BMRBj - BMREntryMaster

Found 1 Document (1.013 seconds)

BMRB: 30231

5UJ5

Solution structure of the oxidized iron-sulfur protein adrenodoxin from Encephalitozoon cuniculi. Seattle Structural Genomics Center for Infectious Disease target EncuA.00705.a

Authors

Buchko, G.W., Seattle Structural Genomics Center for Infectious Disease (SSGCID), S.

Assembly

Adrenodoxin

Entity

1. Adrenodoxin, entity 1 (polymer), 132 monomers, 14358.32 Da Detail

GPGSMDMFSA PDRIPEQIRI FFKTMKQVVP AKAVCGSTVL DVAHKNGVDL EGACEGNLAC STCHVILEEP LYRKLGEPSD KEYDLIDQAF GATGTSRLGC QLRVDKSFEN AVFTVPRATK NMAVDGFKPK PH

2. Adrenodoxin, entity FES (non-polymer), 175.820 Da

Total weight

14534.141 Da

Max. entity weight

14358.32 Da

Source organism

Encephalitozoon cuniculi

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.4 %, Completeness: 70.9 %, Completeness (bb): 79.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	70.9 % (1058 of 1493)	64.4 % (500 of 777)	76.9 % (450 of 585)	82.4 % (108 of 131)
Backbone	79.3 % (614 of 774)	71.4 % (190 of 266)	83.1 % (320 of 385)	84.6 % (104 of 123)
Sidechain	65.6 % (551 of 840)	60.7 % (310 of 511)	73.8 % (237 of 321)	50.0 % (4 of 8)
Aromatic	49.0 % (48 of 98)	49.0 % (24 of 49)	49.0 % (24 of 49)
Methyl	81.6 % (111 of 136)	80.9 % (55 of 68)	82.4 % (56 of 68)

1. entity 1

GPGSMDMFSA PDRIPEQIRI FFKTMKQVVP AKAVCGSTVL DVAHKNGVDL EGACEGNLAC STCHVILEEP LYRKLGEPSD KEYDLIDQAF GATGTSRLGC QLRVDKSFEN AVFTVPRATK NMAVDGFKPK PH

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.1), Details 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] E5, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.3 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5UJ5, Strand ID: A Detail

Release date

2017-01-23

Citation

Solution structure for an Encephalitozoon cuniculi adrenodoxin-like protein in the oxidized state
Shaheen, S., Barrett, K.F., Subramanian, S., Arnold, S., Laureanti, J.A., Myler, P.J., Van Voorhis, W.C., Buchko, G.W.
Protein Sci. (2020), 29, 809-817, PubMed 31912584 , DOI 10.1002/pro.3818 , Abstract

Related entities 1. Adrenodoxin, entity 1, : 1 : 1 : 39 entities Detail

Experiments performed 13 experiments Detail

1 3D 1H-13C NOESY aliphatic

Instrument

Varian VXRS - 750 MHz

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.1), Details 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] E5, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

2 3D 1H-13C NOESY aromatic

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

3 3D HNCACB

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

4 3D 1H-15N NOESY

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

5 3D CBCA(CO)NH

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

6 2D 1H-15N HSQC

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

7 3D HNCO

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

8 2D 1H-13C HSQC aliphatic

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

9 2D 1H-13C HSQC aromatic

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

10 deuterium exchange

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

11 3D C(CO)NH

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

12 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

13 2D HBCBCGCDHD

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 (±0.1) mM
2	E5	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
3	TRIS	natural abundance	20 (±0.2) mM
4	sodium chloride	natural abundance	100 (±2.0) mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30231_5uj5.nef
Input source #2: Coordindates	5uj5.cif
Diamagnetism of the molecular assembly	False (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)
1:54:CYS:SG	2:1:FES:FE1	unknown	unknown	n/a
1:60:CYS:SG	2:1:FES:FE1	unknown	unknown	n/a
1:63:CYS:SG	2:1:FES:FE2	unknown	unknown	n/a
1:100:CYS:SG	2:1:FES:FE2	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	FES	FE2/S2 (INORGANIC) CLUSTER	None

