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Found 1 Document (0.563 seconds)

BMRB: 30295

5VTO

Solution Structure of BlsM

Authors

Kang, M., Doddapaneni, K., Heppner, Z., Wu, Z.

Assembly

Blasticidin M

Entity

1. Blasticidin M (polymer), 163 monomers, 17838.24 × 2 Da Detail

KAGVRSVFLA GPFMGLVNPE TNSMPSAEQL PFLTLIEHFE KQGLEVFNAH RREAWGAQVL TPEECTPLDQ LEIRKADVFV AIPGIPPSPG THVEIGWASA FDKPIVLLLE EGREEEYGFL VRGLGTVAAV EFVHYKDIAL AKPQIDAAIR KVVDRVNNPA ATP

Total weight

35676.48 Da

Max. entity weight

17838.24 Da

Source organism

Streptomyces griseochromogenes

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 80.4 %, Completeness (bb): 93.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.4 % (1516 of 1885)	76.6 % (747 of 975)	84.0 % (629 of 749)	87.0 % (140 of 161)
Backbone	93.2 % (885 of 950)	92.6 % (300 of 324)	93.7 % (447 of 477)	92.6 % (138 of 149)
Sidechain	71.6 % (778 of 1086)	68.7 % (447 of 651)	77.8 % (329 of 423)	16.7 % (2 of 12)
Aromatic	26.0 % (38 of 146)	49.3 % (36 of 73)	0.0 % (0 of 71)	100.0 % (2 of 2)
Methyl	99.0 % (208 of 210)	99.0 % (104 of 105)	99.0 % (104 of 105)

1. entity 1

KAGVRSVFLA GPFMGLVNPE TNSMPSAEQL PFLTLIEHFE KQGLEVFNAH RREAWGAQVL TPEECTPLDQ LEIRKADVFV AIPGIPPSPG THVEIGWASA FDKPIVLLLE EGREEEYGFL VRGLGTVAAV EFVHYKDIAL AKPQIDAAIR KVVDRVNNPA ATP

Show sample condition

Sample #1

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 25 mM sodium phosphate, 2 mM DTT, 25 mM sodium chloride, 2 mM beta-mercaptoethanol, 0.02 % sodium azide, 0.8 mM [U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	25 mM
4	beta-mercaptoethanol	natural abundance	2 mM
5	sodium azide	natural abundance	0.02 %
6	Blasticidin M	[U-15N]	0.8 mM

Sample #2

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.02 % sodium azide, 0.8 mM [U-13C; U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
7	sodium azide	natural abundance		0.02 %
8	Blasticidin M	[U-13C; U-15N]		0.8 mM

Sample #3

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.8 mM [U-100% 13C; U-100% 15N; U-95% 2H] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
9	Blasticidin M	[U-100% 13C; U-100% 15N; U-95% 2H]		0.8 mM

Sample #4

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.8 mM [U-10% 13C; U-100% 15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
10	Blasticidin M	[U-10% 13C; U-100% 15N]		0.8 mM

Sample #5

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 1.25 mM [U-15N] Blasticidin M, 1.25 mM [U-13C; U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
11	Blasticidin M	[U-15N]		1.25 mM
12	Blasticidin M	[U-13C; U-15N]		1.25 mM

Sample #6

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.8 mM [U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
13	Blasticidin M	[U-15N]		0.8 mM

Release date

2018-04-26

Citation

Solution structure of the nucleotide hydrolase BlsM: Implication of its substrate specificity
Kang, M., Doddapaneni, K., Sarni, S., Heppner, Z., Wysocki, V., Wu, Z.
Protein Sci. (2020), 29, 1760-1773, PubMed 31876335 , DOI 10.1002/pro.3812 , Abstract

Related entities 1. Blasticidin M, : 1 : 6 entities Detail

Experiments performed 11 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.8 mM [U-100% 13C; U-100% 15N; U-95% 2H] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
9	Blasticidin M	[U-100% 13C; U-100% 15N; U-95% 2H]		0.8 mM

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	Blasticidin M	[U-100% 13C; U-100% 15N; U-95% 2H]		0.8 mM

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	Blasticidin M	[U-100% 13C; U-100% 15N; U-95% 2H]		0.8 mM

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	Blasticidin M	[U-100% 13C; U-100% 15N; U-95% 2H]		0.8 mM

5 3D HN(COCA)CB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	Blasticidin M	[U-100% 13C; U-100% 15N; U-95% 2H]		0.8 mM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.02 % sodium azide, 0.8 mM [U-13C; U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
7	sodium azide	natural abundance		0.02 %
8	Blasticidin M	[U-13C; U-15N]		0.8 mM

7 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.8 mM [U-10% 13C; U-100% 15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
10	Blasticidin M	[U-10% 13C; U-100% 15N]		0.8 mM

8 3D 15N NOESY-TROSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 25 mM sodium phosphate, 2 mM DTT, 25 mM sodium chloride, 2 mM beta-mercaptoethanol, 0.02 % sodium azide, 0.8 mM [U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	25 mM
4	beta-mercaptoethanol	natural abundance	2 mM
5	sodium azide	natural abundance	0.02 %
6	Blasticidin M	[U-15N]	0.8 mM

