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BMRB: 15811

2K4X

Solution structure of 30S ribosomal protein S27A from Thermoplasma acidophilum

Authors

Wu, B., Yee, A., Fares, C., Lemak, A., Semest, A., Arrowsmith, C.

Assembly

S27A

Entity

1. 30S ribosomal protein S27A (polymer, Thiol state: free and other bound), 55 monomers, 6381.378 Da Detail

MQKRELYEIA DGKLVRKHRF CPRCGPGVFL AEHADRYSCG RCGYTEFKKA KKSKS

2. ZN (non-polymer), 65.409 Da

Total weight

6446.787 Da

Max. entity weight

6381.378 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS21:SG	2:ZN1:ZN
2	na	sing	1:CYS24:SG	2:ZN1:ZN
3	na	sing	1:CYS39:SG	2:ZN1:ZN
4	na	sing	1:CYS42:SG	2:ZN1:ZN

Source organism

Thermoplasma acidophilum

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.7 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.7 % (582 of 664)	86.5 % (307 of 355)	87.5 % (223 of 255)	96.3 % (52 of 54)
Backbone	95.4 % (311 of 326)	93.8 % (106 of 113)	95.6 % (153 of 160)	98.1 % (52 of 53)
Sidechain	82.7 % (321 of 388)	83.1 % (201 of 242)	82.8 % (120 of 145)	0.0 % (0 of 1)
Aromatic	62.9 % (39 of 62)	80.6 % (25 of 31)	45.2 % (14 of 31)
Methyl	97.1 % (33 of 34)	100.0 % (17 of 17)	94.1 % (16 of 17)

1. 30S ribosomal protein S27A

MQKRELYEIA DGKLVRKHRF CPRCGPGVFL AEHADRYSCG RCGYTEFKKA KKSKS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
10	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
11	TRIS	[U-100% 2H]	10 mM
12	sodium chloride	natural abundance	300 mM
13	ZnSO4	natural abundance	10 uM
14	DTT	[U-100% 2H]	10 mM
15	sodium azide	natural abundance	0.01 %
16	benzamidine	natural abundance	10 mM
17	D2O	[U-100% 2H]	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.21 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K4X, Strand ID: A Detail

Release date

2009-04-22

Citation

Solution structure of 30S ribosomal protein S27A from Thermoplasma acidophilum/Northeast Structural Genomics Consortium Target TaT88/Ontario Center for Structural Proteomics target ta1093
Wu, B., Yee, A., Fares, C., Lemak, A., Semest, A., Arrowsmith, C.
Not known

Related entities 1. 30S ribosomal protein S27A, : 1 : 1 : 68 entities Detail

Experiments performed 14 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

3 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

5 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

6 3D C(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

7 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

10 3D CCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
10	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
11	TRIS	[U-100% 2H]	10 mM
12	sodium chloride	natural abundance	300 mM
13	ZnSO4	natural abundance	10 uM
14	DTT	[U-100% 2H]	10 mM
15	sodium azide	natural abundance	0.01 %
16	benzamidine	natural abundance	10 mM
17	D2O	[U-100% 2H]	100 %

14 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	30S ribosomal protein S27A	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	[U-100% 2H]	10 mM
6	sodium azide	natural abundance	0.01 %
7	benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D2O	[U-100% 2H]	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15811_2k4x.nef
Input source #2: Coordindates	2k4x.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:21:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:24:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:39:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:42:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50-----
MQKRELYEIADGKLVRKHRFCPRCGPGVFLAEHADRYSCGRCGYTEFKKAKKSKS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQKRELYEIADGKLVRKHRFCPRCGPGVFLAEHADRYSCGRCGYTEFKKAKKSKS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	55	0	0	100.0

Content subtype: combined_15811_2k4x.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_chem_shift_list_1	Warning	592		100.0 (chain: A, length: 55)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	858 (1)	noe	89.1 (chain: A, length: 55)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	14 (1)	hbond	18.2 (chain: A, length: 55)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	40 (40)	.	50.9 (chain: A, length: 55)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 317
  - ¹³C chemical shifts: 224
  - ¹⁵N chemical shifts: 51
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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	355	316	89.0
¹³C chemical shifts	255	224	87.8
¹⁵N chemical shifts	60	51	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	113	110	97.3
¹³C chemical shifts	110	104	94.5
¹⁵N chemical shifts	53	51	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	242	206	85.1
¹³C chemical shifts	145	120	82.8
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0
¹³C chemical shifts	18	17	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	25	80.6
¹³C chemical shifts	31	14	45.2

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 89.1%
- Total number of restraints: 858
- Weight of restraints: 1.0 (858)
- Potential type of restraints: square-well-parabolic (858)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 18.2%
  - Total number of restraints: 14
  - Weight of restraints: 1.0 (14)
  - Potential type of restraints: square-well-parabolic (14)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - 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: 55, Sequence coverage: 50.9%
- Total number of restraints: 40
- Total number of restraints per polymer type: 40
- Weight of restraints: 1.0 (40)
- Potential type of restraints: square-well-parabolic (40)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords 30S ribosomal protein S27A

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Found 1 Document (0.598 seconds)

BMRB: 15811

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Sample #2

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. 30S ribosomal protein S27A, : 1 : 1 : 68 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 5 contents Detail