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Found 1 Document (3.306 seconds)

BMRB: 17702

2LE8

The protein complex for DNA replication

Authors

LIU, C., WEI, Z., ZHU, G.

Assembly

protein complex for DNA replication

Entity

1. protein comp1 (polymer, Thiol state: not present), 114 monomers, 13285.73 Da Detail

APKASLRLGF SEYSRISNLI VLHLRKVEEE EDESALKRSE LVNWYLKEIE SEIDSEEELI NKKRIIEKVI HRLTHYDHVL IELTQAGLKG STEGSESYEE DPYLVVNPNY LLED

2. protein comp2 (polymer, Thiol state: not present), 29 monomers, 3355.865 Da Detail

SALKGVSQDL LERIRAKEAQ KQLAQMTRW

Total weight

16641.596 Da

Max. entity weight

13285.73 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 70.4 %, Completeness (bb): 77.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	70.4 % (1213 of 1722)	75.6 % (683 of 903)	60.4 % (403 of 667)	83.6 % (127 of 152)
Backbone	77.5 % (660 of 852)	91.0 % (262 of 288)	64.9 % (275 of 424)	87.9 % (123 of 140)
Sidechain	67.4 % (679 of 1008)	68.6 % (422 of 615)	66.4 % (253 of 381)	33.3 % (4 of 12)
Aromatic	26.5 % (26 of 98)	26.5 % (13 of 49)	25.5 % (12 of 47)	50.0 % (1 of 2)
Methyl	79.5 % (140 of 176)	80.7 % (71 of 88)	78.4 % (69 of 88)

1. protein comp1

APKASLRLGF SEYSRISNLI VLHLRKVEEE EDESALKRSE LVNWYLKEIE SEIDSEEELI NKKRIIEKVI HRLTHYDHVL IELTQAGLKG STEGSESYEE DPYLVVNPNY LLED

2. protein comp2

SALKGVSQDL LERIRAKEAQ KQLAQMTRW

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	MES	[U-100% 15N]	25 mM
9	sodium chloride	natural abundance	300 mM
10	glycerol	natural abundance	1 %
11	protein_comp1	[U-100% 13C; U-100% 15N]	0.8 mM
12	protein_comp2	natural abundance	1.0 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	MES	natural abundance	25 mM
16	sodium chloride	natural abundance	300 mM
17	glycerol	natural abundance	1 %
18	protein_comp1	[U-100% 13C; U-100% 15N]	0.8 mM
19	protein_comp2	natural abundance	1.0 mM
20	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	MES	natural abundance	25 mM
22	sodium chloride	natural abundance	300 mM
23	glycerol	natural abundance	1 %
24	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
25	protein_comp1	natural abundance	1.0 mM
26	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 19 models in PDB: 2LE8, Strand ID: A, B Detail

Release date

2012-12-16

Citation

The protein complex for DNA replication
LIU, C., WEI, Z., WU, R., LIANG, C., ZHU, G.
Not known

Related entities 1. protein comp1, : 1 : 1 : 2 : 24 entities Detail

Related entities 2. protein comp2, : 1 : 3 : 81 entities Detail

Interaction partners 1. protein comp1, : 69 : 1 interactors Detail

More details for 70 interactors identified by 26 citations

Interaction partners 2. protein comp2, : 16 : 1 interactors Detail

More details for 17 interactors identified by 8 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	MES	[U-100% 15N]	25 mM
9	sodium chloride	natural abundance	300 mM
10	glycerol	natural abundance	1 %
11	protein_comp1	[U-100% 13C; U-100% 15N]	0.8 mM
12	protein_comp2	natural abundance	1.0 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	MES	[U-100% 15N]	25 mM
9	sodium chloride	natural abundance	300 mM
10	glycerol	natural abundance	1 %
11	protein_comp1	[U-100% 13C; U-100% 15N]	0.8 mM
12	protein_comp2	natural abundance	1.0 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

11 13C/15N filtered-C13 edited NOE

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	MES	natural abundance	25 mM
16	sodium chloride	natural abundance	300 mM
17	glycerol	natural abundance	1 %
18	protein_comp1	[U-100% 13C; U-100% 15N]	0.8 mM
19	protein_comp2	natural abundance	1.0 mM
20	D2O	natural abundance	100 %

12 13C/15N filtered-C13 edited NOE

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	MES	natural abundance	25 mM
22	sodium chloride	natural abundance	300 mM
23	glycerol	natural abundance	1 %
24	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
25	protein_comp1	natural abundance	1.0 mM
26	D2O	natural abundance	100 %

