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- PDB-1rpm: HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU, DOMAIN 1 -

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Basic information

Entry
Database: PDB / ID: 1rpm
TitleHUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU, DOMAIN 1
ComponentsRECEPTOR PROTEIN TYROSINE PHOSPHATASE MU
KeywordsRECEPTOR / PHOSPHATASE / SIGNAL TRANSDUCTION / ADHESION / HYDROLASE
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / retina layer formation / positive regulation of D-glucose transmembrane transport / retinal ganglion cell axon guidance / negative regulation of endothelial cell migration / negative regulation of endothelial cell proliferation / homophilic cell-cell adhesion / phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...transmembrane receptor protein tyrosine phosphatase activity / retina layer formation / positive regulation of D-glucose transmembrane transport / retinal ganglion cell axon guidance / negative regulation of endothelial cell migration / negative regulation of endothelial cell proliferation / homophilic cell-cell adhesion / phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of angiogenesis / adherens junction / neuron projection development / cell-cell junction / lamellipodium / cadherin binding / response to xenobiotic stimulus / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 / : / Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin / Immunoglobulin domain ...Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 / : / Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin / Immunoglobulin domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHoffmann, K.M.V. / Tonks, N.K. / Barford, D.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: The crystal structure of domain 1 of receptor protein-tyrosine phosphatase mu.
Authors: Hoffmann, K.M. / Tonks, N.K. / Barford, D.
History
DepositionSep 11, 1997Processing site: BNL
Revision 1.0Apr 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU
B: RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU


Theoretical massNumber of molelcules
Total (without water)64,3032
Polymers64,3032
Non-polymers00
Water6,305350
1
A: RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU


Theoretical massNumber of molelcules
Total (without water)32,1511
Polymers32,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU


Theoretical massNumber of molelcules
Total (without water)32,1511
Polymers32,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.538, 36.292, 95.381
Angle α, β, γ (deg.)90.00, 95.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0988, -0.0011, 0.9951), (0.0007, -1, -0.0011), (0.9951, 0.0006, 0.0988)
Vector: -0.0122, 21.513, -0.014)

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Components

#1: Protein RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU / D1


Mass: 32151.496 Da / Num. of mol.: 2 / Fragment: CYTOSOLIC MEMBRANE PROXIMAL CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P28827, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 750 MM SODIUM CITRATE, PH 5.5, 2 MM DTT, 0.5 MM EDTA
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
2750 mMsodium cirtate1reservoirpH5.5
32 mMdithiothreitol1reservoir
40.5 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 26733 / % possible obs: 90 % / Redundancy: 4 % / Rsym value: 0.029 / Net I/σ(I): 25.2
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.064 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 112065 / Rmerge(I) obs: 0.03

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.82refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YFO

1yfo


Resolution: 2.3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 -4.3 %RANDOM
Rwork0.195 ---
obs0.195 25566 88.2 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5465 0 0 350 5815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.39
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→8 Å / Total num. of bins used: 8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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