Sequence alignments

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

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

-------110-------120-------130--
QLRVDKSFENAVFTVPRATKNMAVDGFKPKPH
||||||||||||||||||||||||||||||||
QLRVDKSFENAVFTVPRATKNMAVDGFKPKPH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	132	0	0	100.0

Content subtype: combined_30231_5uj5.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_chemical_shifts_1	Warning	1031		87.9 (chain: A, length: 132)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1484 (1)	noe	72.7 (chain: A, length: 132)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	12 (1)	undefined	3.0 (chain: A, length: 132)
3	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	64 (1)	hbond	37.9 (chain: A, length: 132)
4	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	64 (1)	hbond	37.9 (chain: A, length: 132)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_6	OK	138 (138)	.	68.9 (chain: A, length: 132)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 87.9%
- Total number of assignments
  - ¹³C chemical shifts: 443
  - ¹H chemical shifts: 481
  - ¹⁵N chemical shifts: 107
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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 (%)
¹³C chemical shifts	585	443	75.7
¹H chemical shifts	777	481	61.9
¹⁵N chemical shifts	137	107	78.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	264	208	78.8
¹H chemical shifts	266	183	68.8
¹⁵N chemical shifts	123	103	83.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	321	235	73.2
¹H chemical shifts	511	298	58.3
¹⁵N chemical shifts	14	4	28.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	72	56	77.8
¹H chemical shifts	72	55	76.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	49	24	49.0
¹H chemical shifts	49	24	49.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 72.7%
- Total number of restraints: 1484
- Weight of restraints: 1.0 (1484)
- Potential type of restraints: upper-bound-parabolic (1484)
- Range of distance target values: 2.72, 5.5 (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_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 3.0%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: upper-bound-parabolic (12)
  - Range of distance target values: 3.5, 6.5 (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_2
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 37.9%
    - Total number of restraints: 64
    - Weight of restraints: 1.0 (64)
    - Potential type of restraints: upper-bound-parabolic (64)
    - Range of distance target values: 2.0, 3.0 (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: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 37.9%
      - Total number of restraints: 64
        Total hydrogen bond restraints: 64
        O...H-x (too close!): 16
        O...h-N (too close!): 17
        O...H-x: 1
        Long range: 30
        O...H-x (too close!): 14
        O...h-N (too close!): 15
        O...H-x: 1
      - Weight of restraints: 1.0 (64)
        Total hydrogen bond restraints: 1.0 (64)
        O...H-x (too close!): 1.0 (16)
        O...h-N (too close!): 1.0 (17)
        O...H-x: 1.0 (1)
        Long range: 1.0 (30)
        O...H-x (too close!): 1.0 (14)
        O...h-N (too close!): 1.0 (15)
        O...H-x: 1.0 (1)
      - Potential type of restraints: upper-bound-parabolic (64)
        Total hydrogen bond restraints: upper-bound-parabolic (64)
        O...H-x (too close!): upper-bound-parabolic (16)
        O...h-N (too close!): upper-bound-parabolic (17)
        O...H-x: upper-bound-parabolic (1)
        Long range: upper-bound-parabolic (30)
        O...H-x (too close!): upper-bound-parabolic (14)
        O...h-N (too close!): upper-bound-parabolic (15)
        O...H-x: upper-bound-parabolic (1)
      - Range of distance target values: 1.8, 2.7 (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: DYANA/DIANA_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 68.9%
- Total number of restraints: 138
- Total number of restraints per polymer type: 138
- Weight of restraints: 1.0 (138)
- Potential type of restraints: square-well-parabolic (138)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ELECTRON TRANSPORT, SSGCID, Seattle Structural Genomics Center for Infectious Disease, Structural Genomics, infectious diseases, iron-sulfur protein, microsporidosis

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Found 1 Document (1.013 seconds)

BMRB: 30231

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Adrenodoxin, entity 1, : 1 : 1 : 39 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 7 contents Detail