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Found 1 Document (0.596 seconds)

BMRB: 18111

2LMC

Structure of T7 transcription factor Gp2-E. coli RNAp jaw domain complex

Authors

Liu, M.

Assembly

T7 transcription factor Gp2-E. coli RNAp jaw domain complex

Entity

1. T7 transcription factor Gp2-E. coli RNAp jaw domain complex, entity 1 (polymer, Thiol state: all free), 84 monomers, 9338.234 Da Detail

MGSSHHHHHH SSGLVPRGSH MSNVNTGSLS VDNKKFWATV ESSEHSFEVP IYAETLDEAL ELAEWQYVPA GFEVTRVRPC VAPK

2. T7 transcription factor Gp2-E. coli RNAp jaw domain complex, entity 2 (polymer, Thiol state: not present), 84 monomers, 9338.416 Da Detail

MGSSHHHHHH SSGLVPRGSH MKEPAILAEI SGIVSFGKET KGKRRLVITP VDGSDPYEEM IPKWRQLNVF EGERVERGDV ISDG

Total weight

18676.65 Da

Max. entity weight

9338.416 Da

Source organism

Escherichia phage T7 , Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.4 %, Completeness: 69.9 %, Completeness (bb): 72.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	69.9 % (1326 of 1898)	68.8 % (677 of 984)	70.7 % (528 of 747)	72.5 % (121 of 167)
Backbone	72.8 % (719 of 988)	73.9 % (252 of 341)	71.8 % (351 of 489)	73.4 % (116 of 158)
Sidechain	67.9 % (722 of 1063)	66.1 % (425 of 643)	71.0 % (292 of 411)	55.6 % (5 of 9)
Aromatic	58.2 % (99 of 170)	58.8 % (50 of 85)	56.1 % (46 of 82)	100.0 % (3 of 3)
Methyl	84.0 % (131 of 156)	83.3 % (65 of 78)	84.6 % (66 of 78)

1. entity 1

MGSSHHHHHH SSGLVPRGSH MSNVNTGSLS VDNKKFWATV ESSEHSFEVP IYAETLDEAL ELAEWQYVPA GFEVTRVRPC VAPK

2. entity 2

MGSSHHHHHH SSGLVPRGSH MKEPAILAEI SGIVSFGKET KGKRRLVITP VDGSDPYEEM IPKWRQLNVF EGERVERGDV ISDG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Gp2-Jaw complex	[U-100% 13C; U-100% 15N]	300 mM
2	Gp2-Jaw complex	[U-100% 13C; U-100% 15N]	300 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	NaCl	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	water	methyl carbon	internal	indirect	0.25
¹H	water	protons	internal	direct	1.0
¹⁵N	water	nitrogen	internal	indirect	0.1

Referencing offset: -0.05 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	water	methyl carbon	internal	indirect	0.25
¹H	water	protons	internal	direct	1.0
¹⁵N	water	nitrogen	internal	indirect	0.1

Referencing offset: -0.05 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	water	methyl carbon	internal	indirect	0.25
¹H	water	protons	internal	direct	1.0
¹⁵N	water	nitrogen	internal	indirect	0.1

Referencing offset: -0.03 ppm, Outliers: 4 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	water	methyl carbon	internal	indirect	0.25
¹H	water	protons	internal	direct	1.0
¹⁵N	water	nitrogen	internal	indirect	0.1

Referencing offset: 0.51 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2012-01-10

Citation

Structure of T7 transcription factor Gp2-E. coli RNAp jaw domain complex
Liu, M., Matthews, S.J., James, E., Sheppard, C.
Mol. Cell

Related entities 1. T7 transcription factor Gp2-E. coli RNAp jaw domain complex, entity 1, : 1 : 7 entities Detail

Related entities 2. T7 transcription factor Gp2-E. coli RNAp jaw domain complex, entity 2, : 36 entities Detail

Experiments performed 1 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18111_2lmc.nef
Input source #2: Coordindates	2lmc.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----
MGSSHHHHHHSSGLVPRGSHMSNVNTGSLSVDNKKFWATVESSEHSFEVPIYAETLDEALELAEWQYVPAGFEVTRVRPCVAPK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMSNVNTGSLSVDNKKFWATVESSEHSFEVPIYAETLDEALELAEWQYVPAGFEVTRVRPCVAPK

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

--------10--------20--------30--------40--------50--------60--------70--------80----
MGSSHHHHHHSSGLVPRGSHMKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	84	0	0	100.0
B	B	84	0	0	100.0

Content subtype: combined_18111_2lmc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	Bacteriophage_T7_Gp2	Warning	1258		67.9 (chain: A, length: 84), 72.6 (chain: B, length: 84)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Error	2864 (1)	noe	67.9 (chain: A, length: 84), 72.6 (chain: B, length: 84)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	54 (1)	hbond	21.4 (chain: A, length: 84), 20.2 (chain: B, length: 84)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	168 (168)	.	58.3 (chain: A, length: 84), 69.0 (chain: B, length: 84)

Assigned chemical shifts

Saveframe: Bacteriophage_T7_Gp2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 67.9%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 72.6%
- Total number of assignments
  - ¹H chemical shifts: 646
  - ¹³C chemical shifts: 499
  - ¹⁵N chemical shifts: 113
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	483	305	63.1
¹³C chemical shifts	374	242	64.7
¹⁵N chemical shifts	88	56	63.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	108	64.3
¹³C chemical shifts	168	105	62.5
¹⁵N chemical shifts	79	53	67.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	315	197	62.5
¹³C chemical shifts	206	137	66.5
¹⁵N chemical shifts	9	3	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	32	76.2
¹³C chemical shifts	42	33	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	31	60.8
¹³C chemical shifts	49	28	57.1
¹⁵N chemical shifts	2	2	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
64	TRP	CD2	127.915

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	501	329	65.7
¹³C chemical shifts	373	256	68.6
¹⁵N chemical shifts	88	57	64.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	173	121	69.9
¹³C chemical shifts	168	118	70.2
¹⁵N chemical shifts	79	56	70.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	328	208	63.4
¹³C chemical shifts	205	138	67.3
¹⁵N chemical shifts	9	1	11.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	32	78.0
¹³C chemical shifts	41	32	78.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	17	50.0
¹³C chemical shifts	33	16	48.5
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 67.9%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 72.6%
- Total number of restraints: 2864
- Weight of restraints: 1.0 (2864)
- Potential type of restraints: square-well-parabolic (2864)
- Range of distance target values: 1.61, 3.98 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 84, Sequence coverage: 21.4%
    - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 20.2%
  - Total number of restraints: 54
  - Weight of restraints: 1.0 (54)
  - Potential type of restraints: square-well-parabolic (54)
  - Range of distance target values: 2.15, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 58.3%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 69.0%
- Total number of restraints: 168
- Total number of restraints per polymer type: 168
- Weight of restraints: 1.0 (168)
- Potential type of restraints: square-well-parabolic (168)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Gp2-Jaw complex

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Found 1 Document (0.596 seconds)

BMRB: 18111

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. T7 transcription factor Gp2-E. coli RNAp jaw domain complex, entity 1, : 1 : 7 entities Detail

Related entities 2. T7 transcription factor Gp2-E. coli RNAp jaw domain complex, entity 2, : 36 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 5 contents Detail