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Found 1 Document (0.763 seconds)

BMRB: 30020

5IAZ

The C-terminal domain of rice beta-galactosidase 1

Authors

Rimlumduan, T., Hua, Y., Tanaka, T., Ketudat-Cairns, J.

Assembly

beta-galactosidase 1

Entity

1. beta-galactosidase 1 (polymer, Thiol state: all disulfide bound), 122 monomers, 13014.65 Da Detail

GSHMRTVSGV CADVSEYHPN IKNWQIESYG EPEFHTAKVH LKCAPGQTIS AIKFASFGTP LGTCGTFQQG ECHSINSNSV LERKCIGLER CVVAISPSNF GGDPCPEVMK RVAVEAVCST AA

Formula weight

13014.65 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS64:SG
2	disulfide	sing	1:CYS43:SG	1:CYS118:SG
3	disulfide	sing	1:CYS72:SG	1:CYS105:SG
4	disulfide	sing	1:CYS85:SG	1:CYS91:SG

Source organism

Oryza sativa Indica Group

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 90.9 %, Completeness (bb): 93.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.9 % (1213 of 1334)	94.6 % (650 of 687)	85.6 % (447 of 522)	92.8 % (116 of 125)
Backbone	93.5 % (671 of 718)	93.1 % (231 of 248)	94.1 % (334 of 355)	92.2 % (106 of 115)
Sidechain	89.7 % (652 of 727)	95.4 % (419 of 439)	80.2 % (223 of 278)	100.0 % (10 of 10)
Aromatic	49.0 % (48 of 98)	95.9 % (47 of 49)	0.0 % (0 of 48)	100.0 % (1 of 1)
Methyl	99.2 % (121 of 122)	98.4 % (60 of 61)	100.0 % (61 of 61)

1. entity 1

GSHMRTVSGV CADVSEYHPN IKNWQIESYG EPEFHTAKVH LKCAPGQTIS AIKFASFGTP LGTCGTFQQG ECHSINSNSV LERKCIGLER CVVAISPSNF GGDPCPEVMK RVAVEAVCST AA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.5 mM OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
1	D2O	[U-2H]	5 %
2	H2O	natural abundance	95 %
3	OsBGal1 Cter	natural abundance	0.5 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.54 mM OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 100 % [U-2H] D2O, 100% D2O.

#	Name	Isotope labeling	Concentration
6	D2O	[U-2H]	100 %
7	OsBGal1 Cter	natural abundance	0.54 mM
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	20 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.79 mM [U-100% 15N] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
10	D2O	[U-2H]	5 %
11	H2O	natural abundance	95 %
12	OsBGal1 Cter	[U-100% 15N]	0.79 mM
13	sodium chloride	natural abundance	100 mM
14	sodium phosphate	natural abundance	20 mM

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.5 mM [U-100% 13C; U-100% 15N] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.18 mM [U-10% 13C] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
20	D2O	[U-2H]	5 %
21	H2O	natural abundance	95 %
22	OsBGal1 Cter	[U-10% 13C]	0.18 mM
23	sodium chloride	natural abundance	100 mM
24	sodium phosphate	natural abundance	20 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	external	indirect	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.28 ppm, Outliers: 2 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	external	indirect	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.28 ppm, Outliers: 2 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	external	indirect	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.03 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	external	indirect	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.43 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 5IAZ, Strand ID: A Detail

Release date

2016-08-07

Citation

Structure of a plant β-galactosidase C-terminal domain
Rimlumduan, T., Hua, Y., Tanaka, T., Ketudat-Cairns, J.
Biochim. Biophys. Acta (2016), 1864, 1411-1418, PubMed 27451952 , DOI 10.1016/j.bbapap.2016.07.005 , Abstract

Related entities 1. beta-galactosidase 1, : 67 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVANCE DRX - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.5 mM OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
1	D2O	[U-2H]	5 %
2	H2O	natural abundance	95 %
3	OsBGal1 Cter	natural abundance	0.5 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

2 2D 1H-1H NOESY

Instrument

Bruker AVANCE DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.54 mM OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 100 % [U-2H] D2O, 100% D2O.

