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BMRB: 30118

5KIZ

Solution Structure of a repacked version of HIF-2 alpha PAS-B (CASP target)

Authors

Correa, F., Key, J., Kuhlman, B., Gardner, K.H.

Assembly

Endothelial PAS domain-containing protein 1

Entity

1. Endothelial PAS domain-containing protein 1 (polymer, Thiol state: all free), 114 monomers, 13248.96 Da Detail

GEFLDSKTFL SRFSMDMKFT YCDDRITELI GYHPEELLGR SASEFWHALD SENMTKSHQN LCTKGQVVSG QYRMLAKHGG YVWLETQMTV IYNPRNLQPQ CIMAVNYVLS EIEK

Formula weight

13248.96 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 95.6 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.6 % (1302 of 1362)	95.6 % (677 of 708)	95.3 % (505 of 530)	96.8 % (120 of 124)
Backbone	95.4 % (647 of 678)	95.7 % (222 of 232)	94.6 % (317 of 335)	97.3 % (108 of 111)
Sidechain	96.1 % (760 of 791)	95.6 % (455 of 476)	97.0 % (293 of 302)	92.3 % (12 of 13)
Aromatic	97.1 % (134 of 138)	97.1 % (67 of 69)	97.0 % (65 of 67)	100.0 % (2 of 2)
Methyl	94.5 % (104 of 110)	92.7 % (51 of 55)	96.4 % (53 of 55)

1. Endothelial PAS domain-containing protein 1

GEFLDSKTFL SRFSMDMKFT YCDDRITELI GYHPEELLGR SASEFWHALD SENMTKSHQN LCTKGQVVSG QYRMLAKHGG YVWLETQMTV IYNPRNLQPQ CIMAVNYVLS EIEK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

LACS Plot; CA

Referencing offset: -0.3 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.3 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2016-08-10

Citation

Computational Repacking of HIF-2α Cavity Replaces Water-Based Stabilized Core
Correa, F., Key, J., Kuhlman, B., Gardner, K.H.
Structure (2016), 24, 1918-1927, PubMed 27667693 , DOI 10.1016/j.str.2016.08.014 , Abstract

Related entities 1. Endothelial PAS domain-containing protein 1, : 1 : 261 entities Detail

Interaction partners 1. Endothelial PAS domain-containing protein 1, : 31 interactors Detail

More details for 31 interactors identified by 19 citations

Experiments performed 9 experiments Detail

1 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

2 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

4 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

5 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

6 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

7 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HIF-2 alpha D1	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Tris	natural abundance		50 mM
5	NaCl	natural abundance		20 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30118_5kiz.nef
Input source #2: Coordindates	5kiz.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

--240-------250-------260-------270-------280-------290-------300-------310-------320-------330-----
GEFLDSKTFLSRFSMDMKFTYCDDRITELIGYHPEELLGRSASEFWHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQMTVIYNPRNLQPQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GEFLDSKTFLSRFSMDMKFTYCDDRITELIGYHPEELLGRSASEFWHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQMTVIYNPRNLQPQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--340---------
CIMAVNYVLSEIEK
||||||||||||||
CIMAVNYVLSEIEK
-------110----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	114	0	0	100.0

Content subtype: combined_30118_5kiz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1322		99.1 (chain: A, length: 114)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3310 (1)	noe	99.1 (chain: A, length: 114)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	28 (1)	hbond	22.8 (chain: A, length: 114)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	186 (186)	.	96.5 (chain: A, length: 114)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 695
  - ¹³C chemical shifts: 505
  - ¹⁵N chemical shifts: 122
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 99.1%
- Total number of restraints: 3310
- Weight of restraints: 1.0 (3310)
- Potential type of restraints: square-well-parabolic (3310)
- Range of distance target values: 1.74, 3.42 (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_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 22.8%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: square-well-parabolic (28)
  - Range of distance target values: 2.05, 3.05 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 96.5%
- Total number of restraints: 186
- Total number of restraints per polymer type: 186
- Weight of restraints: 1.0 (186)
- Potential type of restraints: square-well-parabolic (186)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Cavity, Repacking, Rosetta, TRANSCRIPTION