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- PDB-2kwb: Minimal Constraint Solution NMR Structure of Translationally-cont... -

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Basic information

Entry
Database: PDB / ID: 2kwb
TitleMinimal Constraint Solution NMR Structure of Translationally-controlled tumor protein (TCTP) from C.elegans, Northeast Structural Genomics Consortium Target WR73
ComponentsTranslationally-controlled tumor protein homolog
KeywordsMETAL BINDING PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / 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. / Cooper, B. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Minimal Constraint Solution NMR Structure of Translationally-controlled tumor protein (TCTP) from C.elegans, Northeast Structural Genomics Consortium Target WR73
Authors: Aramini, J.M. / Rossi, P. / Cort, J.R. / Cooper, B. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T.
History
DepositionApr 2, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: Minimal Constraint NMR Structure
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
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: 2-12,14-16,18-38,66-106,111-146,152-181: (A) RMSD (ORDERED RESIDUES): BB, 1.0, HEAVY ATOM, 1.5. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 89.0%, ADDITIONALLY ALLOWED, 10.9%, GENEROUSLY ALLOWED, 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, -0.31/-1.83. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 20.78/-2.04 (E) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 55. 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]: 1,13,17,39-65,107-110,147-151,182-183.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.82 mM [U-13C; U-15N; U-2H; ILVFY-1H] WR73, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.85 mM [U-5% 13C; U-100% 15N] WR73, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.82 mMWR73-1[U-13C; U-15N; U-2H; ILVFY-1H]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
50 uMDSS-61
0.02 %sodium azide-71
0.85 mMWR73-8[U-5% 13C; U-100% 15N]2
20 mMMES-92
100 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
50 uMDSS-132
0.02 %sodium azide-142
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
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddarddata analysis
Sparky3Goddardpeak picking
Sparky3Goddardchemical shift assignment
TopSpin2.1Bruker Biospincollection
VnmrJVariancollection
PSVS1.4Bhattacharya and Montelionestructure validation
TALOSplusCornilescu, Delaglio and Baxdihedral angle constraints
PdbStat5.1Tejero and Montelionepdb coordinate analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL MINIMAL CONSTRAINT STRUCTURES ARE BASED ON A TOTAL OF 976 CONFORMATIONALLY-RESTRICTING DISTANCE CONSTRAINTS, 272 DIHEDRAL ANGLE CONSTRAINTS, AND 126 HYDROGEN BOND CONSTRAINTS (7.6 ...Details: THE FINAL MINIMAL CONSTRAINT STRUCTURES ARE BASED ON A TOTAL OF 976 CONFORMATIONALLY-RESTRICTING DISTANCE CONSTRAINTS, 272 DIHEDRAL ANGLE CONSTRAINTS, AND 126 HYDROGEN BOND CONSTRAINTS (7.6 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 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: 976 / NOE intraresidue total count: 89 / NOE long range total count: 351 / NOE medium range total count: 248 / NOE sequential total count: 288
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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