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Found 1 Document (5.372 seconds)

BMRB: 25502

2MZU

Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals

Authors

Chi, C.N., Strotz, D., Riek, R., Voegeli, B.

Assembly

Peptidyl-prolyl cis-trans isomerase A

Entity

1. Peptidyl-prolyl cis-trans isomerase A, entity 1 (polymer, Thiol state: free and disulfide bound), 165 monomers, 18012.29 Da Detail

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

2. 4-[(E)-(4-hydroxynaphthalen-1-yl)diazenyl]benzenesulfonic acid (non-polymer), 328.342 Da

Total weight

18340.63 Da

Max. entity weight

18012.29 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 84.5 %, Completeness (bb): 84.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.5 % (1603 of 1897)	95.7 % (944 of 986)	66.0 % (488 of 739)	99.4 % (171 of 172)
Backbone	84.4 % (825 of 978)	97.1 % (337 of 347)	69.9 % (330 of 472)	99.4 % (158 of 159)
Sidechain	86.1 % (913 of 1061)	95.0 % (607 of 639)	71.6 % (293 of 409)	100.0 % (13 of 13)
Aromatic	46.9 % (91 of 194)	86.6 % (84 of 97)	6.3 % (6 of 96)	100.0 % (1 of 1)
Methyl	88.9 % (128 of 144)	97.2 % (70 of 72)	80.6 % (58 of 72)

1. entity 1

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

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1.5 mM
2	sodium phosphate	natural abundance		150 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.0
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.0

Referencing offset: 0.33 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.0
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.0

Referencing offset: 0.33 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.0
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.0

Referencing offset: -0.09 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2015-04-19

Citation

Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals
Chi, C.N., Strotz, D., Riek, R., Voegeli, B.
J. Biomol. NMR (2015), 62, 63-69, PubMed 25749872 , DOI 10.1007/s10858-015-9917-8 , Abstract

Related entities 1. Peptidyl-prolyl cis-trans isomerase A, entity 1, : 1 : 102 : 7 : 198 entities Detail

Interaction partners 1. Peptidyl-prolyl cis-trans isomerase A, entity 1, : 83 interactors Detail

More details for 83 interactors identified by 34 citations

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25502_2mzu.nef
Input source #2: Coordindates	2mzu.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

Chain assignments

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

Content subtype: combined_25502_2mzu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1595		100.0 (chain: A, length: 165)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	281 (1)	noe	83.0 (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%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM

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

Total number of assignments
- ¹H chemical shifts: 977
- ¹³C chemical shifts: 445
- ¹⁵N chemical shifts: 173

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
32	THR	HG1	7.753
40	SER	HG	3.437
41	THR	HG1	6.692
51	SER	HG	4.885
62	CYS	HG	1.618
73	THR	HG1	5.773
77	SER	HG	5.102
92	HIS	HD1	12.134
107	THR	HG1	4.673
110	SER	HG	4.926
119	THR	HG1	3.054
126	HIS	HD1	8.175
152	THR	HG1	5.012

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	986	964	97.8
¹³C chemical shifts	739	445	60.2
¹⁵N chemical shifts	178	173	97.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	347	344	99.1
¹³C chemical shifts	330	164	49.7
¹⁵N chemical shifts	159	156	98.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	639	620	97.0
¹³C chemical shifts	409	281	68.7
¹⁵N chemical shifts	19	17	89.5

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	77	100.0
¹³C chemical shifts	77	58	75.3

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	82	84.5
¹³C chemical shifts	96	0	0.0
¹⁵N chemical shifts	1	1	100.0

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: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 83.0%
- Total number of restraints: 281
- Weight of restraints: 1.0 (281)
- Potential type of restraints: upper-bound-parabolic (281)
- Range of distance target values: 0.0, 10.35 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Cyclophilin A

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Found 1 Document (5.372 seconds)

BMRB: 25502

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Peptidyl-prolyl cis-trans isomerase A, entity 1, : 1 : 102 : 7 : 198 entities Detail

Interaction partners 1. Peptidyl-prolyl cis-trans isomerase A, entity 1, : 83 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail