283 ---
all0.2269 15643 --
obs0.2269 14147 90.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.989 Å20 Å29.097 Å2
2--7.884 Å20 Å2
3----21.873 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 0 94 2236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006464
X-RAY DIFFRACTIONc_angle_deg1.27794
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.278

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