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BMRB: 26053

2NDA

Solution structure of MapZ extracellular domain second subdomain

Authors

Jean, N.L., Manuse, S., Guinot, M., Bougault, C.M., Grangeasse, C., Simorre, J.

Assembly

MapZ SY

Entity

1. MapZ SY (polymer, Thiol state: all free), 113 monomers, 12301.29 Da Detail

GHMSRSEVNM GLSSAGVAVQ RSASRVAYNQ SAIDDSNNSA WDFADGVLEQ ILATSRSRGY ITGDQYILER VNIVNGNGYY NLYKPDGTYL FTLNCKTGYF VGNGAGHADD LDY

Formula weight

12301.29 Da

Source organism

Streptococcus pneumoniae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.6 %, Completeness: 89.3 %, Completeness (bb): 91.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.3 % (1102 of 1234)	89.2 % (562 of 630)	89.3 % (426 of 477)	89.8 % (114 of 127)
Backbone	91.7 % (620 of 676)	89.5 % (213 of 238)	94.5 % (308 of 326)	88.4 % (99 of 112)
Sidechain	87.5 % (576 of 658)	89.0 % (349 of 392)	84.5 % (212 of 251)	100.0 % (15 of 15)
Aromatic	59.0 % (72 of 122)	67.2 % (41 of 61)	50.0 % (30 of 60)	100.0 % (1 of 1)
Methyl	99.1 % (113 of 114)	98.2 % (56 of 57)	100.0 % (57 of 57)

1. MapZ SY

GHMSRSEVNM GLSSAGVAVQ RSASRVAYNQ SAIDDSNNSA WDFADGVLEQ ILATSRSRGY ITGDQYILER VNIVNGNGYY NLYKPDGTYL FTLNCKTGYF VGNGAGHADD LDY

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.09 ppm, Outliers: 4 Detail

LACS Plot; CB

Referencing offset: 0.09 ppm, Outliers: 4 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.05 ppm, Outliers: 7 Detail

Protein Blocks Logo

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

Release date

2016-06-26

Citation

Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ
Manuse, S., Jean, N.L., Guinot, M., Lavergne, J., Laguri, C., Bougault, C.M., Van Nieuwenhze, M.S., Grangeasse, C., Simorre, J.
Nat. Commun. (2016), 7, 12071-12071, PubMed 27346279 , DOI 10.1038/ncomms12071 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26052 released on 2016-06-26
Title Solution structure of MapZ extracellular domain first subdomain

Related entities 1. MapZ SY, : 1 : 1 entities Detail

Interaction partners 1. MapZ SY, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC/HMQC

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

2 3D HN(CA)CO

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

4 3D HNCACB

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

5 3D HN(CO)CACB

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

6 3D C(CO)NH

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

9 3D H(CCO)NH

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

10 2D 1H-13C HSQC/HMQC

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

11 2D 1H-13C HSQC/HMQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

12 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	MapZ_extra2	[U-100% 13C; U-100% 15N]		2.5 mM
2	Tris	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	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_26053_2nda.nef
Input source #2: Coordindates	2nda.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
GHMSRSEVNMGLSSAGVAVQRSASRVAYNQSAIDDSNNSAWDFADGVLEQILATSRSRGYITGDQYILERVNIVNGNGYYNLYKPDGTYLFTLNCKTGYF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMSRSEVNMGLSSAGVAVQRSASRVAYNQSAIDDSNNSAWDFADGVLEQILATSRSRGYITGDQYILERVNIVNGNGYYNLYKPDGTYLFTLNCKTGYF

-------110---
VGNGAGHADDLDY
|||||||||||||
VGNGAGHADDLDY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_26053_2nda.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	1100		95.6 (chain: A, length: 113)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	4185 (1)	noe	92.0 (chain: A, length: 113)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	160 (160)	.	84.1 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 95.6%
- Total number of assignments
  - ¹H chemical shifts: 561
  - ¹³C chemical shifts: 426
  - ¹⁵N chemical shifts: 113
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 92.0%
- Total number of restraints: 4138
- Weight of restraints: 1.0 (4138)
- Potential type of restraints: square-well-parabolic (4138)
- Range of distance target values: 1.43, 4.06 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 84.1%
- Total number of restraints: 160
- Total number of restraints per polymer type: 160
- Weight of restraints: 1.0 (160)
- Potential type of restraints: square-well-parabolic (160)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords FtsZ, MapZ, division, peptidoglycan