BMRBj - BMREntryMaster

Found 1 Document (0.791 seconds)

BMRB: 17818

2LGO

Solution NMR structure of a FKBP-type peptidyl-prolyl cis-trans isomerase from Giardia lamblia. Seattle Structural Genomics Center for Infectious Disease (SSGCID) target GilaA.00840.a

Authors

Buchko, G.W.

Assembly

FKBP-type peptidyl-prolyl cis-trans isomerase

Entity

1. FKBP-type peptidyl-prolyl cis-trans isomerase (polymer, Thiol state: not present), 130 monomers, 14138.98 Da Detail

MAHHHHHHMG TLEAQTQGPG SMSAQLEKKV LTPGDGVTKP QAGKKVTVHY DGRFPDGKQF DSSRSRGKPF QFTLGAGEVI KGWDQGVATM TLGEKALFTI PYQLAYGERG YPPVIPPKAT LVFEVELLAV

Formula weight

14138.98 Da

Source organism

Giardia lamblia ATCC 50803

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.6 %, Completeness: 77.9 %, Completeness (bb): 79.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.9 % (1164 of 1495)	80.7 % (627 of 777)	71.5 % (421 of 589)	89.9 % (116 of 129)
Backbone	79.2 % (602 of 760)	86.1 % (229 of 266)	69.8 % (261 of 374)	93.3 % (112 of 120)
Sidechain	78.6 % (667 of 849)	77.9 % (398 of 511)	80.5 % (265 of 329)	44.4 % (4 of 9)
Aromatic	51.5 % (68 of 132)	56.1 % (37 of 66)	47.7 % (31 of 65)	0.0 % (0 of 1)
Methyl	90.9 % (120 of 132)	90.9 % (60 of 66)	90.9 % (60 of 66)

1. FKBP

MAHHHHHHMG TLEAQTQGPG SMSAQLEKKV LTPGDGVTKP QAGKKVTVHY DGRFPDGKQF DSSRSRGKPF QFTLGAGEVI KGWDQGVATM TLGEKALFTI PYQLAYGERG YPPVIPPKAT LVFEVELLAV

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
7	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
8	sodium chloride	natural abundance	100 mM
9	TRIS	natural abundance	20 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	100 %

LACS Plot; CA

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

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2011-08-16

Citation

Solution structure of a putative FKBP-type peptidyl-propyl cis-trans isomerase from Giardia lamblia
Buchko, G.W., Hewitt, S.N., Van Voorhis, W.C., Myler, P.J.
J. Biomol. NMR (2013), 57, 369-374, PubMed 24293257 , DOI 10.1007/s10858-013-9797-8 , Abstract

Related entities 1. FKBP-type peptidyl-prolyl cis-trans isomerase, : 1 : 176 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

3 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

4 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

6 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

7 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

11 deuterium exchange

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
7	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
8	sodium chloride	natural abundance	100 mM
9	TRIS	natural abundance	20 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	100 %

12 3D C(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

13 2D HBCBCGCDCDHD

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

14 2D HBCBCGCDCEHE

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7 (±0.2)

#	Name	Isotope labeling	Concentration
1	FKBP	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 mM
3	TRIS	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17818_2lgo.nef
Input source #2: Coordindates	2lgo.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

None

Sequence alignments

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

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

-------110-------120-------130
PYQLAYGERGYPPVIPPKATLVFEVELLAV
||||||||||||||||||||||||||||||
PYQLAYGERGYPPVIPPKATLVFEVELLAV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	130	0	0	100.0

Content subtype: combined_17818_2lgo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1098		93.1 (chain: A, length: 130)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2087 (1)	noe	86.9 (chain: A, length: 130)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	76 (1)	hbond	38.5 (chain: A, length: 130)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	150 (150)	.	78.5 (chain: A, length: 130)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 93.1%
- Total number of assignments
  - ¹³C chemical shifts: 378
  - ¹H chemical shifts: 604
  - ¹⁵N chemical shifts: 116
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
49	HIS	HD1	12.47
49	HIS	ND1	145.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	589	378	64.2
¹H chemical shifts	777	603	77.6
¹⁵N chemical shifts	133	115	86.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	260	121	46.5
¹H chemical shifts	266	225	84.6
¹⁵N chemical shifts	120	111	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	329	257	78.1
¹H chemical shifts	511	378	74.0
¹⁵N chemical shifts	13	4	30.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	70	61	87.1
¹H chemical shifts	70	61	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	65	31	47.7
¹H chemical shifts	66	37	56.1
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 86.9%
- Total number of restraints: 2087
- Weight of restraints: 1.0 (2087)
- Potential type of restraints: square-well-parabolic (2087)
- Range of distance target values: 2.08, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 38.5%
  - Total number of restraints: 76
  - Weight of restraints: 1.0 (76)
  - Potential type of restraints: square-well-parabolic (76)
  - Range of distance target values: 1.9, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 78.5%
- Total number of restraints: 150
- Total number of restraints per polymer type: 150
- Weight of restraints: 1.0 (150)
- Potential type of restraints: square-well-parabolic (150)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords giardiasis, infectious diesease, isomerase, SSGCID

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.791 seconds)

BMRB: 17818

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. FKBP-type peptidyl-prolyl cis-trans isomerase, : 1 : 176 entities Detail

Experiments performed 14 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail