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- PDB-2loy: Refined Miminal Constraint Solution NMR Structure of Translationa... -

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Basic information

Entry
Database: PDB / ID: 2loy
TitleRefined Miminal Constraint Solution NMR Structure of Translationally-controlled tumor protein (TCTP) from Caenorhabditis elegans, Northeast Structural Genomics Consortium Target WR73
ComponentsTranslationally-controlled tumor protein homolog
KeywordsMETAL BINDING PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


calcium ion binding / endoplasmic reticulum / 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 homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsAramini, J.M. / Rossi, P. / Cort, J.R. / Lee, H. / Janjua, H. / Maglaqui, M. / Cooper, B. / Xiao, R. / Acton, T.B. / Everett, J.K. ...Aramini, J.M. / Rossi, P. / Cort, J.R. / Lee, H. / Janjua, H. / Maglaqui, M. / Cooper, B. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
Authors: Lange, O.F. / Rossi, P. / Sgourakis, N.G. / Song, Y. / Lee, H.W. / Aramini, J.M. / Ertekin, A. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionJan 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Aug 18, 2021Group: Data collection / Database references / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translationally-controlled tumor protein homolog


Theoretical massNumber of molelcules
Total (without water)21,6431
Polymers21,6431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translationally-controlled tumor protein homolog / TCTP


Mass: 21642.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F25H2.11, tct-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q93573

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Refinement of minimal constraint structure with residual dipolar couplings
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N TROSY-HSQC
1312D 1H-13C HSQC aliphatic
1413D HNCO
1513D HN(CA)CO
1613D TROSY-HN(CA)CB
1713D TROSY-HN(CO)CACB
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 15N-15N-1H NOESY
11113D 13C-13C-1H NOESY
11213D 15N-13C-1H NOESY
11313D 13C-15N-1H NOESY
11413D C(CO)NH TOCSY
11522D 1H-13C HSQC high resolution
1163NH J-MODULATION (RDC)
NMR detailsText: THE PROTEIN IS MONOMERIC AT 298 K BY 15N T1/T2 RELAXATION AND STATIC LIGHT SCATTERING. THE STRUCTURE IS A MINIMAL CONSTRAINT STRUCTURE DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. ALL ...Text: THE PROTEIN IS MONOMERIC AT 298 K BY 15N T1/T2 RELAXATION AND STATIC LIGHT SCATTERING. THE STRUCTURE IS A MINIMAL CONSTRAINT STRUCTURE DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN METHYL ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE NUMBERS 1 TO 183, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,18-38,66-106,111-146,152-162,164-181: (A) RMSD (ORDERED RESIDUES): BB, 1.0, HEAVY ATOM, 1.6. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.8%, ALLOWED, 2.9%, DISALLOWED, 0.2%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.28/-0.79, ALL, -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.30/-1.10 (E) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 40. (F) AGREEMENT WITH N-H RESIDUAL DIPOLAR COUPLINGS: CORRELATION COEFFICIENT (R): 0.985; Qrms: 0.171. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,13-17,39-65,107-110,147-151,163,182-183.

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.85 mM [U-5% 13C; U-100% 15N] WR73.004, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution30.6 mM [U-5% 13C; U-100% 15N] WR73.011, 11.55 mg/ml Pf1 phage, 12 mM MES, 400 mM NaCl, 6 mM DTT, 3 mM Cacl2, 90% H2O/10% D2Osample_390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.822 mMWR73.009[U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H]1
0.02 %NaN3natural abundance1
10 mMDTTnatural abundance1
5 mMCaCl2natural abundance1
100 mMNaClnatural abundance1
1 %Proteinase Inhibitorsnatural abundance1
20 mMMESnatural abundance1
50 uMDSSnatural abundance1
0.85 mMWR73.004[U-5% 13C; U-100% 15N]2
0.02 %NaN3natural abundance2
10 mMDTTnatural abundance2
5 mMCaCl2natural abundance2
100 mMNaClnatural abundance2
1 %Proteinase Inhibitorsnatural abundance2
20 mMMESnatural abundance2
10 %D2Onatural abundance2
50 uMDSSnatural abundance2
0.6 mMWR73.011[U-5% 13C; U-100% 15N]3
11.55 mg/mLPf1 phagenatural abundance3
12 mMMESnatural abundance3
400 mMNaClnatural abundance3
6 mMDTTnatural abundance3
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1Bruker Biospindata collection
VnmrJVariandata collection
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3Goddarddata analysis
Sparky3Goddardpeak picking
TALOS+Shen, Cornilescu, Delaglio and Baxdihedral angle constraints
PALESPALES (Zweckstetter, Bax)rdc analysis
PSVS1.4Bhattacharya, Montelionestructure validation
PSVS1.4Bhattacharya, Montelionequality assessment
PdbStat5.5Tejero, Montelionedata analysis
MolProbity3.19Richardsonstructure validation
MolProbity3.19Richardsonquality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL RDC-REFINED MINIMAL CONSTRAINT STRUCTURES ARE BASED ON A TOTAL OF 970 CONFORMATIONALLY-RESTRICTING DISTANCE CONSTRAINTS, 293 DIHEDRAL ANGLE CONSTRAINTS, 126 HYDROGEN BOND ...Details: THE FINAL RDC-REFINED MINIMAL CONSTRAINT STRUCTURES ARE BASED ON A TOTAL OF 970 CONFORMATIONALLY-RESTRICTING DISTANCE CONSTRAINTS, 293 DIHEDRAL ANGLE CONSTRAINTS, 126 HYDROGEN BOND CONSTRAINTS, and 99 N-H RESIDUAL DIPOLAR COUPLINGS FROM A SINGLE ALIGNMENT IN PHAGE. (7.7 CONSTRAINTS PER RESIDUE, 2.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 183 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 FINAL STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.
NMR constraintsNOE constraints total: 970
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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