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Found 1 Document (0.579 seconds)

BMRB: 19438

2MCF

tgam

Authors

Yang, Y., Montet de Guillen, K., Roumestand, C.

Assembly

Tgam

Entity

1. Tgam (polymer), 148 monomers, 16733.12 Da Detail

MKYDVVIIPE SFHRFDKHNM EHICPPMVIG DRSYDIAMEI VNGVDRVIKA SFNASVEELE GEDCDVLYRK YTLEKEGKKG IVHVKLRKIT ENCPPVDGNR CSVLEFERDI ECIVKAIEEC LAKGELNSKL EGKPIPNPLL GLDSTRTG

Formula weight

16733.12 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 52.5 %, Completeness (bb): 96.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.5 % (909 of 1731)	37.6 % (341 of 908)	63.9 % (432 of 676)	92.5 % (136 of 147)
Backbone	96.9 % (845 of 872)	98.0 % (292 of 298)	96.1 % (417 of 434)	97.1 % (136 of 140)
Sidechain	20.0 % (199 of 997)	8.2 % (50 of 610)	39.2 % (149 of 380)	0.0 % (0 of 7)
Aromatic	0.0 % (0 of 88)	0.0 % (0 of 44)	0.0 % (0 of 44)
Methyl	6.6 % (11 of 166)	4.8 % (4 of 83)	8.4 % (7 of 83)

1. Tgam

MKYDVVIIPE SFHRFDKHNM EHICPPMVIG DRSYDIAMEI VNGVDRVIKA SFNASVEELE GEDCDVLYRK YTLEKEGKKG IVHVKLRKIT ENCPPVDGNR CSVLEFERDI ECIVKAIEEC LAKGELNSKL EGKPIPNPLL GLDSTRTG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 (±0.1) K, pH 6.60 (±0.01)

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %

LACS Plot; CA

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

Referencing offset: -0.25 ppm, Outliers: 4 Detail

LACS Plot; CB

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

Referencing offset: -0.25 ppm, Outliers: 4 Detail

LACS Plot; HA

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

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2MCF, Strand ID: A Detail

Release date

2014-09-01

Citation

Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans
Yang, Y., Montet de Guillen, K., Roumestand, C.
Proteomics (2015), 15, 114-123, PubMed 25359407 , DOI 10.1002/pmic.201300535 , Abstract

Related entities 1. Tgam, : 1 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19438_2mcf.nef
Input source #2: Coordindates	2mcf.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:24:CYS:SG	A:120:CYS:SG	oxidized, CA 53.13, CB 42.47 ppm	oxidized, CA 58.48, CB 39.42 ppm	2.037
A:64:CYS:SG	A:93:CYS:SG	oxidized, CA 57.17, CB 41.21 ppm	oxidized, CA 52.61, CB 42.09 ppm	2.016
A:101:CYS:SG	A:112:CYS:SG	unknown, CA 55.27 ppm	oxidized, CA 59.29, CB 41.91 ppm	2.028

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
MKYDVVIIPESFHRFDKHNMEHICPPMVIGDRSYDIAMEIVNGVDRVIKASFNASVEELEGEDCDVLYRKYTLEKEGKKGIVHVKLRKITENCPPVDGNR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKYDVVIIPESFHRFDKHNMEHICPPMVIGDRSYDIAMEIVNGVDRVIKASFNASVEELEGEDCDVLYRKYTLEKEGKKGIVHVKLRKITENCPPVDGNR

-------110-------120-------130-------140--------
CSVLEFERDIECIVKAIEECLAKGELNSKLEGKPIPNPLLGLDSTRTG
||||||||||||||||||||||||||||||||||||||||||||||||
CSVLEFERDIECIVKAIEECLAKGELNSKLEGKPIPNPLLGLDSTRTG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0

Content subtype: combined_19438_2mcf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	848		100.0 (chain: A, length: 148)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1949 (1)	noe	100.0 (chain: A, length: 148)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	26 (1)	noe	11.5 (chain: A, length: 148)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	40 (1)	hbond	16.9 (chain: A, length: 148)
4	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	38 (1)	hbond	14.9 (chain: A, length: 148)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_6	OK	234 (234)	.	83.8 (chain: A, length: 148)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 295
  - ¹³C chemical shifts: 417
  - ¹⁵N chemical shifts: 136
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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	908	295	32.5
¹³C chemical shifts	676	417	61.7
¹⁵N chemical shifts	155	136	87.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	298	295	99.0
¹³C chemical shifts	296	283	95.6
¹⁵N chemical shifts	140	136	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	610	0	0.0
¹³C chemical shifts	380	134	35.3
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	0	0.0
¹³C chemical shifts	87	5	5.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	0	0.0
¹³C chemical shifts	44	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 100.0%
- Total number of restraints: 1947
- Weight of restraints: 1.0 (1947)
- Potential type of restraints: upper-bound-parabolic (1947)
- Range of distance target values: 2.2, 7.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 11.5%
  - Total number of restraints: 26
  - Weight of restraints: 1.0 (26)
  - Potential type of restraints: upper-bound-parabolic (26)
  - Range of distance target values: 2.2, 4.8 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 16.9%
    - Total number of restraints: 40
    - Weight of restraints: 1.0 (40)
    - Potential type of restraints: upper-bound-parabolic (40)
    - Range of distance target values: 2.2, 4.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_5
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 14.9%
      - Total number of restraints: 38
        Total hydrogen bond restraints: 38
      - Weight of restraints: 1.0 (38)
        Total hydrogen bond restraints: 1.0 (38)
      - Potential type of restraints: upper-bound-parabolic (38)
        Total hydrogen bond restraints: upper-bound-parabolic (38)
      - Range of distance target values: 1.8, 2.7 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 83.8%
- Total number of restraints: 234
- Total number of restraints per polymer type: 234
- Weight of restraints: 1.0 (234)
- Potential type of restraints: square-well-parabolic (234)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords tgam

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Found 1 Document (0.579 seconds)

BMRB: 19438

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Tgam, : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail