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BMRB: 15295

2JQV

Solution structure At3g28950.1 from Arabidopsis thaliana

Authors

Volkman, B.F., de la Cruz, N.B., Peterson, F.C.

Assembly

At3g28950.1

Entity

1. At3g28950.1 (polymer, Thiol state: all free), 165 monomers, 18574.55 Da Detail

STSSDPQSHN VFVYGSILEP AVAAVILDRT ADTVPAVLHG YHRYKLKGLP YPCIVSSDSG KVNGKVITGV SDAELNNFDV IEGNDYERVT VEVVRMDNSE KVKVETYVWV NKDDPRMYGE WDFEEWRVVH AEKFVETFRK MLEWNKNPNG KSMEEAVGSL LSSGD

Formula weight

18574.55 Da

Source organism

Arabidopsis thaliana

Exptl. method

solution NMR

Refine. method

AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT.

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.0 %, Completeness: 84.6 %, Completeness (bb): 92.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.6 % (1604 of 1897)	82.1 % (804 of 979)	86.7 % (646 of 745)	89.0 % (154 of 173)
Backbone	92.5 % (903 of 976)	90.7 % (303 of 334)	92.8 % (449 of 484)	95.6 % (151 of 158)
Sidechain	78.4 % (843 of 1075)	77.7 % (501 of 645)	81.7 % (339 of 415)	20.0 % (3 of 15)
Aromatic	61.2 % (104 of 170)	69.4 % (59 of 85)	51.9 % (42 of 81)	75.0 % (3 of 4)
Methyl	89.9 % (160 of 178)	89.9 % (80 of 89)	89.9 % (80 of 89)

1. At3g28950.1

STSSDPQSHN VFVYGSILEP AVAAVILDRT ADTVPAVLHG YHRYKLKGLP YPCIVSSDSG KVNGKVITGV SDAELNNFDV IEGNDYERVT VEVVRMDNSE KVKVETYVWV NKDDPRMYGE WDFEEWRVVH AEKFVETFRK MLEWNKNPNG KSMEEAVGSL LSSGD

Show sample condition

Sample

Solvent system 95% H2O, 5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.75 mM At3g28950.1 U-15N/13C, 10 mM MOPS, 100 mM sodium chloride, 5 mM DTT

#	Name	Isotope labeling	Concentration
1	At3g28950.1	[U-100% 13C; U-100% 15N]	0.75 mM
2	MOPS	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	5 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.59 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.59 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.31 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JQV, Strand ID: A Detail

Release date

2007-08-14

Citation

Solution structure of At3g28950 from Arabidopsis thaliana
de la Cruz, N.B., Peterson, F.C., Volkman, B.F.
Proteins (2008), 71, 546-551, PubMed 18214976 , DOI 10.1002/prot.21936 , Abstract

Related entities 1. At3g28950.1, : 1 : 1 : 15 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15295_2jqv.nef
Input source #2: Coordindates	2jqv.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
STSSDPQSHNVFVYGSILEPAVAAVILDRTADTVPAVLHGYHRYKLKGLPYPCIVSSDSGKVNGKVITGVSDAELNNFDVIEGNDYERVTVEVVRMDNSE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STSSDPQSHNVFVYGSILEPAVAAVILDRTADTVPAVLHGYHRYKLKGLPYPCIVSSDSGKVNGKVITGVSDAELNNFDVIEGNDYERVTVEVVRMDNSE

-------110-------120-------130-------140-------150-------160-----
KVKVETYVWVNKDDPRMYGEWDFEEWRVVHAEKFVETFRKMLEWNKNPNGKSMEEAVGSLLSSGD
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KVKVETYVWVNKDDPRMYGEWDFEEWRVVHAEKFVETFRKMLEWNKNPNGKSMEEAVGSLLSSGD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	165	0	0	100.0

Content subtype: combined_15295_2jqv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1530		93.9 (chain: A, length: 165)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2912 (1)	noe	88.5 (chain: A, length: 165)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	189 (189)	.	81.2 (chain: A, length: 165)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 93.9%
- Total number of assignments
  - ¹H chemical shifts: 769
  - ¹³C chemical shifts: 612
  - ¹⁵N chemical shifts: 149
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	979	769	78.5
¹³C chemical shifts	745	612	82.1
¹⁵N chemical shifts	180	149	82.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	334	293	87.7
¹³C chemical shifts	330	294	89.1
¹⁵N chemical shifts	158	146	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	645	476	73.8
¹³C chemical shifts	415	318	76.6
¹⁵N chemical shifts	22	3	13.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	93	80	86.0
¹³C chemical shifts	93	78	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	51	60.0
¹³C chemical shifts	81	32	39.5
¹⁵N chemical shifts	4	3	75.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 88.5%
- Total number of restraints: 2910
- Weight of restraints: 1.0 (2910)
- Potential type of restraints: upper-bound-parabolic (2910)
- Range of distance target values: 2.05, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 81.2%
- Total number of restraints: 189
- Total number of restraints per polymer type: 189
- Weight of restraints: 1.0 (189)
- Potential type of restraints: square-well-parabolic (189)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords At3g28950.1, Center for Eukaryotic Structural Genomics, Protein Structure Initiative, PSI, Structural Genomics

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Found 1 Document (0.739 seconds)

BMRB: 15295

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. At3g28950.1, : 1 : 1 : 15 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail