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- PDB-7cc7: Tetratricopeptide repeat (TPR) domain of protein tyrosine phospha... -

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Basic information

Entry
Database: PDB / ID: 7cc7
TitleTetratricopeptide repeat (TPR) domain of protein tyrosine phosphatase-interacting protein 51 (PTPIP51)
ComponentsRegulator of microtubule dynamics protein 3
KeywordsLIPID TRANSPORT / TPR / PTPIP51 / mitochondria / endoplasmic reticulum / MAM / phopsphplipid
Function / homology
Function and homology information


organelle membrane contact site / intercellular bridge / mitotic spindle pole / spindle microtubule / intracellular calcium ion homeostasis / microtubule binding / mitochondrial outer membrane / membrane => GO:0016020 / cell differentiation / apoptotic process ...organelle membrane contact site / intercellular bridge / mitotic spindle pole / spindle microtubule / intracellular calcium ion homeostasis / microtubule binding / mitochondrial outer membrane / membrane => GO:0016020 / cell differentiation / apoptotic process / mitochondrion / nucleus
Similarity search - Function
Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
PARA-TOLUENE SULFONATE / Regulator of microtubule dynamics protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsLee, B.I. / Park, T.H. / Yeo, H.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002545 Korea, Republic Of
CitationJournal: Embo Rep. / Year: 2021
Title: Phospholipid transfer function of PTPIP51 at mitochondria-associated ER membranes.
Authors: Yeo, H.K. / Park, T.H. / Kim, H.Y. / Jang, H. / Lee, J. / Hwang, G.S. / Ryu, S.E. / Park, S.H. / Song, H.K. / Ban, H.S. / Yoon, H.J. / Lee, B.I.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2May 12, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.4Jun 23, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.5Mar 27, 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: Regulator of microtubule dynamics protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4034
Polymers26,9661
Non-polymers4363
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-1 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.025, 80.025, 202.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Regulator of microtubule dynamics protein 3 / hRMD-3 / Cerebral protein 10 / Protein FAM82A2 / Protein FAM82C / Protein tyrosine phosphatase- ...hRMD-3 / Cerebral protein 10 / Protein FAM82A2 / Protein FAM82C / Protein tyrosine phosphatase-interacting protein 51 / TCPTP-interacting protein 51


Mass: 26966.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: RMDN3, FAM82A2, FAM82C, PTPIP51, hucep-10, UNQ3122/PRO10274
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96TC7
#2: Chemical ChemComp-TSU / PARA-TOLUENE SULFONATE / P-Toluenesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl pH 8.0 and 30% (w/v) SOKALAN CP-42

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 68214 / % possible obs: 99 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Rsym value: 0.068 / Net I/σ(I): 58.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 3.27 / Num. unique obs: 4398 / CC1/2: 0.759 / Rpim(I) all: 0.353 / Rrim(I) all: 0.851 / Rsym value: 0.742 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→37.25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.901 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 3417 5 %RANDOM
Rwork0.1917 ---
obs0.1928 64737 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.13 Å2 / Biso mean: 22.49 Å2 / Biso min: 12.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.45→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 28 224 2076
Biso mean--28.17 33.32 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171769
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.6322564
X-RAY DIFFRACTIONr_angle_other_deg1.5781.5784116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6035230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8123.301103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64315350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.31511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
LS refinement shellResolution: 1.451→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 261 -
Rwork0.257 4637 -
all-4898 -
obs--98.39 %

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