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- PDB-2ljw: Solution NMR structure of Alr2454 protein from Nostoc sp. strain ... -

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Basic information

Entry
Database: PDB / ID: 2ljw
TitleSolution NMR structure of Alr2454 protein from Nostoc sp. strain PCC 7120, Northeast Structural Genomics Consortium Target NsR264
ComponentsAlr2454 protein
KeywordsStructural Genomics / Unknown Function / novel fold / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-BIOLOGY / Protein Structure Initiative
Function / homologyProtein of unknown function DUF3067 / Protein of unknown function DUF3067 / Domain of unknown function (DUF3067) / HIT family, subunit A / 2-Layer Sandwich / Alpha Beta / Alr2454 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsAramini, J.M. / Lee, D. / Ciccosanti, C. / Janjua, H. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267.
Authors: Aramini, J.M. / Petrey, D. / Lee, D.Y. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T.
History
DepositionSep 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Aug 22, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_database_status / 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_database_remark.text / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650 HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alr2454 protein


Theoretical massNumber of molelcules
Total (without water)12,9931
Polymers12,9931
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 Alr2454 protein


Mass: 12992.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr2454 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8YUA0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY aliphatic
1513D 1H-13C NOESY aromatic
1622D 1H-13C HSQC high resolution (L/V methyl stereoassignment)
1713D HNCO
1813D HN(CA)CO
1913D HNCA
11013D HN(CO)CA
11113D CBCA(CO)NH
11213D HN(CA)CB
11313D HBHA(CO)NH
11413D (H)CCH-TOCSY
11513D CCH-TOCSY
11613D (H)CCH-COSY
11711D 15N T1 and T2
11812D 1H-15N hetNOE
NMR detailsText: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HIS6): BACKBONE, 99.4%, SIDE CHAIN, 98.3%, AROMATICS, 96.6%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100.0%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 104, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 1-100: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 0.9. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.8%, ADDITIONALLY ALLOWED, 3.1%, DISALLOWED, 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.15/-0.28, ALL, -0.03/-0.18. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 12.51/-0.62 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 104): RECALL, 0.976, PRECISION, 0.934, F-MEASURE, 0.955, DP-SCORE, 0.817. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE FINAL SIX HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.01 mM [U-100% 13C; U-100% 15N] NsR264, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.567 mM [U-5% 13C; U-100% 15N] NsR264, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.01 mMNsR264-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
50 uMDSS-71
0.567 mMNsR264-8[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-92
100 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
0.02 %sodium azide-132
50 uMDSS-142
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement, structure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionerpf analysis
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospindata analysis
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.112Goddarddata analysis
Sparky3.112Goddardpeak picking
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
TALOS+Shen, Cornilescu, Delaglio and Baxdihedral angle constraints
PSVS1.4Bhattacharya and Montelionestructure quality analysis
MolProbity3.18Richardsonstructure quality analysis
PdbStat5.4Tejero & Montelionepdb coordinate analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2478 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 162 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (25.4 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2478 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 162 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (25.4 CONSTRAINTS PER RESIDUE, 6.8 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 104 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: 2478 / NOE intraresidue total count: 688 / NOE long range total count: 709 / NOE medium range total count: 462 / NOE sequential total count: 619
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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