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Found 1 Document (0.774 seconds)

BMRB: 16024

2KAJ

NMR structrure of gallium subsituted ferredoxin

Authors

Xu, X., Ubbink, M., Knaff, D.B.

Assembly

Ga-substituted Ferredoxin

Entity

1. Ferredoxin (polymer, Thiol state: free and other bound), 96 monomers, 10231.99 Da Detail

ASYTVKLITP DGESSIECSD DTYILDAAEE AGLDLPYSCR AGACSTCAGK ITAGSVDQSD QSFLDDDQIE AGYVLTCVAY PTSDCTIETH KEEDLY

2. GA (non-polymer), 69.723 Da

Total weight

10301.713 Da

Max. entity weight

10231.99 Da

Source organism

Synechocystis sp. PCC 6803

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.7 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	98.7 % (590 of 598)	98.6 % (495 of 502)	99.0 % (95 of 96)
Backbone	99.0 % (285 of 288)	99.0 % (193 of 195)	98.9 % (92 of 93)
Sidechain	98.4 % (305 of 310)	98.4 % (302 of 307)	100.0 % (3 of 3)
Aromatic	90.3 % (28 of 31)	90.3 % (28 of 31)
Methyl	98.1 % (52 of 53)	98.1 % (52 of 53)

1. Ferredoxin

ASYTVKLITP DGESSIECSD DTYILDAAEE AGLDLPYSCR AGACSTCAGK ITAGSVDQSD QSFLDDDQIE AGYVLTCVAY PTSDCTIETH KEEDLY

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GaFd	[U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM

Sample #2

Solvent system 99%D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
3	GaFd	natural abundance		2 mM
4	sodium phosphate	natural abundance		50 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2KAJ, Strand ID: A Detail

Release date

2010-07-26

Citation

Structural and functional characterization of the ga-substituted ferredoxin from Synechocystis sp. PCC6803, a mimic of the native protein
Xu, X., Scanu, S., Chung, J., Hirasawa, M., Knaff, D.B., Ubbink, M.
Biochemistry (2010), 49, 7790-7797, PubMed 20690702 , DOI 10.1021/bi100712g , Abstract

Related entities 1. Ferredoxin, : 1 : 5 : 3 : 210 entities Detail

Interaction partners 1. Ferredoxin, : 4 interactors Detail

More details for 4 interactors identified by 4 citations

Experiments performed 5 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16024_2kaj.nef
Input source #2: Coordindates	2kaj.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)
1:44:CYS:SG	2:1:GA:GA	unknown	unknown	n/a
1:47:CYS:SG	2:1:GA:GA	unknown	unknown	n/a
1:77:CYS:SG	2:1:GA:GA	unknown	unknown	n/a
1:39:CYS:SG	2:1:GA:GA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	GA	GALLIUM (III) ION	Distance restraints

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90------
ASYTVKLITPDGESSIECSDDTYILDAAEEAGLDLPYSCRAGACSTCAGKITAGSVDQSDQSFLDDDQIEAGYVLTCVAYPTSDCTIETHKEEDLY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ASYTVKLITPDGESSIECSDDTYILDAAEEAGLDLPYSCRAGACSTCAGKITAGSVDQSDQSFLDDDQIEAGYVLTCVAYPTSDCTIETHKEEDLY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0

Content subtype: combined_16024_2kaj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	590		100.0 (chain: A, length: 96)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	4 (1)	undefined	4.2 (chain: A, length: 96), 100.0 (chain: B, length: 1)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2763 (1)	noe	100.0 (chain: A, length: 96)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	17 (1)	noe	22.9 (chain: A, length: 96)
4	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	4 (1)	undefined	4.2 (chain: A, length: 96), 100.0 (chain: B, length: 1)
5	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	36 (1)	hbond	26.0 (chain: A, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 494
  - ¹⁵N chemical shifts: 96
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
90	HIS	HD1	7.058

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	502	493	98.2
¹⁵N chemical shifts	97	96	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	195	193	99.0
¹⁵N chemical shifts	93	92	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	307	300	97.7
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	52	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	28	90.3

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 4.2%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 4
- Weight of restraints: 1.0 (4)
- Potential type of restraints: upper-bound-parabolic (4)
- Range of distance target values: 2.2, 2.2 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 100.0%
  - Total number of restraints: 2763
  - Weight of restraints: 1.0 (2763)
  - Potential type of restraints: upper-bound-parabolic (2763)
  - Range of distance target values: 2.52, 6.72 (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
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 22.9%
    - Total number of restraints: 17
    - Weight of restraints: 1.0 (17)
    - Potential type of restraints: upper-bound-parabolic (17)
    - Range of distance target values: 4.5, 5.5 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_5
      - Status: Warning
      - Experiment type: undefined
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 4.2%
        Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
        - X | X
      - Total number of restraints: 4
        Total other bond restraints: 4
      - Weight of restraints: 1.0 (4)
        Total other bond restraints: 1.0 (4)
      - Potential type of restraints: upper-bound-parabolic (4)
        Total other bond restraints: upper-bound-parabolic (4)
      - Range of distance target values: 2.4, 2.4 (Å)
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
      - Distance restraints on contact map
        Chain_ID_1: B - Chain_ID_2: B
        None
      - Saveframe: DYANA/DIANA_distance_constraints_4
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 26.0%
        Total number of restraints: 36
        Total hydrogen bond restraints: 36
        O...H-x: 3
        O...h-N: 3
        Long range: 30
        O...H-x: 15
        O...h-N: 15
        Weight of restraints: 1.0 (36)
        Total hydrogen bond restraints: 1.0 (36)
        O...H-x: 1.0 (3)
        O...h-N: 1.0 (3)
        Long range: 1.0 (30)
        O...H-x: 1.0 (15)
        O...h-N: 1.0 (15)
        Potential type of restraints: upper-bound-parabolic (36)
        Total hydrogen bond restraints: upper-bound-parabolic (36)
        O...H-x: upper-bound-parabolic (3)
        O...h-N: upper-bound-parabolic (3)
        Long range: upper-bound-parabolic (30)
        O...H-x: upper-bound-parabolic (15)
        O...h-N: upper-bound-parabolic (15)
        Range of distance target values: 2.4, 3.3 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Distance restraints on contact map

Keywords ferredoxin, iron-sulfur

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Found 1 Document (0.774 seconds)

BMRB: 16024

Sample #1

Sample #2

Related entities 1. Ferredoxin, : 1 : 5 : 3 : 210 entities Detail

Interaction partners 1. Ferredoxin, : 4 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail