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- PDB-5o9k: Crystal structure of Murine Histmaine-Releasing Factor (HRF/TCTP) -

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Basic information

Entry
Database: PDB / ID: 5o9k
TitleCrystal structure of Murine Histmaine-Releasing Factor (HRF/TCTP)
ComponentsTranslationally-controlled tumor protein
KeywordsIMMUNE SYSTEM / Immunoglobulin E / Allergy / Histamine Releasing Factor / TCTP / HRF / P23 / P21 / Fortilin
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 / multivesicular body / spindle pole / DNA-binding transcription factor binding / calcium ion binding / extracellular space / nucleoplasm / nucleus / 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. / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.014 Å
AuthorsDore, K.A. / Kashiwakura, J. / McDonnell, J.M. / Gould, H.J. / Kawakami, T. / Sutton, B.J. / Davies, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100090 United Kingdom
CitationJournal: Mol. Immunol. / Year: 2017
Title: Crystal structures of murine and human Histamine-Releasing Factor (HRF/TCTP) and a model for HRF dimerisation in mast cell activation.
Authors: Dore, K.A. / Kashiwakura, J.I. / McDonnell, J.M. / Gould, H.J. / Kawakami, T. / Sutton, B.J. / Davies, A.M.
History
DepositionJun 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2053
Polymers41,1132
Non-polymers921
Water00
1
A: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)20,5561
Polymers20,5561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Translationally-controlled tumor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6482
Polymers20,5561
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.530, 99.850, 57.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Translationally-controlled tumor protein / TCTP / 21 kDa polypeptide / p21 / p23


Mass: 20556.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Murine histamine-releasing factor with C-terminal His-tag
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tpt1, Trt
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P63028
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.1M Tris-HCl pH8.4, 23% (w/v) PEG 2000 MME and 0.01M nickel chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 A
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 4.01→57.06 Å / Num. obs: 3606 / % possible obs: 98.5 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.081 / Net I/σ(I): 9
Reflection shellResolution: 4.01→4.63 Å / Redundancy: 12 % / Rmerge(I) obs: 1.892 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1200 / CC1/2: 0.877 / Rpim(I) all: 0.554 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YZ1

1yz1


Resolution: 4.014→57.059 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.3416 156 4.99 %
Rwork0.2996 --
obs0.3017 3125 85.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.014→57.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 6 0 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012206
X-RAY DIFFRACTIONf_angle_d0.3612987
X-RAY DIFFRACTIONf_dihedral_angle_d5.7321298
X-RAY DIFFRACTIONf_chiral_restr0.039339
X-RAY DIFFRACTIONf_plane_restr0.002386
LS refinement shellResolution: 4.0142→57.0647 Å
RfactorNum. reflection% reflection
Rfree0.3416 156 -
Rwork0.2996 2969 -
obs--86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6211-0.0673-0.44620.39-0.0660.40320.5084-0.30390.37440.3852-0.1195-0.4788-0.00060.19190.89571.41370.7475-0.0279-0.29350.29710.633217.1172106.322787.6918
20.1951-0.35680.12940.6696-0.31870.5521-0.89930.2319-0.6641.1195-0.0179-0.2945-1.4115-0.9858-0.09761.73070.43530.02261.39750.31491.327618.834298.6418101.3533
30.148-0.05960.02480.05240.05070.1621-0.28640.61240.60330.2728-0.1502-0.0894-0.0663-0.1681-0.00381.8659-0.1686-0.36210.7380.07961.351422.217107.133192.0683
40.92520.24020.42540.82120.44640.9920.29250.1753-0.0866-0.4230.3073-0.6881-0.3802-0.51431.60520.00730.8623-0.1341.10240.41080.49825.2463116.6926129.6827
50.33040.06540.130.07530.05620.04910.62820.05230.0434-0.5265-0.3882-0.24840.0427-0.04480.12042.03921.3384-0.07172.67680.36681.090717.4821109.3568124.6769
60.0537-0.0150.04110.0699-0.12050.14230.7150.7499-0.0763-0.6351-0.6956-0.46490.07070.32850.00030.9487-0.07490.05782.21120.29531.1511-2.2052122.0463116.1021
70.1572-0.0936-0.03410.04250.00620.1084-0.2461-0.1875-0.5777-0.4395-0.10410.12670.52690.9699-01.11850.2372-0.03081.89460.2241.365910.2863116.4543120.7711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 170 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 32 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 84 )
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 127 )
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 170 )

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