13 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	25 mM
2	sodium chloride	natural abundance	300 mM
3	glycerol	natural abundance	1 %
4	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
5	protein_comp1	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

14 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	MES	[U-100% 15N]	25 mM
9	sodium chloride	natural abundance	300 mM
10	glycerol	natural abundance	1 %
11	protein_comp1	[U-100% 13C; U-100% 15N]	0.8 mM
12	protein_comp2	natural abundance	1.0 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

15 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	MES	natural abundance	25 mM
16	sodium chloride	natural abundance	300 mM
17	glycerol	natural abundance	1 %
18	protein_comp1	[U-100% 13C; U-100% 15N]	0.8 mM
19	protein_comp2	natural abundance	1.0 mM
20	D2O	natural abundance	100 %

16 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	MES	natural abundance	25 mM
22	sodium chloride	natural abundance	300 mM
23	glycerol	natural abundance	1 %
24	protein_comp2	[U-100% 13C; U-100% 15N]	0.8 mM
25	protein_comp1	natural abundance	1.0 mM
26	D2O	natural abundance	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17702_2le8.nef
Input source #2: Coordindates	2le8.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----
APKASLRLGFSEYSRISNLIVLHLRKVEEEEDESALKRSELVNWYLKEIESEIDSEEELINKKRIIEKVIHRLTHYDHVLIELTQAGLKGSTEGSESYEE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
APKASLRLGFSEYSRISNLIVLHLRKVEEEEDESALKRSELVNWYLKEIESEIDSEEELINKKRIIEKVIHRLTHYDHVLIELTQAGLKGSTEGSESYEE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---110--------
DPYLVVNPNYLLED
||||||||||||||
DPYLVVNPNYLLED
-------110----

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

380-----390-------400--------
SALKGVSQDLLERIRAKEAQKQLAQMTRW
|||||||||||||||||||||||||||||
SALKGVSQDLLERIRAKEAQKQLAQMTRW
--------10--------20---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	114	0	0	100.0
B	B	29	0	0	100.0

Content subtype: combined_17702_2le8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1127		99.1 (chain: A, length: 114), 96.6 (chain: B, length: 29)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	2183 (1)	noe	95.6 (chain: A, length: 114), 69.0 (chain: B, length: 29)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	160 (160)	.	69.3 (chain: A, length: 114), 86.2 (chain: B, length: 29)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 99.1%
  - Entity_assembly_ID: B, Chain length: 29, Sequence coverage: 96.6%
- Total number of assignments
  - ¹H chemical shifts: 639
  - ¹³C chemical shifts: 363
  - ¹⁵N chemical shifts: 125
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	714	489	68.5
¹³C chemical shifts	535	282	52.7
¹⁵N chemical shifts	124	104	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	229	215	93.9
¹³C chemical shifts	228	109	47.8
¹⁵N chemical shifts	111	103	92.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	485	274	56.5
¹³C chemical shifts	307	173	56.4
¹⁵N chemical shifts	13	1	7.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	48	67.6
¹³C chemical shifts	71	47	66.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	11	25.6
¹³C chemical shifts	42	10	23.8
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	149	78.8
¹³C chemical shifts	132	81	61.4
¹⁵N chemical shifts	37	21	56.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	45	76.3
¹³C chemical shifts	58	23	39.7
¹⁵N chemical shifts	29	18	62.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	130	104	80.0
¹³C chemical shifts	74	58	78.4
¹⁵N chemical shifts	8	3	37.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0
¹³C chemical shifts	18	18	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	0	0.0
¹³C chemical shifts	5	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 95.6%
  - Entity_assembly_ID: B, Chain length: 29, Sequence coverage: 69.0%
- Total number of restraints: 2181
- Weight of restraints: 1.0 (2181)
- Potential type of restraints: square-well-parabolic (2181)
- Range of distance target values: 1.27, 3.4 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 69.3%
  - Entity_assembly_ID: B, Chain length: 29, Sequence coverage: 86.2%
- Total number of restraints: 160
- Total number of restraints per polymer type: 160
- Weight of restraints: 1.0 (160)
- Potential type of restraints: square-well-parabolic (160)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DNA replication

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Found 1 Document (3.306 seconds)

BMRB: 17702

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. protein comp1, : 1 : 1 : 2 : 24 entities Detail

Related entities 2. protein comp2, : 1 : 3 : 81 entities Detail

Interaction partners 1. protein comp1, : 69 : 1 interactors Detail

Interaction partners 2. protein comp2, : 16 : 1 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail