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BMRB: 18725

2LYH

Structure of Faap24 residues 141-215

Authors

Wienk, H., Slootweg, J., Kaptein, R., Boelens, R., Folkers, G.E.

Assembly

Faap24

Entity

1. Faap24 (polymer, Thiol state: not present), 95 monomers, 10392.94 Da Detail

MGSSHHHHHH SSHMLVPRGS SKNPLLGKKR ALLLSEPSLL RTVQQIPGVG KVKAPLLLQK FPSIQQLSNA SIGELEQVVG QAVAQQIHAF FTQPR

Formula weight

10392.94 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.5 %, Completeness: 79.5 %, Completeness (bb): 87.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.5 % (892 of 1122)	78.9 % (465 of 589)	80.1 % (347 of 433)	80.0 % (80 of 100)
Backbone	87.8 % (488 of 556)	87.4 % (166 of 190)	88.5 % (246 of 278)	86.4 % (76 of 88)
Sidechain	73.7 % (482 of 654)	74.9 % (299 of 399)	73.7 % (179 of 243)	33.3 % (4 of 12)
Aromatic	35.5 % (22 of 62)	41.9 % (13 of 31)	29.0 % (9 of 31)
Methyl	87.5 % (98 of 112)	92.9 % (52 of 56)	82.1 % (46 of 56)

1. Faap24

MGSSHHHHHH SSHMLVPRGS SKNPLLGKKR ALLLSEPSLL RTVQQIPGVG KVKAPLLLQK FPSIQQLSNA SIGELEQVVG QAVAQQIHAF FTQPR

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

LACS Plot; CA

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 2.7 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2013-04-28

Citation

The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition
Wienk, H., Slootweg, J.C., Speerstra, S., Kaptein, R., Boelens, R., Folkers, G.E.
Nucleic Acids Res. (2013), 41, 6739-6749, PubMed 23661679 , DOI 10.1093/nar/gkt354 , Abstract

Related entities 1. Faap24, : 1 : 6 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 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

5 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

6 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

7 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

9 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	FAAP24	[U-100% 13C; U-100% 15N]		0.2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	PMSF	natural abundance		0.2 mM
5	D2O	natural abundance		7 %
6	H2O	natural abundance		93 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18725_2lyh.nef
Input source #2: Coordindates	2lyh.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

--120-----130-------140-------150-------160-------170-------180-------190-------200-------210-----
MGSSHHHHHHSSHMLVPRGSLEPSKNPLLGKKRALLLSEPSLLRTVQQIPGVGKVKAPLLLQKFPSIQQLSNASIGELEQVVGQAVAQQIHAFFTQPR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSHMLVPRGSLEPSKNPLLGKKRALLLSEPSLLRTVQQIPGVGKVKAPLLLQKFPSIQQLSNASIGELEQVVGQAVAQQIHAFFTQPR
--------10--------20--------30--------40--------50--------60--------70--------80--------90--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	98	0	0	100.0

Content subtype: combined_18725_2lyh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	874		84.7 (chain: A, length: 98)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1546 (1)	noe	79.6 (chain: A, length: 98)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	120 (120)	.	83.7 (chain: A, length: 98)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 84.7%
- Total number of assignments
  - ¹H chemical shifts: 454
  - ¹³C chemical shifts: 341
  - ¹⁵N chemical shifts: 79
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 79.6%
- Total number of restraints: 1533
- Weight of restraints: 1.0 (1533)
- Potential type of restraints: square-well-parabolic (1533)
- Range of distance target values: 1.21, 2.75 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 83.7%
- Total number of restraints: 120
- Total number of restraints per polymer type: 120
- Weight of restraints: 1.0 (120)
- Potential type of restraints: square-well-parabolic (120)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA-binding protein, Fanconi anemia, interstrand crosslink repair