9 3D HMQC-NOESY-HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	sodium azide	natural abundance		0.02 %
8	Blasticidin M	[U-13C; U-15N]		0.8 mM

10 3D 15N/13C-filtered 13C-edited NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 1.25 mM [U-15N] Blasticidin M, 1.25 mM [U-13C; U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
11	Blasticidin M	[U-15N]		1.25 mM
12	Blasticidin M	[U-13C; U-15N]		1.25 mM

11 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 308 (±0.1) K, pH 6.50 (±0.05), Details 0.8 mM [U-15N] Blasticidin M, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
13	Blasticidin M	[U-15N]		0.8 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30295_5vto.nef
Input source #2: Coordindates	5vto.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

-------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-
KAGVRSVFLAGPFMGLVNPETNSMPSAEQLPFLTLIEHFEKQGLEVFNAHRREAWGAQVLTPEECTPLDQLEIRKADVFVAIPGIPPSPGTHVEIGWASA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KAGVRSVFLAGPFMGLVNPETNSMPSAEQLPFLTLIEHFEKQGLEVFNAHRREAWGAQVLTPEECTPLDQLEIRKADVFVAIPGIPPSPGTHVEIGWASA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------120-------130-------140-------150-------160-------170----
FDKPIVLLLEEGREEEYGFLVRGLGTVAAVEFVHYKDIALAKPQIDAAIRKVVDRVNNPAATP
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FDKPIVLLLEEGREEEYGFLVRGLGTVAAVEFVHYKDIALAKPQIDAAIRKVVDRVNNPAATP
-------110-------120-------130-------140-------150-------160---

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

------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-
KAGVRSVFLAGPFMGLVNPETNSMPSAEQLPFLTLIEHFEKQGLEVFNAHRREAWGAQVLTPEECTPLDQLEIRKADVFVAIPGIPPSPGTHVEIGWASA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KAGVRSVFLAGPFMGLVNPETNSMPSAEQLPFLTLIEHFEKQGLEVFNAHRREAWGAQVLTPEECTPLDQLEIRKADVFVAIPGIPPSPGTHVEIGWASA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------320-------330-------340-------350-------360-------370----
FDKPIVLLLEEGREEEYGFLVRGLGTVAAVEFVHYKDIALAKPQIDAAIRKVVDRVNNPAATP
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FDKPIVLLLEEGREEEYGFLVRGLGTVAAVEFVHYKDIALAKPQIDAAIRKVVDRVNNPAATP
-------110-------120-------130-------140-------150-------160---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	163	0	0	100.0
B	B	163	0	0	100.0

Content subtype: combined_30295_5vto.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1476		98.8 (chain: A, length: 163)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3928 (1)	noe	94.5 (chain: A, length: 163), 94.5 (chain: B, length: 163)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	348 (1)	hbond	73.6 (chain: A, length: 163), 73.6 (chain: B, length: 163)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	350 (350)	.	66.3 (chain: A, length: 163), 65.6 (chain: B, length: 163)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 163, Sequence coverage: 98.8%
- Total number of assignments
  - ¹H chemical shifts: 715
  - ¹³C chemical shifts: 621
  - ¹⁵N chemical shifts: 140
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
110	SER	HG	5.13

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	975	713	73.1
¹³C chemical shifts	749	621	82.9
¹⁵N chemical shifts	169	140	82.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	324	297	91.7
¹³C chemical shifts	326	297	91.1
¹⁵N chemical shifts	149	138	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	651	416	63.9
¹³C chemical shifts	423	324	76.6
¹⁵N chemical shifts	20	2	10.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	105	98.1
¹³C chemical shifts	107	106	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	33	45.2
¹³C chemical shifts	71	0	0.0
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 163, Sequence coverage: 94.5%
  - Entity_assembly_ID: B, Chain length: 163, Sequence coverage: 94.5%
- Total number of restraints: 3902
- Weight of restraints: 1.0 (3902)
- Potential type of restraints: square-well-parabolic (3902)
- Range of distance target values: 2.25, 4.4 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 163, Sequence coverage: 73.6%
    - Entity_assembly_ID: B, Chain length: 163, Sequence coverage: 73.6%
  - Total number of restraints: 348
  - Weight of restraints: 1.0 (348)
  - Potential type of restraints: square-well-parabolic (348)
  - Range of distance target values: 1.9, 2.9 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 163, Sequence coverage: 66.3%
  - Entity_assembly_ID: B, Chain length: 163, Sequence coverage: 65.6%
- Total number of restraints: 350
- Total number of restraints per polymer type: 350
- Weight of restraints: 1.0 (350)
- Potential type of restraints: square-well-parabolic (350)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Deaminase, biosynthesis, cytosine, hydrolase

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Found 1 Document (0.563 seconds)

BMRB: 30295

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Related entities 1. Blasticidin M, : 1 : 6 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail