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BMRB: 25104

2MS4

CYCLOPHILIN A COMPLEXED WITH A FRAGMENT OF CRK-II

Authors

Jankowski, W., Saleh, T., Rossi, P., Kalodimos, C.

Assembly

CYCLOPHILIN A COMPLEXED WITH A FRAGMENT OF CRK-II

Entity

1. CYCLOPHILIN A COMPLEXED WITH A FRAGMENT OF CRK-II, entity 1 (polymer), 165 monomers, 18012.29 Da Detail

MVNPTVFFDI AVDGEPLGRV SFELFADKVP KTAENFRALS TGEKGFGYKG SCFHRIIPGF MCQGGDFTRH NGTGGKSIYG EKFEDENFIL KHTGPGILSM ANAGPNTNGS QFFICTAKTE WLDGKHVVFG KVKEGMNIVE AMERFGSRNG KTSKKITIAD CGQLE

2. CYCLOPHILIN A COMPLEXED WITH A FRAGMENT OF CRK-II, entity 2 (polymer, Thiol state: not present), 9 monomers, 955.0198 Da Detail

PEPGPYAQP

Total weight

18967.309 Da

Max. entity weight

18012.29 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 85.9 %, Completeness (bb): 93.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.9 % (1717 of 1999)	84.4 % (879 of 1042)	86.1 % (671 of 779)	93.8 % (167 of 178)
Backbone	93.5 % (957 of 1024)	94.8 % (343 of 362)	91.4 % (455 of 498)	97.0 % (159 of 164)
Sidechain	79.7 % (897 of 1125)	78.8 % (536 of 680)	81.9 % (353 of 431)	57.1 % (8 of 14)
Aromatic	74.8 % (151 of 202)	75.2 % (76 of 101)	74.0 % (74 of 100)	100.0 % (1 of 1)
Methyl	98.6 % (144 of 146)	98.6 % (72 of 73)	98.6 % (72 of 73)

1. entity 1

MVNPTVFFDI AVDGEPLGRV SFELFADKVP KTAENFRALS TGEKGFGYKG SCFHRIIPGF MCQGGDFTRH NGTGGKSIYG EKFEDENFIL KHTGPGILSM ANAGPNTNGS QFFICTAKTE WLDGKHVVFG KVKEGMNIVE AMERFGSRNG KTSKKITIAD CGQLE

2. entity 2

PEPGPYAQP

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MS4, Strand ID: A, B Detail

Release date

2015-09-09

Citation

STRUCTURAL BASIS FOR THE REGULATION OF CRKII BY CYCLOPHILIN A
Jankowski, W., Saleh, T., Rossi, P., Kalodimos, C.
Not known

Related entities 1. CYCLOPHILIN A COMPLEXED WITH A FRAGMENT OF CRK-II, entity 1, : 2 : 7 : 99 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

6 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

7 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.8 mM
2	H20	natural abundance		90 %
3	D20	natural abundance		10 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25104_2ms4.nef
Input source #2: Coordindates	2ms4.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
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM

-------110-------120-------130-------140-------150-------160-----
ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

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

--220----
PEPGPYAQP
|||||||||
PEPGPYAQP
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	165	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_25104_2ms4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1711		100.0 (chain: A, length: 165), 44.4 (chain: B, length: 9)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2958 (1)	noe	97.0 (chain: A, length: 165), 22.2 (chain: B, length: 9)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	2967 (1)	noe	97.0 (chain: A, length: 165), 44.4 (chain: B, length: 9)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	135 (1)	hbond	55.2 (chain: A, length: 165), 66.7 (chain: B, length: 9)
4	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	135 (1)	hbond	55.2 (chain: A, length: 165), 66.7 (chain: B, length: 9)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	364 (364)	.	97.0 (chain: A, length: 165)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	365 (365)	.	97.0 (chain: A, length: 165)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 44.4%
- Total number of assignments
  - ¹³C chemical shifts: 670
  - ¹H chemical shifts: 874
  - ¹⁵N chemical shifts: 167
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 97.0%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 22.2%
- Total number of restraints: 2958
- Weight of restraints: 1.0 (2958)
- Potential type of restraints: square-well-parabolic (2958)
- Range of distance target values: 2.36, 4.43 (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_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 97.0%
    - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 44.4%
  - Total number of restraints: 2967
  - Weight of restraints: 1.0 (2967)
  - Potential type of restraints: square-well-parabolic (2967)
  - Range of distance target values: 2.36, 4.43 (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: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 55.2%
      - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 66.7%
    - Total number of restraints: 135
    - Weight of restraints: 1.0 (135)
    - Potential type of restraints: square-well-parabolic (135)
    - Range of distance target values: 2.0, 3.05 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_7
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 55.2%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM | | |||||| | || ||||||| |||| |||||||||| | | | |||||| |||| || | | | | |||| ...P.V.FDIAVD.E.LG.VSFELFA.KVPK.AENFRALSTG..G..Y..S.FHRIIP..MCQG...........KS..G..F.......K.T..GILS. --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140-------150-------160----- ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE || | ||||| ||||| | ||| |||||||| ||| | | |||||| AN.....N..QFFIC...TEWLD.....F.KVK..MNIVEAME.FGS..G..S.KITIAD -------110-------120-------130-------140-------150-------160
        Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 66.7%
        --220---- PEPGPYAQP ||||| | .EPGPY.Q --220---
      - Total number of restraints: 135
        Long range restraints, | i - j | >= 5 : 1
        Total hydrogen bond restraints: 134
        O...H-x: 28
        O...h-N: 28
        Long range: 71
        O...h-N: 37
        O...H-x: 34
        Inter-chain: 7
        O...h-N: 7
      - Weight of restraints: 1.0 (135)
        Long range restraints, | i - j | >= 5 : 1.0 (1)
        Total hydrogen bond restraints: 1.0 (134)
        O...H-x: 1.0 (28)
        O...h-N: 1.0 (28)
        Long range: 1.0 (71)
        O...h-N: 1.0 (37)
        O...H-x: 1.0 (34)
        Inter-chain: 1.0 (7)
        O...h-N: 1.0 (7)
      - Potential type of restraints: square-well-parabolic (135)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (1)
        Total hydrogen bond restraints: square-well-parabolic (134)
        O...H-x: square-well-parabolic (28)
        O...h-N: square-well-parabolic (28)
        Long range: square-well-parabolic (71)
        O...h-N: square-well-parabolic (37)
        O...H-x: square-well-parabolic (34)
        Inter-chain: square-well-parabolic (7)
        O...h-N: square-well-parabolic (7)
      - Range of distance target values: 2.0, 3.05 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Chain_ID_1: B - Chain_ID_2: B
        None
        Chain_ID_1: A - Chain_ID_2: B

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 97.0%
- Total number of restraints: 364
- Total number of restraints per polymer type: 364
- Weight of restraints: 1.0 (364)
- Potential type of restraints: square-well-parabolic (364)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_6
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 97.0%
  - Total number of restraints: 365
  - Total number of restraints per polymer type: 365
  - Weight of restraints: 1.0 (365)
  - Potential type of restraints: square-well-parabolic (365)
  - Plot of Phi-Psi angle restraints
  - Plot of Chi1-Chi2 angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords CYCLOPHILIN A