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- PDB-6izb: Flexible loop truncated human TCTP -

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Basic information

Entry
Database: PDB / ID: 6izb
TitleFlexible loop truncated human TCTP
ComponentsTranslationally-controlled tumor protein
KeywordsIMMUNE SYSTEM / alpha/beta fold / flexible loop truncated / dimer / disulfide bond
Function / homology
Function and homology information


negative regulation of ectoderm development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / stem cell population maintenance / cytoplasmic microtubule / multivesicular body / response to virus / intracellular calcium ion homeostasis / spindle pole / calcium ion transport / regulation of apoptotic process ...negative regulation of ectoderm development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / stem cell population maintenance / cytoplasmic microtubule / multivesicular body / response to virus / intracellular calcium ion homeostasis / spindle pole / calcium ion transport / regulation of apoptotic process / DNA-binding transcription factor binding / calcium ion binding / negative regulation of apoptotic process / extracellular space / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Translationally controlled tumor protein (TCTP) domain signature 1. / Translationally controlled tumour protein, conserved site / Translationally controlled tumor protein (TCTP) domain signature 2. / Translationally controlled tumour protein / Translationally controlled tumour protein (TCTP) domain / Translationally controlled tumour protein / Translationally controlled tumor protein (TCTP) domain profile. / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily
Similarity search - Domain/homology
Translationally-controlled tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 1.899 Å
AuthorsShin, D.H. / Kim, M.S.
CitationJournal: To Be Published
Title: Flexible loop truncated human TCTP
Authors: Shin, D.H. / Kim, M.S.
History
DepositionDec 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)17,9591
Polymers17,9591
Non-polymers00
Water1,63991
1
A: Translationally-controlled tumor protein

A: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)35,9172
Polymers35,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area2190 Å2
ΔGint-10 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.295, 69.295, 146.062
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

21A-268-

HOH

31A-290-

HOH

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Components

#1: Protein Translationally-controlled tumor protein / TCTP / Fortilin / Histamine-releasing factor / HRF / p23


Mass: 17958.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13693
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 25 % (w/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.37 Å / Num. obs: 17029 / % possible obs: 99.5 % / Redundancy: 36.1 % / Net I/σ(I): 45.7
Reflection shellResolution: 1.9→1.97 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementResolution: 1.899→46.366 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 852 5 %
Rwork0.2196 --
obs0.2209 17028 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→46.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 91 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191242
X-RAY DIFFRACTIONf_angle_d1.1871663
X-RAY DIFFRACTIONf_dihedral_angle_d18.322478
X-RAY DIFFRACTIONf_chiral_restr0.069174
X-RAY DIFFRACTIONf_plane_restr0.009214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8991-2.01810.29281340.25312543X-RAY DIFFRACTION97
2.0181-2.17390.27661390.23722655X-RAY DIFFRACTION100
2.1739-2.39270.2691400.2212662X-RAY DIFFRACTION100
2.3927-2.73890.23241400.21942676X-RAY DIFFRACTION100
2.7389-3.45050.25531450.22212728X-RAY DIFFRACTION100
3.4505-46.37940.2311540.21152912X-RAY DIFFRACTION100

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