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BMRB: 17995

2LKI

Solution NMR structure of holo acyl carrier protein NE2163 from nitrosomonas europaea. Northeast structural genomics consortium target NET1

Authors

Lemak, A., Srisailam, S., Lukin, J., Yee, A., Montecchio, M., Semesi, A., Arrowsmith, C.

Assembly

NE2163

Entity

1. NE2163 (polymer, Thiol state: not present), 105 monomers, 11730.90 Da Detail

MGSSHHHHHH SSGRENLYFQ GHMQHLEAVR NILGDVLNLG ERKHTLTASS VLLGNIPELD SMAVVNVITA LEEYFDFSVD DDEISAQTFE TLGSLALFVE HKLSH

2. PNS (non-polymer, Thiol state: not present), 358.348 Da

Total weight

12089.248 Da

Max. entity weight

11730.9 Da

Source organism

Nitrosomonas europaea

Exptl. method

Refine. method

restrained molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 82.9 %, Completeness: 75.9 %, Completeness (bb): 79.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.9 % (899 of 1185)	75.0 % (452 of 603)	76.4 % (359 of 470)	78.6 % (88 of 112)
Backbone	79.5 % (499 of 628)	77.3 % (167 of 216)	81.2 % (250 of 308)	78.8 % (82 of 104)
Sidechain	73.4 % (481 of 655)	73.6 % (285 of 387)	73.1 % (190 of 260)	75.0 % (6 of 8)
Aromatic	35.5 % (39 of 110)	43.6 % (24 of 55)	27.3 % (15 of 55)
Methyl	94.4 % (119 of 126)	92.1 % (58 of 63)	96.8 % (61 of 63)

1. NE2163

MGSSHHHHHH SSGRENLYFQ GHMQHLEAVR NILGDVLNLG ERKHTLTASS VLLGNIPELD SMAVVNVITA LEEYFDFSVD DDEISAQTFE TLGSLALFVE HKLSH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2011-11-16

Citation

Solution structure of acyl carrier protein from Nitrosomonas europaea
Srisailam, S., Lukin, J., Yee, A., Semesi, A., Arrowsmith, C.
Proteins (2006), 64, 800-803, PubMed 16741959 , DOI 10.1002/prot.21016 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 6769 released on 2007-02-05
Title Complete assignments of a hypothetical protein NE2066, from Nitrosomonas_europaea. Northeast Structural Genomics Consortium Target NeT1.

Related entities 1. NE2163, : 1 : 4 entities Detail

Experiments performed 12 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

6 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

10 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

11 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

12 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NE2163	[U-13C; U-15N]		1.0 mM
2	MOPS	natural abundance		10 mM
3	sodium chloride	natural abundance		450 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17995_2lki.nef
Input source #2: Coordindates	2lki.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)
1:61:SER:OG	2:1:PNS:P24	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	PNS	4'-PHOSPHOPANTETHEINE	Assigned chemical shifts, Distance restraints

Sequence alignments

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

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

80---
HKLSH
|||||
HKLSH
-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0

Content subtype: combined_17995_2lki.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	908		79.0 (chain: A, length: 105), 100.0 (chain: B, length: 1)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2453 (1)	noe	79.0 (chain: A, length: 105), 100.0 (chain: B, length: 1)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	39 (1)	noe	5.7 (chain: A, length: 105), 100.0 (chain: B, length: 1)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	28 (1)	hbond	29.5 (chain: A, length: 105)
4	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	66 (1)	hbond	46.7 (chain: A, length: 105)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	146 (146)	.	79.0 (chain: A, length: 105)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_7	OK	54 (54)	.	51.4 (chain: A, length: 105)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 79.0%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 468
  - ¹³C chemical shifts: 354
  - ¹⁵N chemical shifts: 86
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 79.0%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 2453
- Weight of restraints: 1.0 (2453)
- Potential type of restraints: square-well-parabolic (2453)
- Range of distance target values: 2.25, 3.9 (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: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 5.7%
    - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 2.65, 6.25 (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: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 29.5%
    - Total number of restraints: 28
    - Weight of restraints: 1.0 (28)
    - Potential type of restraints: square-well-parabolic (28)
    - Range of distance target values: 1.95, 3.38 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_6
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 46.7%
      - Total number of restraints: 66
        Total hydrogen bond restraints: 66
        O...H-x: 33
        O...h-N: 33
      - Weight of restraints: 1.0 (66)
        Total hydrogen bond restraints: 1.0 (66)
        O...H-x: 1.0 (33)
        O...h-N: 1.0 (33)
      - Potential type of restraints: square-well-parabolic (66)
        Total hydrogen bond restraints: square-well-parabolic (66)
        O...H-x: square-well-parabolic (33)
        O...h-N: square-well-parabolic (33)
      - Range of distance target values: 1.95, 3.2 (Å)
      - Histogram of 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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 79.0%
- Total number of restraints: 146
- Total number of restraints per polymer type: 146
- Weight of restraints: 1.0 (146)
- Potential type of restraints: square-well-parabolic (146)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_7

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 51.4%

------------------------------10--------20--------30--------40--------50--------60--------70--------
MGSSHHHHHHSSGRENLYFQGHMQHLEAVRNILGDVLNLGERKHTLTASSVLLGNIPELDSMAVVNVITALEEYFDFSVDDDEISAQTFETLGSLALFVE
                          |  |||||| |||| |  ||||  |||||| |||| |||||||| |||| || |||| | ||||| | | ||  
..........................E..RNILGD.LNLG.R..TLTA..VLLGNI.ELDS.AVVNVITA.EEYF.FS.DDDE.S.QTFET.G.L.LF  
------------------------------10--------20--------30--------40--------50--------60--------70------  

80---
HKLSH

Total number of restraints: 54
Potential type of restraints: undefined (54)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords acyl carrier, fatty acid biosynthesis, helical bundle, lipid synthesis, phosphopantetheine