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Found 1 Document (1.198 seconds)

BMRB: 15913

2K78

Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin

Authors

Villareal, V.A., Pilpa, R.M., Robson, S.A., Fadeev, E.A., Clubb, R.T.

Assembly

IsdC

Entity

1. IsdC (polymer, Thiol state: not present), 147 monomers, 16595.16 Da Detail

MGSSHHHHHH SSGLVPRGSH MSANAADSGT LNYEVYKYNT NDTSIANDYF NKPAKYIKKN GKLYVQITVN HSHWITGMSI EGHKENIISK NTAKDERTSE FEVSKLNGKI DGKIDVYIDE KVNGKPFKYD HHYNITYKFN GPTDVAG

2. ZNH (non-polymer), 626.051 Da

Total weight

17221.21 Da

Max. entity weight

16595.16 Da

Source organism

Staphylococcus aureus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.1 %, Completeness: 73.4 %, Completeness (bb): 85.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.4 % (1252 of 1706)	70.8 % (627 of 885)	74.3 % (492 of 662)	83.6 % (133 of 159)
Backbone	85.1 % (744 of 874)	85.4 % (258 of 302)	84.4 % (362 of 429)	86.7 % (124 of 143)
Sidechain	64.5 % (624 of 967)	63.3 % (369 of 583)	66.8 % (246 of 368)	56.3 % (9 of 16)
Aromatic	28.9 % (52 of 180)	34.4 % (31 of 90)	22.5 % (20 of 89)	100.0 % (1 of 1)
Methyl	92.7 % (115 of 124)	91.9 % (57 of 62)	93.5 % (58 of 62)

1. IsdC

MGSSHHHHHH SSGLVPRGSH MSANAADSGT LNYEVYKYNT NDTSIANDYF NKPAKYIKKN GKLYVQITVN HSHWITGMSI EGHKENIISK NTAKDERTSE FEVSKLNGKI DGKIDVYIDE KVNGKPFKYD HHYNITYKFN GPTDVAG

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	sodium azide	natural abundance	0.01 %
11	IsdC	natural abundance	1.1 mM
12	ZNH	natural abundance	2.3 mM
13	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 30 models in PDB: 2K78, Strand ID: A Detail

Release date

2008-08-13

Citation

The IsdC protein from Staphylococcus aureus uses a flexible binding pocket to capture heme
Villareal, V.A., Pilpa, R.M., Robson, S.A., Fadeev, E.A., Clubb, R.T.
J. Biol. Chem. (2008), 283, 31591-31600, PubMed 18715872 , DOI 10.1074/jbc.M801126200 , Abstract

Related entities 1. IsdC, : 1 : 3 : 7 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	sodium azide	natural abundance	0.01 %
11	IsdC	natural abundance	1.1 mM
12	ZNH	natural abundance	2.3 mM
13	D2O	natural abundance	100 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

4 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

5 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

6 3D HNHA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

7 3D HCCH-COSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	sodium azide	natural abundance	0.01 %
11	IsdC	natural abundance	1.1 mM
12	ZNH	natural abundance	2.3 mM
13	D2O	natural abundance	100 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	sodium azide	natural abundance	0.01 %
11	IsdC	natural abundance	1.1 mM
12	ZNH	natural abundance	2.3 mM
13	D2O	natural abundance	100 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

10 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

11 3D HNHB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 302 K, pH 6

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	sodium azide	natural abundance	0.01 %
4	IsdC	[U-100% 13C; U-100% 15N]	1.3 mM
5	ZNH	natural abundance	2.1 mM
6	D2O	[U-100% 2H]	7 %
7	H2O	natural abundance	93 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15913_2k78.nef
Input source #2: Coordindates	2k78.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZNH	PROTOPORPHYRIN IX CONTAINING ZN	Distance restraints

Sequence alignments

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

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

----110-------120-------130-------140-------150
FEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG
|||||||||||||||||||||||||||||||||||||||||||||||
FEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG
-------110-------120-------130-------140-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	147	0	0	100.0

Content subtype: combined_15913_2k78.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1225		85.0 (chain: A, length: 147)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2847 (1)	noe	84.4 (chain: A, length: 147)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	34 (1)	noe	8.2 (chain: A, length: 147), 100.0 (chain: B, length: 1)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	83 (1)	hbond	31.3 (chain: A, length: 147)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	208 (208)	.	77.6 (chain: A, length: 147)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 85.0%
- Total number of assignments
  - ¹H chemical shifts: 607
  - ¹³C chemical shifts: 488
  - ¹⁵N chemical shifts: 130
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	885	607	68.6
¹³C chemical shifts	662	488	73.7
¹⁵N chemical shifts	161	130	80.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	302	254	84.1
¹³C chemical shifts	294	244	83.0
¹⁵N chemical shifts	143	121	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	583	353	60.5
¹³C chemical shifts	368	244	66.3
¹⁵N chemical shifts	18	9	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	57	87.7
¹³C chemical shifts	65	58	89.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	27	30.0
¹³C chemical shifts	89	20	22.5
¹⁵N chemical shifts	1	1	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: 147, Sequence coverage: 84.4%
- Total number of restraints: 2818
- Weight of restraints: 1.0 (2818)
- Potential type of restraints: square-well-parabolic (2818)
- Range of distance target values: 2.1, 3.9 (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_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 8.2%
    - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
  - Total number of restraints: 34
  - Weight of restraints: 1.0 (34)
  - Potential type of restraints: square-well-parabolic (34)
  - Range of distance target values: 2.0, 3.6 (Å)
  - Histogram of 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: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 31.3%
    - Total number of restraints: 83
    - Weight of restraints: 1.0 (83)
    - Potential type of restraints: square-well-parabolic (83)
    - 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
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 77.6%
- Total number of restraints: 208
- Total number of restraints per polymer type: 208
- Weight of restraints: 1.0 (208)
- Potential type of restraints: square-well-parabolic (208)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords heme, Isd, IsdC, NEAT domain, NMR complex

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Found 1 Document (1.198 seconds)

BMRB: 15913

Sample #1

Sample #2

Related entities 1. IsdC, : 1 : 3 : 7 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 6 contents Detail