BMRBj - BMREntryMaster

Found 1 Document (0.722 seconds)

BMRB: 25435

2MXX

Structure of Amylase binding Protein A of Streptococcous gordonii: a potential receptor for human salivary amylase enzyme

Authors

Sethi, A., Mohanty, B., Ramasubbu, N., Gooley, P.R.

Assembly

Amylase binding Protein A

Entity

1. Amylase binding Protein A (polymer, Thiol state: not present), 179 monomers, 19141.52 Da Detail

MADEATDAAR NNDGAYYLQT QFTNADKVNE YLAQHDGEIR AEAAADPAVV AAKAALDAVE GGSHNYGEVK AAYEAAFNNA FNAVRNKYVQ RFQATYNNAT EQEGKTYIQG ETPEQANARY LKRVGAANNQ NPAAEDKGAT TPASKEEAKK SEAAAKNAGK AAGKALPKTS AVKHHHHHH

Formula weight

19141.52 Da

Source organism

Streptococcus gordonii str. Challis

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, energy minimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.1 %, Completeness: 84.2 %, Completeness (bb): 94.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.2 % (1634 of 1940)	81.9 % (820 of 1001)	86.2 % (638 of 740)	88.4 % (176 of 199)
Backbone	94.7 % (1008 of 1064)	93.7 % (341 of 364)	95.4 % (502 of 526)	94.8 % (165 of 174)
Sidechain	75.3 % (786 of 1044)	75.2 % (479 of 637)	77.5 % (296 of 382)	44.0 % (11 of 25)
Aromatic	34.7 % (50 of 144)	45.8 % (33 of 72)	23.6 % (17 of 72)
Methyl	98.8 % (166 of 168)	98.8 % (83 of 84)	98.8 % (83 of 84)

1. entity

MADEATDAAR NNDGAYYLQT QFTNADKVNE YLAQHDGEIR AEAAADPAVV AAKAALDAVE GGSHNYGEVK AAYEAAFNNA FNAVRNKYVQ RFQATYNNAT EQEGKTYIQG ETPEQANARY LKRVGAANNQ NPAAEDKGAT TPASKEEAKK SEAAAKNAGK AAGKALPKTS AVKHHHHHH

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 50 mM Sodium Phosphate, 100 mM NaCl at pH 5.8, 15N13C-labeled AbpA (325 uM), Temperature = 298 K

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

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: -0.12 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: -0.12 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: 0.13 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: 0.0 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2015-05-10

Citation

Structure of amylase-binding protein A of Streptococcus gordonii: a potential receptor for human salivary α-amylase enzyme
Sethi, A., Mohanty, B., Ramasubbu, N., Gooley, P.R.
Protein Sci. (2015), 24, 1013-1018, PubMed 25739638 , DOI 10.1002/pro.2671 , Abstract

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 50 mM Sodium Phosphate, 100 mM NaCl at pH 5.8, 15N13C-labeled AbpA (325 uM), Temperature = 298 K

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D HNCACO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 3D CccoNH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

6 3D HcccoNH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 3D 15N resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

8 3D 13Cali resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

9 3D 13Caro resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

10 2D 15N{1H}-NOE

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AbpA	U-98% 13C; U-98% 15N	325 uM
2	Sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25435_2mxx.nef
Input source #2: Coordindates	2mxx.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

------30--------40--------50--------60--------70--------80--------90-------100-------110-------120--
MADEATDAARNNDGAYYLQTQFTNADKVNEYLAQHDGEIRAEAAADPAVVAAKAALDAVEGGSHNYGEVKAAYEAAFNNAFNAVRNKYVQRFQATYNNAT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MADEATDAARNNDGAYYLQTQFTNADKVNEYLAQHDGEIRAEAAADPAVVAAKAALDAVEGGSHNYGEVKAAYEAAFNNAFNAVRNKYVQRFQATYNNAT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----130-------140-------150-------160-------170-------180-------190-------200-
EQEGKTYIQGETPEQANARYLKRVGAANNQNPAAEDKGATTPASKEEAKKSEAAAKNAGKAAGKALPKTSAVKHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EQEGKTYIQGETPEQANARYLKRVGAANNQNPAAEDKGATTPASKEEAKKSEAAAKNAGKAAGKALPKTSAVKHHHHHH
-------110-------120-------130-------140-------150-------160-------170---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	179	0	0	100.0

Content subtype: combined_25435_2mxx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1642		96.1 (chain: A, length: 179)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2043 (1)	noe	94.4 (chain: A, length: 179)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 179, Sequence coverage: 96.1%
- Total number of assignments
  - ¹³C chemical shifts: 640
  - ¹H chemical shifts: 825
  - ¹⁵N chemical shifts: 177
- 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 (%)
¹³C chemical shifts	740	640	86.5
¹H chemical shifts	1001	825	82.4
¹⁵N chemical shifts	205	177	86.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	358	344	96.1
¹H chemical shifts	364	345	94.8
¹⁵N chemical shifts	174	165	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	382	296	77.5
¹H chemical shifts	637	480	75.4
¹⁵N chemical shifts	31	12	38.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	85	83	97.6
¹H chemical shifts	85	83	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	72	15	20.8
¹H chemical shifts	72	30	41.7

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 179, Sequence coverage: 94.4%
- Total number of restraints: 2043
- Weight of restraints: 1.0 (2043)
- Potential type of restraints: upper-bound-parabolic (2043)
- 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 AbpA, Streptococcous gordonii, amylase binding protein, amylase enzyme

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Found 1 Document (0.722 seconds)

BMRB: 25435

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail