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BMRB: 25284

2MVU

Solution Structure of the 3,7-dioxo-octyl Actinorhodin Acyl Carrier Protein from Streptomyces coelicolor

Authors

Dong, X., Bailey, C., Williams, C., Crosby, J., Simpson, T.J., Willis, C.L., Crump, M.P.

Assembly

3,7-dioxo-octyl Actinorhodin Acyl Carrier Protein

Entity

1. 3,7-dioxo-octyl Actinorhodin Acyl Carrier Protein, entity (polymer, Thiol state: not present), 86 monomers, 9232.119 Da Detail

MATLLTTDDL RRALVESAGE TDGTDLSGDF LDLRFEDIGY DSLALMETAA RLESRYGVSI PDDVAGRVDT PRELLDLING ALAEAA

2. 3,7-dioxo-octyl Actinorhodin Acyl Carrier Protein, entity SDO (non-polymer), 482.529 Da

Total weight

9714.648 Da

Max. entity weight

9232.119 Da

Entity Connection

covalent 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	1:SER42:OG	2:SDO1:P24

Source organism

Streptomyces coelicolor

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 93.9 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.9 % (855 of 911)	93.3 % (431 of 462)	93.7 % (341 of 364)	97.6 % (83 of 85)
Backbone	98.0 % (502 of 512)	97.7 % (173 of 177)	98.4 % (247 of 251)	97.6 % (82 of 84)
Sidechain	90.2 % (431 of 478)	90.5 % (258 of 285)	89.6 % (172 of 192)	100.0 % (1 of 1)
Aromatic	11.1 % (4 of 36)	11.1 % (2 of 18)	11.1 % (2 of 18)
Methyl	99.2 % (119 of 120)	98.3 % (59 of 60)	100.0 % (60 of 60)

1. entity

MATLLTTDDL RRALVESAGE TDGTDLSGDF LDLRFEDIGY DSLALMETAA RLESRYGVSI PDDVAGRVDT PRELLDLING ALAEAA

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

Protein Blocks Logo

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

Release date

2015-10-18

Citation

ACP-ligand recognition: Selection of derivatized aromatic biosynthetic intermediates
Dong, X., Bailey, C., Williams, C., Crosby, J., Simpson, T.J., Willis, C.L., Crump, M.P.
Org. Biomol. Chem.

Related entities 1. 3,7-dioxo-octyl Actinorhodin Acyl Carrier Protein, entity, : 1 : 10 : 3 : 64 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

2 3D CBCA(CO)NH

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

3 3D CBCA(CO)NH

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

4 3D HNCO

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

5 3D HNCA

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

6 3D HNCACB

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

7 3D C(CO)NH

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

8 3D 1H-15N NOESY

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

9 3D 1H-13C NOESY

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

10 3D H(CCO)NH

Instrument

Agilent Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.5 (±0.2) mM
2	potassium phosphate	natural abundance		20 (±2.0) mM
3	H2O	natural abundance		95 (±1.0) %
4	D2O	natural abundance		5 (±1.0) %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25284_2mvu.nef
Input source #2: Coordindates	2mvu.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:42:SER:OG	2:1:SDO:P24	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	SDO	N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide	Assigned chemical shifts

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80------
MATLLTTDDLRRALVESAGETDGTDLSGDFLDLRFEDIGYDSLALMETAARLESRYGVSIPDDVAGRVDTPRELLDLINGALAEAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MATLLTTDDLRRALVESAGETDGTDLSGDFLDLRFEDIGYDSLALMETAARLESRYGVSIPDDVAGRVDTPRELLDLINGALAEAA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	86	0	0	100.0

Content subtype: combined_25284_2mvu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	874		98.8 (chain: A, length: 86), 100.0 (chain: B, length: 1)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	3621 (1)	noe	98.8 (chain: A, length: 86)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	117 (117)	.	81.4 (chain: A, length: 86)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 98.8%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 449
  - ¹³C chemical shifts: 339
  - ¹⁵N chemical shifts: 86
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 98.8%
- Total number of restraints: 3576
- Weight of restraints: 1.0 (3576)
- Potential type of restraints: square-well-parabolic (3576)
- Range of distance target values: 1.75, 6.2 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- 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: 86, Sequence coverage: 81.4%
- Total number of restraints: 117
- Total number of restraints per polymer type: 117
- Weight of restraints: 1.0 (117)
- Potential type of restraints: square-well-parabolic (117)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ACP, Actinorhodin, biosynthetic intermediates, ligand recognition