#	Name	Isotope labeling	Concentration
6	D2O	[U-2H]	100 %
7	OsBGal1 Cter	natural abundance	0.54 mM
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	20 mM

3 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.79 mM [U-100% 15N] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
10	D2O	[U-2H]	5 %
11	H2O	natural abundance	95 %
12	OsBGal1 Cter	[U-100% 15N]	0.79 mM
13	sodium chloride	natural abundance	100 mM
14	sodium phosphate	natural abundance	20 mM

4 3D HNHA

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
10	D2O	[U-2H]	5 %
11	H2O	natural abundance	95 %
12	OsBGal1 Cter	[U-100% 15N]	0.79 mM
13	sodium chloride	natural abundance	100 mM
14	sodium phosphate	natural abundance	20 mM

5 2D 1H-15N HSQC

Instrument

Varian UNITY INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.5 mM [U-100% 13C; U-100% 15N] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

6 2D 1H-13C HSQC

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

7 3D HNCO

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

8 3D CBCA(CO)NH

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

9 3D HNCACB

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

10 3D HCCH-TOCSY

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

11 3D C(CO)NH

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

12 3D HBCBCACOCAHA

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

13 3D 1H-13C NOESY

Instrument

Varian UNITY INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	D2O	[U-2H]	5 %
16	H2O	natural abundance	95 %
17	OsBGal1 Cter	[U-100% 13C; U-100% 15N]	0.5 mM
18	sodium chloride	natural abundance	100 mM
19	sodium phosphate	natural abundance	20 mM

14 2D 1H-13C HSQC

Instrument

Bruker AVANCE DRX - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 0.18 mM [U-10% 13C] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
20	D2O	[U-2H]	5 %
21	H2O	natural abundance	95 %
22	OsBGal1 Cter	[U-10% 13C]	0.18 mM
23	sodium chloride	natural abundance	100 mM
24	sodium phosphate	natural abundance	20 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30020_5iaz.nef
Input source #2: Coordindates	5iaz.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:732:CYS:SG	A:785:CYS:SG	oxidized, CA 53.6, CB 49.3 ppm	oxidized, CA 57.2, CB 37.9 ppm	2.019
A:764:CYS:SG	A:839:CYS:SG	oxidized, CA 52.9, CB 40.7 ppm	oxidized, CA 55.1, CB 44.9 ppm	2.019
A:793:CYS:SG	A:826:CYS:SG	oxidized, CA 52.9, CB 40.2 ppm	oxidized, CA 54.6, CB 44.6 ppm	2.019
A:806:CYS:SG	A:812:CYS:SG	oxidized, CA 57.0, CB 44.5 ppm	oxidized, CA 53.9, CB 46.4 ppm	2.02

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

------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-
GSHMRTVSGVCADVSEYHPNIKNWQIESYGEPEFHTAKVHLKCAPGQTISAIKFASFGTPLGTCGTFQQGECHSINSNSVLERKCIGLERCVVAISPSNF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMRTVSGVCADVSEYHPNIKNWQIESYGEPEFHTAKVHLKCAPGQTISAIKFASFGTPLGTCGTFQQGECHSINSNSVLERKCIGLERCVVAISPSNF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------830-------840---
GGDPCPEVMKRVAVEAVCSTAA
||||||||||||||||||||||
GGDPCPEVMKRVAVEAVCSTAA
-------110-------120--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	122	0	0	100.0

Content subtype: combined_30020_5iaz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1211		96.7 (chain: A, length: 122)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	12 (1)	undefined	6.6 (chain: A, length: 122)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	3215 (1)	noe	96.7 (chain: A, length: 122)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	75 (75)	.	58.2 (chain: A, length: 122)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 653
  - ¹³C chemical shifts: 444
  - ¹⁵N chemical shifts: 114
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
741	ASN	CG	177.2
744	ASN	CG	177.0
746	GLN	CD	180.4
768	GLN	CD	179.1
780	THR	HG1	5.14
789	GLN	CD	180.7
790	GLN	CD	179.0
798	SER	HG	6.38
799	ASN	CG	176.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	687	651	94.8
¹³C chemical shifts	522	437	83.7
¹⁵N chemical shifts	129	114	88.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	248	232	93.5
¹³C chemical shifts	244	220	90.2
¹⁵N chemical shifts	115	104	90.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	439	419	95.4
¹³C chemical shifts	278	217	78.1
¹⁵N chemical shifts	14	10	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	61	96.8
¹³C chemical shifts	63	61	96.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	47	95.9
¹³C chemical shifts	48	0	0.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 6.6%
- Total number of restraints: 12
- Weight of restraints: 1.0 (12)
- Potential type of restraints: square-well-parabolic (12)
- Range of distance target values: 1.0, 1.55 (Å)
- Histogram of 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: 122, Sequence coverage: 96.7%
  - Total number of restraints: 3214
  - Weight of restraints: 1.0 (3214)
  - Potential type of restraints: square-well-parabolic (3214)
  - Range of distance target values: 1.25, 7.0 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 58.2%
- Total number of restraints: 75
- Total number of restraints per polymer type: 75
- Weight of restraints: 1.0 (75)
- Potential type of restraints: square-well-parabolic (75)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HYDROLASE, beta-sandwich, exoglycosidase, glycoside hydrolase

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Found 1 Document (0.763 seconds)

BMRB: 30020

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. beta-galactosidase 1, : 67 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 5 contents Detail