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BMRB: 18801

2M08

The solution structure of NmPin, the parvuline of Nitrosopumilus maritimus

Authors

Lederer, C., Bayer, P.

Assembly

NmPin

Entity

1. NmPin (polymer, Thiol state: all free), 93 monomers, 10179.77 Da Detail

GPSNKIKCSH ILVSKQSEAL AIMEKLKSGE KFGKLAKELS IDSGSAKKNG NLGYFTKGMM VKPFEDAAFK LQVGEVSEPI KSEFGYHIIK RFG

Formula weight

10179.77 Da

Source organism

Nitrosopumilus maritimus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.0 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.0 % (1024 of 1113)	93.4 % (548 of 587)	88.6 % (382 of 431)	98.9 % (94 of 95)
Backbone	98.0 % (541 of 552)	98.4 % (190 of 193)	97.4 % (262 of 269)	98.9 % (89 of 90)
Sidechain	87.9 % (566 of 644)	90.9 % (358 of 394)	82.9 % (203 of 245)	100.0 % (5 of 5)
Aromatic	64.3 % (54 of 84)	100.0 % (42 of 42)	28.6 % (12 of 42)
Methyl	100.0 % (86 of 86)	100.0 % (43 of 43)	100.0 % (43 of 43)

1. entity

GPSNKIKCSH ILVSKQSEAL AIMEKLKSGE KFGKLAKELS IDSGSAKKNG NLGYFTKGMM VKPFEDAAFK LQVGEVSEPI KSEFGYHIIK RFG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for side-chain asignment and NOE-spectra

#	Name	Isotope labeling	Type	Concentration
4	entity	[U-99% 13C; U-99% 15N]		1 mM
5	potassium phosphate	natural abundance		50 mM
6	DSS	natural abundance		2 uM

LACS Plot; CA

Referencing offset: 2.35 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.35 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -1.63 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M08, Strand ID: A Detail

Release date

2016-06-29

Citation

NmPin from the marine thaumarchaeote Nitrosopumilus maritimus is an active membrane associated prolyl isomerase
Hoppstock, L., Trusch, F., Lederer, C., van West, P., Koenneke, M., Bayer, P.
BMC Biol. (2016), 14, 53-53, PubMed 27349962 , DOI 10.1186/s12915-016-0274-1 , Abstract

Related entities 1. NmPin, : 1 : 241 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

2 2D 1H-13C HSQC

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

3 2D 1H-1H TOCSY

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

4 2D 1H-1H COSY

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

5 2D 1H-1H NOESY

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

6 3D CBCA(CO)NH

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

7 3D HNCACB

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for backbone assignment and 2D-spectra

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	DSS	natural abundance		2 uM

8 3D HCCH-TOCSY

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for side-chain asignment and NOE-spectra

#	Name	Isotope labeling	Type	Concentration
4	entity	[U-99% 13C; U-99% 15N]		1 mM
5	potassium phosphate	natural abundance		50 mM
6	DSS	natural abundance		2 uM

9 3D HCCH-COSY

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for side-chain asignment and NOE-spectra

#	Name	Isotope labeling	Type	Concentration
4	entity	[U-99% 13C; U-99% 15N]		1 mM
5	potassium phosphate	natural abundance		50 mM
6	DSS	natural abundance		2 uM

10 3D 1H-13C NOESY

Instrument

Bruker Ultrashield - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 301.5 K, pH 6.5, Details used for side-chain asignment and NOE-spectra

#	Name	Isotope labeling	Type	Concentration
4	entity	[U-99% 13C; U-99% 15N]		1 mM
5	potassium phosphate	natural abundance		50 mM
6	DSS	natural abundance		2 uM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18801_2m08.nef
Input source #2: Coordindates	2m08.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---
GPSNKIKCSHILVSKQSEALAIMEKLKSGEKFGKLAKELSIDSGSAKKNGNLGYFTKGMMVKPFEDAAFKLQVGEVSEPIKSEFGYHIIKRFG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPSNKIKCSHILVSKQSEALAIMEKLKSGEKFGKLAKELSIDSGSAKKNGNLGYFTKGMMVKPFEDAAFKLQVGEVSEPIKSEFGYHIIKRFG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	93	0	0	100.0

Content subtype: combined_18801_2m08.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1032		100.0 (chain: A, length: 93)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2266 (1)	noe	98.9 (chain: A, length: 93)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 554
  - ¹³C chemical shifts: 384
  - ¹⁵N chemical shifts: 94
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 98.9%
- Total number of restraints: 2266
- Weight of restraints: 1.0 (2266)
- Potential type of restraints: upper-bound-parabolic (2266)
- Range of distance target values: 2.4, 5.5 (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

Keywords Thaumarchaeota, archaeal, membrane, parvulin, sdPar