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BMRB: 19625

2MHC

TNPX

Authors

Headey, S.J., Sivakumaran, A., Adams, V., Rodgers, A.J.W., Rood, J.I., Scanlon, M.J., Wilce, M.C.J.

Assembly

TNPX

Entity

1. TNPX (polymer, Thiol state: not present), 120 monomers, 13776.08 Da Detail

GSRTSRITAL YERLSRDDDL TGESNSITNQ KKYLEDYARR NGFENIRHFT DDGFSGVNFN RPGFQSLIKE VEAGNVETLI VKDMSRLGRN YLQVGFYTEV LFPQKNVRFL AINNSIDSNN

Formula weight

13776.08 Da

Source organism

Clostridium perfringens

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.1 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.1 % (1316 of 1414)	93.5 % (691 of 739)	92.0 % (497 of 540)	94.8 % (128 of 135)
Backbone	97.6 % (699 of 716)	97.2 % (240 of 247)	97.4 % (342 of 351)	99.2 % (117 of 118)
Sidechain	89.9 % (727 of 809)	91.7 % (451 of 492)	88.3 % (265 of 300)	64.7 % (11 of 17)
Aromatic	66.1 % (82 of 124)	85.5 % (53 of 62)	46.8 % (29 of 62)
Methyl	96.6 % (114 of 118)	94.9 % (56 of 59)	98.3 % (58 of 59)

1. TNPX

GSRTSRITAL YERLSRDDDL TGESNSITNQ KKYLEDYARR NGFENIRHFT DDGFSGVNFN RPGFQSLIKE VEAGNVETLI VKDMSRLGRN YLQVGFYTEV LFPQKNVRFL AINNSIDSNN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

LACS Plot; CA

Referencing offset: -1.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -1.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.6 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MHC, Strand ID: A Detail

Release date

2014-11-23

Citation

Solution structure and DNA binding of the catalytic domain of the large serine resolvase TnpX
Headey, S.J., Sivakumaran, A., Adams, V., Rodgers, A.J.W., Scanlon, J.I., Wilce, M.C.J.
J. Mol. Recognit. (2015), 28, 316-324, PubMed 25720550 , DOI 10.1002/jmr.2446 , Abstract

Related entities 1. TNPX, : 1 : 3 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

4 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

5 3D HN(CA)CO 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

6 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

7 3D (H)C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

8 3D HC(C)H-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

9 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

10 3D (H)CCH-TOCSY 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

12 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

13 2D 1H-1 NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

14 2D 1H-15N NOE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.4MM [U-98% 13C

#	Name	Isotope labeling	Type	Concentration
1	TNPX	[U-99% 13C; U-99% 15N]		0.4 mM
2	D2O	natural abundance		10 %
3	sodium chloride	natural abundance		150 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		90 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19625_2mhc.nef
Input source #2: Coordindates	2mhc.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
GSRTSRITALYERLSRDDDLTGESNSITNQKKYLEDYARRNGFENIRHFTDDGFSGVNFNRPGFQSLIKEVEAGNVETLIVKDMSRLGRNYLQVGFYTEV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSRTSRITALYERLSRDDDLTGESNSITNQKKYLEDYARRNGFENIRHFTDDGFSGVNFNRPGFQSLIKEVEAGNVETLIVKDMSRLGRNYLQVGFYTEV

-------110-------120
LFPQKNVRFLAINNSIDSNN
||||||||||||||||||||
LFPQKNVRFLAINNSIDSNN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	120	0	0	100.0

Content subtype: combined_19625_2mhc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1380		99.2 (chain: A, length: 120)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2324 (1)	noe	99.2 (chain: A, length: 120)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 756
  - ¹³C chemical shifts: 494
  - ¹⁵N chemical shifts: 130
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 99.2%
- Total number of restraints: 2324
- Weight of restraints: 1.0 (2324)
- Potential type of restraints: square-well-parabolic (2324)
- Range of distance target values: 2.12, 3.65 (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

Keywords RECOMBINATION, SERINE RESOLVASE, TNPX