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Found 1 Document (0.596 seconds)

BMRB: 17414

2L8L

Structure of an engineered splicing intein mutant based on Mycobacterium tuberculosis RecA

Authors

Du, Z., Wang, C.

Assembly

RecA

Entity

1. RecA (polymer), 139 monomers, 15340.26 Da Detail

CLAEGTRIFD PVTGTTHRIE DVVGGRKPIH VVAAAKDGTL HARPVVSWFD QGTRDVIGLR IAGGAILWAT PDHKVLTEYG WRAAGELRKG DRVAVRDVET GELRYSVIRE VLPTRRARTF DLEVEELHTL VAEGVVVHN

Formula weight

15340.26 Da

Source organism

Mycobacterium tuberculosis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 75.1 %, Completeness (bb): 81.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.1 % (1170 of 1557)	89.3 % (712 of 797)	51.9 % (322 of 621)	97.8 % (136 of 139)
Backbone	81.6 % (672 of 824)	98.3 % (282 of 287)	64.3 % (259 of 403)	97.8 % (131 of 134)
Sidechain	70.6 % (606 of 858)	84.3 % (430 of 510)	49.9 % (171 of 343)	100.0 % (5 of 5)
Aromatic	40.6 % (43 of 106)	75.5 % (40 of 53)	0.0 % (0 of 50)	100.0 % (3 of 3)
Methyl	70.7 % (140 of 198)	94.9 % (94 of 99)	46.5 % (46 of 99)

1. RecA

CLAEGTRIFD PVTGTTHRIE DVVGGRKPIH VVAAAKDGTL HARPVVSWFD QGTRDVIGLR IAGGAILWAT PDHKVLTEYG WRAAGELRKG DRVAVRDVET GELRYSVIRE VLPTRRARTF DLEVEELHTL VAEGVVVHN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	1 mM
4	entity	[U-98% 13C; U-98% 15N]	0.15 ~ 0.2 mM
5	H2O	natural abundance	90 %
6	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: 0.56 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: 0.56 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: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L8L, Strand ID: A Detail

Release date

2012-01-03

Citation

pK(a) coupling at the intein active site: implications for the coordination mechanism of protein splicing with a conserved aspartate
Du, Z., Zheng, Y., Liu, Y., Belfort, M., Wang, C.
J. Am. Chem. Soc. (2011), 133, 10275-10282, PubMed 21604815 , DOI 10.1021/ja203209f , Abstract

Related entities 1. RecA, : 1 : 4 : 17 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17414_2l8l.nef
Input source #2: Coordindates	2l8l.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	Error

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
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGLRIAGGAILWATPDHKVLTEYGWRAAGELRKGDRVAVRDVET
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGLRIAGGAILWATPDHKVLTEYGWRAAGELRKGDRVAVRDVET

-------110-------120-------130---------
GELRYSVIREVLPTRRARTFDLEVEELHTLVAEGVVVHN
|||||||||||||||||||||||||||||||||||||||
GELRYSVIREVLPTRRARTFDLEVEELHTLVAEGVVVHN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	139	0	0	100.0

Content subtype: combined_17414_2l8l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1138		99.3 (chain: A, length: 139)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	1801 (1)	noe	100.0 (chain: A, length: 139)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	4 (1)	hbond	1.4 (chain: A, length: 139)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	163 (162)	.	90.6 (chain: A, length: 139)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	94 (94)	.	67.6 (chain: A, length: 139)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_7	OK	118 (118)	.	81.3 (chain: A, length: 139)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 99.3%
- Total number of assignments
  - ¹H chemical shifts: 714
  - ¹³C chemical shifts: 287
  - ¹⁵N chemical shifts: 137
- Completeness of assignments
- Redox state of CYS
- Peptide bond of PRO
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 100.0%
- Total number of restraints: 1801
- Weight of restraints: 1.0 (1801)
- Potential type of restraints: square-well-parabolic (1801)
- Range of distance target values: 2.4, 7.8 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 1.4%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 2.05, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 90.6%
- Total number of restraints: 162
- Total number of restraints per polymer type: 162
- Weight of restraints: 1.0 (162)
- Potential type of restraints: square-well-parabolic (162)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 67.6%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGLRIAGGAILWATPDHKVLTEYGWRAAGELRKGDRVAVRDVET
  | ||| ||  ||||||||||||||| | ||| | |||||||  ||   ||  || | ||| ||| | |  ||| | || |  ||||| || | |||||
..A.GTR.FD..TGTTHRIEDVVDGRK.I.VVA.A.DGTLHAR..VS...QG..DV.G.RIA.GAI.W.T..HKV.T.YG.R..GELRK.DR.A.RDVET
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130---------
GELRYSVIREVLPTRRARTFDLEVEELHTLVAEGVVVHN
||| |||||||| || | | |   |    ||||||||| 
GEL.YSVIREVL.TR.A.T.D...E....LVAEGVVVH 
-------110-------120-------130--------

Total number of restraints: 94
Potential type of restraints: undefined (94)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Saveframe: CNS/XPLOR_dipolar_coupling_7

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 81.3%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGLRIAGGAILWATPDHKVLTEYGWRAAGELRKGDRVAVRDVET
 ||||||||| |||| ||||||||||| ||||| ||||||||| ||||| ||| || | ||| ||||| | ||||||||||| |||||| || | |||||
.LAEGTRIFD.VTGT.HRIEDVVDGRK.IHVVA.AKDGTLHAR.VVSWF.QGT.DV.G.RIA.GAILW.T.DHKVLTEYGWR.AGELRK.DR.A.RDVET
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130---------
GELRYSVIREVLPTRRARTFDLEVEELHTLVAEGVVVHN
||| |||| ||| |||||||| ||| | ||||||||   
GEL.YSVI.EVL.TRRARTFD.EVE.L.TLVAEGVV   
-------110-------120-------130------

Total number of restraints: 118
Potential type of restraints: undefined (118)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords intein, Mtu, nmr, RecA, splicing

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Found 1 Document (0.596 seconds)

BMRB: 17414

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RecA, : 1 : 4 : 17 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail