BMRBj - BMREntryMaster

Found 1 Document (0.784 seconds)

BMRB: 19869

2MMV

ZapA mutant dimer from B. stearothermophilus

Authors

Nogueira, M., Sforca, M., Zeri, A.

Assembly

ZapA homodimer

Entity

1. ZapA homodimer (polymer, Thiol state: not present), 86 monomers, 9886.297 × 2 Da Detail

GSHMTEQPKT RVSVRIYGQD YTIVGAESPA HIRLVAAFVD DKMHEFSEKQ PMLDVPKLAV LTAVQIASEY LKLKEEYQRL REQLKK

Total weight

19772.594 Da

Max. entity weight

9886.297 Da

Source organism

Geobacillus stearothermophilus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.9 %, Completeness: 78.9 %, Completeness (bb): 77.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.9 % (818 of 1037)	86.0 % (468 of 544)	67.9 % (275 of 405)	85.2 % (75 of 88)
Backbone	77.2 % (392 of 508)	91.2 % (156 of 171)	63.1 % (161 of 255)	91.5 % (75 of 82)
Sidechain	82.0 % (502 of 612)	83.6 % (312 of 373)	81.5 % (190 of 233)	0.0 % (0 of 6)
Aromatic	51.6 % (33 of 64)	68.8 % (22 of 32)	34.4 % (11 of 32)
Methyl	90.2 % (92 of 102)	90.2 % (46 of 51)	90.2 % (46 of 51)

1. ZapA

GSHMTEQPKT RVSVRIYGQD YTIVGAESPA HIRLVAAFVD DKMHEFSEKQ PMLDVPKLAV LTAVQIASEY LKLKEEYQRL REQLKK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [U-13C, 15N]; Mutant

#	Name	Isotope labeling	Concentration
4	ZapA	[U-13C; U-15N]	0.3 mM
5	sodium phosphate	natural abundance	50 mM
6	potassium chloride	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details Before the acquisition, this mixture was lyophilized and resuspended in deuterium.

#	Name	Isotope labeling	Concentration
7	ZapA	[U-13C; U-15N]	0.3 mM
8	ZapA	natural abundance	0.3 mM
9	sodium phosphate	natural abundance	50 mM
10	potassium chloride	natural abundance	50 mM

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: -0.49 ppm, Outliers: 1 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: -0.49 ppm, Outliers: 1 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: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-06-14

Related entities 1. ZapA homodimer, : 1 : 15 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [U-13C, 15N]; Mutant

#	Name	Isotope labeling	Concentration
4	ZapA	[U-13C; U-15N]	0.3 mM
5	sodium phosphate	natural abundance	50 mM
6	potassium chloride	natural abundance	50 mM

2 2D 13C-15N CHSQC

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

3 3D 1H-13C NOESY aromatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

4 3D 1H-13C NOESY aliphatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [U-13C, 15N]; Mutant

#	Name	Isotope labeling	Concentration
4	ZapA	[U-13C; U-15N]	0.3 mM
5	sodium phosphate	natural abundance	50 mM
6	potassium chloride	natural abundance	50 mM

5 3D CBCA(CO)NH

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

6 3D HNCO

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

7 3D HBHA(CO)NH

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

8 3D HNCACB

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

9 3D 13C-15N filtered NOESY C13 HSQC

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details Before the acquisition, this mixture was lyophilized and resuspended in deuterium.

#	Name	Isotope labeling	Concentration
7	ZapA	[U-13C; U-15N]	0.3 mM
8	ZapA	natural abundance	0.3 mM
9	sodium phosphate	natural abundance	50 mM
10	potassium chloride	natural abundance	50 mM

10 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

11 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
7	ZapA	[U-13C; U-15N]	0.3 mM
8	ZapA	natural abundance	0.3 mM
9	sodium phosphate	natural abundance	50 mM
10	potassium chloride	natural abundance	50 mM

12 3D 15N - NOESY-HSQC

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

13 3D 15N - TOCSY -HSQC

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.3 MM [15N]; Mutant

#	Name	Isotope labeling	Concentration
1	ZapA	[U-15N]	0.3 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	50 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19869_2mmv.nef
Input source #2: Coordindates	2mmv.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------
GSHMTEQPKTRVSVRIYGQDYTIVGAESPAHIRLVAAFVDDKMHEFSEKQPMLDVPKLAVLTAVQIASEYLKLKEEYQRLREQLKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMTEQPKTRVSVRIYGQDYTIVGAESPAHIRLVAAFVDDKMHEFSEKQPMLDVPKLAVLTAVQIASEYLKLKEEYQRLREQLKK

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60--------70--------80------
GSHMTEQPKTRVSVRIYGQDYTIVGAESPAHIRLVAAFVDDKMHEFSEKQPMLDVPKLAVLTAVQIASEYLKLKEEYQRLREQLKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMTEQPKTRVSVRIYGQDYTIVGAESPAHIRLVAAFVDDKMHEFSEKQPMLDVPKLAVLTAVQIASEYLKLKEEYQRLREQLKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	86	0	0	100.0
B	B	86	0	0	100.0

Content subtype: combined_19869_2mmv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	803		91.9 (chain: A, length: 86)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3307 (1)	noe	91.9 (chain: A, length: 86), 91.9 (chain: B, length: 86)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 91.9%
- Total number of assignments
  - ¹H chemical shifts: 463
  - ¹³C chemical shifts: 266
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	544	463	85.1
¹³C chemical shifts	405	266	65.7
¹⁵N chemical shifts	93	74	79.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	171	155	90.6
¹³C chemical shifts	172	79	45.9
¹⁵N chemical shifts	82	74	90.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	373	308	82.6
¹³C chemical shifts	233	187	80.3
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	46	85.2
¹³C chemical shifts	54	46	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	22	68.8
¹³C chemical shifts	32	11	34.4

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 91.9%
  - Entity_assembly_ID: B, Chain length: 86, Sequence coverage: 91.9%
- Total number of restraints: 3294
- Weight of restraints: 1.0 (3294)
- Potential type of restraints: upper-bound-parabolic (3294)
- Range of distance target values: 1.93, 5.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords B. stearothermophilus, ZapA, dimer, protein

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Found 1 Document (0.784 seconds)

BMRB: 19869

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ZapA homodimer, : 1 : 15 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 3 contents Detail