BMRBj - BMREntryMaster

Found 1 Document (0.961 seconds)

BMRB: 25127

2MSN

NMR structure of a putative phosphoglycolate phosphatase (NP_346487.1) from Streptococcus pneumoniae TIGR4

Authors

Jaudzems, K., Serrano, P., Pedrini, B., Geralt, M., Wuthrich, K.

Assembly

putative phosphoglycolate phosphatase

Entity

1. putative phosphoglycolate phosphatase (polymer, Thiol state: not present), 208 monomers, 23684.22 Da Detail

GHMQKTAFIW DLDGTLLDSY EAILSGIEET FAQFSIPYDK EKVREFIFKY SVQDLLVRVA EDRNLDVEVL NQVRAQSLAE KNAQVVLMPG AREVLAWADE SGIQQFIYTH KGNNAFTILK DLGVESYFTE ILTSQSGFVR KPSPEAATYL LDKYQLNSDN TYYIGDRTLD VEFAQNSGIQ SINFLESTYE GNHRIQALAD ISRIFETK

Formula weight

23684.22 Da

Source organism

Streptococcus pneumoniae TIGR4

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.5 %, Completeness: 82.4 %, Completeness (bb): 71.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.4 % (2029 of 2461)	85.2 % (1082 of 1270)	75.3 % (724 of 962)	97.4 % (223 of 229)
Backbone	71.7 % (889 of 1240)	62.6 % (265 of 423)	69.5 % (426 of 613)	97.1 % (198 of 204)
Sidechain	94.2 % (1336 of 1418)	96.5 % (817 of 847)	90.5 % (494 of 546)	100.0 % (25 of 25)
Aromatic	77.5 % (183 of 236)	94.1 % (111 of 118)	60.3 % (70 of 116)	100.0 % (2 of 2)
Methyl	99.6 % (247 of 248)	99.2 % (123 of 124)	100.0 % (124 of 124)

1. entity

GHMQKTAFIW DLDGTLLDSY EAILSGIEET FAQFSIPYDK EKVREFIFKY SVQDLLVRVA EDRNLDVEVL NQVRAQSLAE KNAQVVLMPG AREVLAWADE SGIQQFIYTH KGNNAFTILK DLGVESYFTE ILTSQSGFVR KPSPEAATYL LDKYQLNSDN TYYIGDRTLD VEFAQNSGIQ SINFLESTYE GNHRIQALAD ISRIFETK

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: 0.05 ppm, Outliers: 4 Detail

LACS Plot; CB

Referencing offset: 0.05 ppm, Outliers: 4 Detail

LACS Plot; HA

Referencing offset: 0.08 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2014-09-21

Related entities 1. putative phosphoglycolate phosphatase, : 1 : 2 : 1 : 130 entities Detail

Experiments performed 8 experiments Detail

1 5D APSY-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

2 4D APSY-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

3 4D APSY-HNCOCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

4 4D APSY-HNCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

5 5D APSY-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.5 (±0.1) mM
2	D2O	[U-100% 2H]		5 (±0.5) %
3	sodium azide	natural abundance		0.03 (±0.01) %
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±2.0) mM
6	H2O	natural abundance		95 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25127_2msn.nef
Input source #2: Coordindates	2msn.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	.	Not matched with CCD	None

Sequence alignments

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

---                                                                                                 
.GH                                                                                                 
 ||                                                                                                 
-GHMQKTAFIWDLDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVAEDRNLDVEVLNQVRAQSLAEKNAQVVLMPGAREVLAWAD
 ---------10--------20--------30--------40--------50--------60--------70--------80--------90-------1

                                                                                                    
                                                                                                    
                                                                                                    
ESGIQQFIYTHKGNNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFLESTYEGNHRIQALA
00-------110-------120-------130-------140-------150-------160-------170-------180-------190-------2

         
         
         
DISRIFETK
00-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	208	1	0	100.0

Content subtype: combined_25127_2msn.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1961		No information
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Error	4628	noe	No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Error
- Experiment type: noe

Keywords putative phosphoglycolate phosphatase, haloacid dehalogenase like hydrolase