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BMRB: 17448

2L9D

Solution structure of the protein YP_546394.1, the first structural representative of the pfam family PF12112

Authors

MOHANTY, B., SERRANO, P., GERALT, M., HORST, R., WUTHRICH, K.

Assembly

protein YP 546394.1

Entity

1. protein YP 546394.1 (polymer, Thiol state: all free), 108 monomers, 12019.58 Da Detail

GMGTTEKSGI KEIIIQGLTR AGKPFRPSDW VDRMCSTYAS FGADRKLRYS PYLKPRVIEG VRCLAVDLKL KDTNPEGFNQ LMHFATENQL NILDAEGNSI DAAQVTEI

Formula weight

12019.58 Da

Source organism

Methylobacillus flagellatus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.2 %, Completeness (bb): 98.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.2 % (1226 of 1249)	98.0 % (639 of 652)	98.1 % (475 of 484)	99.1 % (112 of 113)
Backbone	98.6 % (629 of 638)	98.6 % (217 of 220)	98.4 % (310 of 315)	99.0 % (102 of 103)
Sidechain	98.0 % (696 of 710)	97.7 % (422 of 432)	98.5 % (264 of 268)	100.0 % (10 of 10)
Aromatic	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (39 of 39)	100.0 % (1 of 1)
Methyl	100.0 % (118 of 118)	100.0 % (59 of 59)	100.0 % (59 of 59)

1. YP 546394.1

GMGTTEKSGI KEIIIQGLTR AGKPFRPSDW VDRMCSTYAS FGADRKLRYS PYLKPRVIEG VRCLAVDLKL KDTNPEGFNQ LMHFATENQL NILDAEGNSI DAAQVTEI

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 50 mM sodium chloride, 20mM sodium phosphate, 4.5 mM sodium azide, 1.2 mM [U-98% 13C, U-98% 15N]

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

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: 0.09 ppm, Outliers: 6 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: 0.09 ppm, Outliers: 6 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: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CO

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: -0.19 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L9D, Strand ID: A Detail

Release date

2011-03-07

Citation

Solution structure of the protein YP_546394.1, the first structural representative of the pfam family PF12112
MOHANTY, B., SERRANO, P., GERALT, M., HORST, R., WUTHRICH, K.
Not known

Related entities 1. protein YP 546394.1, : 1 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 50 mM sodium chloride, 20mM sodium phosphate, 4.5 mM sodium azide, 1.2 mM [U-98% 13C, U-98% 15N]

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

3 4D APSY - HACANH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

4 5D APSY - HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

5 5D APSY - CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

6 15N resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

7 13Cali resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

8 13Caro resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YP_546394.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17448_2l9d.nef
Input source #2: Coordindates	2l9d.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
GMGTTEKSGIKEIIIQGLTRAGKPFRPSDWVDRMCSTYASFGADRKLRYSPYLKPRVIEGVRCLAVDLKLKDTNPEGFNQLMHFATENQLNILDAEGNSI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMGTTEKSGIKEIIIQGLTRAGKPFRPSDWVDRMCSTYASFGADRKLRYSPYLKPRVIEGVRCLAVDLKLKDTNPEGFNQLMHFATENQLNILDAEGNSI

--------
DAAQVTEI
||||||||
DAAQVTEI

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_17448_2l9d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1227		99.1 (chain: A, length: 108)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2762 (1)	noe	98.1 (chain: A, length: 108)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	438 (435)	.	100.0 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 639
  - ¹³C chemical shifts: 471
  - ¹⁵N chemical shifts: 117
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	652	639	98.0
¹³C chemical shifts	484	471	97.3
¹⁵N chemical shifts	120	117	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	220	216	98.2
¹³C chemical shifts	216	207	95.8
¹⁵N chemical shifts	103	101	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	432	423	97.9
¹³C chemical shifts	268	264	98.5
¹⁵N chemical shifts	17	16	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	61	98.4
¹³C chemical shifts	62	61	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	40	100.0
¹³C chemical shifts	39	39	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 98.1%
- Total number of restraints: 2762
- Weight of restraints: 1.0 (2762)
- Potential type of restraints: upper-bound-parabolic (2762)
- Range of distance target values: 2.44, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 100.0%
- Total number of restraints: 435
- Total number of restraints per polymer type: 435
- Weight of restraints: 1.0 (435)
- Potential type of restraints: square-well-parabolic (435)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Methylobacillus flagellatus KT, PG9854E

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Found 1 Document (0.626 seconds)

BMRB: 17448

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. protein YP 546394.1, : 1 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 4 contents Detail