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- PDB-6ize: Dimeric human TCTP -

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Basic information

Entry
Database: PDB / ID: 6ize
TitleDimeric human TCTP
ComponentsTranslationally-controlled tumor protein
KeywordsIMMUNE SYSTEM / alpha/beta fold / dimer / disulfide bond
Function / homology
Function and homology information


negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cytoplasmic microtubule / multivesicular body / response to virus / spindle pole / intracellular calcium ion homeostasis / calcium ion transport / regulation of apoptotic process / calcium ion binding / negative regulation of apoptotic process ...negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cytoplasmic microtubule / multivesicular body / response to virus / spindle pole / intracellular calcium ion homeostasis / calcium ion transport / regulation of apoptotic process / calcium ion binding / negative regulation of apoptotic process / extracellular space / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
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. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 ...Translationally controlled tumor protein (TCTP) domain signature 1. / Translationally controlled tumour protein, conserved site / Translationally controlled tumor protein (TCTP) domain signature 2. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Translationally-controlled tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.29 Å
AuthorsShin, D.H. / Kim, M.S.
CitationJournal: To Be Published
Title: Dimeric 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 23, 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

Downloads & links

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Assembly

Deposited unit
A: Translationally-controlled tumor protein
B: Translationally-controlled tumor protein
C: Translationally-controlled tumor protein
D: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)78,4774
Polymers78,4774
Non-polymers00
Water2,882160
1
A: Translationally-controlled tumor protein
B: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)39,2392
Polymers39,2392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area14730 Å2
MethodPISA
2
C: Translationally-controlled tumor protein
D: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)39,2392
Polymers39,2392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-11 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.772, 55.772, 195.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 19619.344 Da / Num. of mol.: 4
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.: 160 / 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: 1.94 Å3/Da / Density % sol: 36.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.2 M ammonium acetate, 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.29→55.72 Å / Num. obs: 29992 / % possible obs: 99.9 % / Redundancy: 13.3 % / Net I/σ(I): 25.6
Reflection shellResolution: 2.29→2.37 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementResolution: 2.29→32.051 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.89
RfactorNum. reflection% reflection
Rfree0.2731 1857 6.19 %
Rwork0.215 --
obs0.2187 29992 92.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.29→32.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 0 160 4844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124774
X-RAY DIFFRACTIONf_angle_d1.3176384
X-RAY DIFFRACTIONf_dihedral_angle_d21.511850
X-RAY DIFFRACTIONf_chiral_restr0.057676
X-RAY DIFFRACTIONf_plane_restr0.007812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1493-2.20740.32421170.2721659X-RAY DIFFRACTION73
2.2074-2.27230.36871160.28071903X-RAY DIFFRACTION81
2.2723-2.34560.3781390.28582043X-RAY DIFFRACTION87
2.3456-2.42940.33231290.26272143X-RAY DIFFRACTION92
2.4294-2.52670.32991460.27632211X-RAY DIFFRACTION94
2.5267-2.64160.33231380.26312216X-RAY DIFFRACTION95
2.6416-2.78080.3481520.27122255X-RAY DIFFRACTION97
2.7808-2.95490.33621510.24872283X-RAY DIFFRACTION98
2.9549-3.18290.30031470.2342285X-RAY DIFFRACTION98
3.1829-3.50280.29071560.21682323X-RAY DIFFRACTION100
3.5028-4.00890.24951640.19422314X-RAY DIFFRACTION99
4.0089-5.04760.22751490.16412251X-RAY DIFFRACTION96
5.0476-32.05450.21871530.1962249X-RAY DIFFRACTION96

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