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Found 1 Document (0.727 seconds)

BMRB: 34304

6H5H

A computationally designed dRP lyase domain reconstructed from two heterologous fragments

Authors

ElGamacy, M., Coles, M., Lupas, A.N.

Assembly

polb4

Entity

1. polb4 (polymer, Thiol state: not present), 121 monomers, 13421.08 Da Detail

MKHHHHHHPM SDYDIPTTEN LYFQGAMGGQ ETLNGALVNM LKEEGNKALS VGNIDDALQY YAAAITLDKY PHKIKSGAEA KKLPGVGTKI AEKIDEFLAT GKLRKLEKIR QDDTSSSINF L

Formula weight

13421.08 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Refine. method

simulated annealingNOESY back-calculation

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 59.5 %, Completeness: 54.4 %, Completeness (bb): 56.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	54.4 % (764 of 1404)	53.6 % (392 of 731)	54.8 % (299 of 546)	57.5 % (73 of 127)
Backbone	56.8 % (408 of 718)	56.5 % (140 of 248)	56.7 % (200 of 353)	58.1 % (68 of 117)
Sidechain	52.9 % (422 of 797)	52.2 % (252 of 483)	54.3 % (165 of 304)	50.0 % (5 of 10)
Aromatic	30.6 % (30 of 98)	30.6 % (15 of 49)	30.6 % (15 of 49)
Methyl	68.0 % (87 of 128)	65.6 % (42 of 64)	70.3 % (45 of 64)

1. entity 1

MKHHHHHHPM SDYDIPTTEN LYFQGAMGGQ ETLNGALVNM LKEEGNKALS VGNIDDALQY YAAAITLDKY PHKIKSGAEA KKLPGVGTKI AEKIDEFLAT GKLRKLEKIR QDDTSSSINF L

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	polb4	[U-15N]		500 uM
2	potassium phosphate	natural abundance		150 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 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: 0.23 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: 0.23 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: -0.07 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: -0.39 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 22 models in PDB: 6H5H, Strand ID: A Detail

Release date

2018-12-02

Citation

Asymmetric protein design from conserved supersecondary structures
ElGamacy, M., Coles, M., Lupas, A.N.
J. Struct. Biol. (2018), 204, 380-387, PubMed 30558718 , DOI 10.1016/j.jsb.2018.10.010 , Abstract

Related entities 1. polb4, : 1 entities Detail

Experiments performed 10 experiments Detail

1 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 mM

2 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 mM

3 3D C(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 mM

4 3D H(CCO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 mM

5 3D 15N-HSQC NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	polb4	[U-15N]		500 uM
2	potassium phosphate	natural abundance		150 mM

6 3D 13C-HSQC NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 mM

7 3D CNH-NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 mM

8 3D NNH-NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	polb4	[U-15N]		500 uM
2	potassium phosphate	natural abundance		150 mM

9 3D CCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-13C; U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	polb4	[U-13C; U-15N]		500 uM
4	potassium phosphate	natural abundance		150 mM

10 2D 15N-filtered NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 7.1, Details 500 uM [U-15N] polb4, 150 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	polb4	[U-15N]		500 uM
2	potassium phosphate	natural abundance		150 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34304_6h5h.nef
Input source #2: Coordindates	6h5h.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
MKHHHHHHPMSDYDIPTTENLYFQGAMGGQETLNGALVNMLKEEGNKALSVGNIDDALQYYAAAITLDKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLAT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKHHHHHHPMSDYDIPTTENLYFQGAMGGQETLNGALVNMLKEEGNKALSVGNIDDALQYYAAAITLDKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLAT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--------80--------90-
GKLRKLEKIRQDDTSSSINFL
|||||||||||||||||||||
GKLRKLEKIRQDDTSSSINFL
-------110-------120-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	121	0	0	100.0

Content subtype: combined_34304_6h5h.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	668		49.6 (chain: A, length: 121)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	93 (1)	noe	34.7 (chain: A, length: 121)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	93 (1)	noe	34.7 (chain: A, length: 121)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	51 (1)	hbond	51.2 (chain: A, length: 121)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	51 (1)	hbond	51.2 (chain: A, length: 121)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 49.6%
- Total number of assignments
  - ¹H chemical shifts: 350
  - ¹³C chemical shifts: 257
  - ¹⁵N chemical shifts: 61
- Completeness of assignments
- 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: 121, Sequence coverage: 34.7%
- Total number of restraints: 93
- Weight of restraints: 1.0 (93)
- Potential type of restraints: square-well-parabolic (93)
- Range of distance target values: 1.75, 2.9 (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: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 34.7%
  - Total number of restraints: 93
  - Weight of restraints: 1.0 (93)
  - Potential type of restraints: square-well-parabolic (93)
  - Range of distance target values: 1.75, 2.9 (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: 121, Sequence coverage: 51.2%
    - Total number of restraints: 51
    - Weight of restraints: 1.0 (51)
    - Potential type of restraints: square-well-parabolic (51)
    - Range of distance target values: 2.2, 2.2 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_5
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 51.2%
        --------------------------------------10--------20--------30--------40--------50--------60--------70 MKHHHHHHPMSDYDIPTTENLYFQGAMGGQETLNGALVNMLKEEGNKALSVGNIDDALQYYAAAITLDKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLAT | ||||||||||||||||||||||||||||||||||||| | | | |||||| ||||||||||||||| ...............................T.NGALVNMLKEEGNKALSVGNIDDALQYYAAAITLDKY.H.I..G.EAKKLP.VGTKIAEKIDEFLAT --------------------------------------10--------20--------30--------40--------50--------60--------70 --------80--------90- GKLRKLEKIRQDDTSSSINFL
      - Total number of restraints: 51
        Total hydrogen bond restraints: 51
        O...H-x: 46
        Long range: 5
        O...H-x: 5
      - Weight of restraints: 1.0 (51)
        Total hydrogen bond restraints: 1.0 (51)
        O...H-x: 1.0 (46)
        Long range: 1.0 (5)
        O...H-x: 1.0 (5)
      - Potential type of restraints: square-well-parabolic (51)
        Total hydrogen bond restraints: square-well-parabolic (51)
        O...H-x: square-well-parabolic (46)
        Long range: square-well-parabolic (5)
        O...H-x: square-well-parabolic (5)
      - Range of distance target values: 2.2, 2.2 (Å)
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Keywords Protein design, UNKNOWN FUNCTION, dRP lyase domain

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Found 1 Document (0.727 seconds)

BMRB: 34304

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. polb4, : 1 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail