BMRBj - BMREntryMaster

Found 1 Document (0.842 seconds)

BMRB: 30777

7JH1

Solution structure of a reconstructed XCL1 ancestor

Authors

Tyler, R.C., Peterson, F.C., Volkman, B.F.

Assembly

XCL1 ancestor

Entity

1. XCL1 ancestor (polymer, Thiol state: all disulfide bound), 64 monomers, 7463.924 Da Detail

ARKSCCLKYT KRPLPLKRIK SYTIQSNEAC NIKAIIFTTK KGRKICANPN EKWVQKAMKH LDKK

Formula weight

7463.924 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS30:SG
2	disulfide	sing	1:CYS6:SG	1:CYS46:SG

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 86.6 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.6 % (709 of 819)	81.3 % (356 of 438)	93.5 % (289 of 309)	88.9 % (64 of 72)
Backbone	96.3 % (364 of 378)	96.0 % (121 of 126)	97.4 % (186 of 191)	93.4 % (57 of 61)
Sidechain	80.8 % (407 of 504)	75.3 % (235 of 312)	91.2 % (165 of 181)	63.6 % (7 of 11)
Aromatic	66.7 % (28 of 42)	66.7 % (14 of 21)	65.0 % (13 of 20)	100.0 % (1 of 1)
Methyl	96.8 % (60 of 62)	96.8 % (30 of 31)	96.8 % (30 of 31)

1. entity 1

ARKSCCLKYT KRPLPLKRIK SYTIQSNEAC NIKAIIFTTK KGRKICANPN EKWVQKAMKH LDKK

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-99% 13C; U-99% 15N] Anc.0, 20 mM sodium phosphate, 0.02 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	Anc.0	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %

Release date

2020-07-23

Citation

Evolution of fold switching in a metamorphic protein
Kleist, A.B., Prehoda, K.E., Babu, M.M., Peterson, F.C., Volkman, B.F., Dishman, A.F., Tyler, R.C., Fox, J.C.
Science (2021), 371, 86-90, PubMed 33384377 , DOI 10.1126/science.abd8700 , Abstract

Related entities 1. XCL1 ancestor, : 1 : 295 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30777_7jh1.nef
Input source #2: Coordindates	7jh1.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:5:CYS:SG	A:30:CYS:SG	oxidized, CA 55.572, CB 41.948 ppm	oxidized, CA 52.743, CB 42.142 ppm	2.031
A:6:CYS:SG	A:46:CYS:SG	oxidized, CA 56.766, CB 41.462 ppm	oxidized, CA 55.785, CB 43.501 ppm	2.035

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----
ARKSCCLKYTKRPLPLKRIKSYTIQSNEACNIKAIIFTTKKGRKICANPNEKWVQKAMKHLDKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ARKSCCLKYTKRPLPLKRIKSYTIQSNEACNIKAIIFTTKKGRKICANPNEKWVQKAMKHLDKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	64	0	0	100.0

Content subtype: combined_30777_7jh1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	709		98.4 (chain: A, length: 64)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1256 (1)	noe	93.8 (chain: A, length: 64)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	6 (1)	undefined	6.2 (chain: A, length: 64)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	92 (92)	.	93.8 (chain: A, length: 64)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 356
  - ¹³C chemical shifts: 289
  - ¹⁵N chemical shifts: 64
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	438	356	81.3
¹³C chemical shifts	309	289	93.5
¹⁵N chemical shifts	72	64	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	121	96.0
¹³C chemical shifts	128	124	96.9
¹⁵N chemical shifts	61	57	93.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	235	75.3
¹³C chemical shifts	181	165	91.2
¹⁵N chemical shifts	11	7	63.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	31	96.9
¹³C chemical shifts	32	31	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	14	66.7
¹³C chemical shifts	20	13	65.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 93.8%
- Total number of restraints: 1256
- Weight of restraints: 1.0 (1256)
- Potential type of restraints: upper-bound-parabolic (1256)
- Range of distance target values: 2.18, 5.5 (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
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 6.2%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 93.8%
- Total number of restraints: 92
- Total number of restraints per polymer type: 92
- Weight of restraints: 1.0 (92)
- Potential type of restraints: square-well-parabolic (92)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CYTOKINE, ancestral reconstruction, chemokine, metamorphic protein

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Found 1 Document (0.842 seconds)

BMRB: 30777

Sample

Related entities 1. XCL1 ancestor, : 1 : 295 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail