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Found 1 Document (1.899 seconds)

BMRB: 18112

2LMD

Minimal Constraints Solution NMR Structure of Prospero Homeobox protein 1 from Homo sapiens. Northeast Structural Genomics Consortium Target HR4660B.

Authors

Rossi, P., Lange, O.A., Lee, H., Maglaqui, M., Janjua, H., Ciccosanti, C., Zhao, L., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T.

Assembly

HR4660B

Entity

1. HR4660B (polymer, Thiol state: all free), 174 monomers, 20691.50 Da Detail

MGHHHHHHSH MAMQEGLSPN HLKKAKLMFF YTRYPSSNML KTYFSDVKFN RCITSQLIKW FSNFREFYYI QMEKYARQAI NDGVTSTEEL SITRDCELYR ALNMHYNKAN DFEVPERFLE VAQITLREFF NAIIAGKDVD PSWKKAIYKV ICKLDSEVPE IFKSPNCLQE LLHE

Formula weight

20691.5 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.0 %, Completeness: 59.3 %, Completeness (bb): 79.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	59.3 % (1279 of 2157)	50.8 % (572 of 1127)	65.8 % (555 of 844)	81.7 % (152 of 186)
Backbone	79.8 % (824 of 1032)	75.4 % (261 of 346)	80.1 % (415 of 518)	88.1 % (148 of 168)
Sidechain	44.3 % (574 of 1295)	39.8 % (311 of 781)	52.2 % (259 of 496)	22.2 % (4 of 18)
Aromatic	39.1 % (100 of 256)	39.1 % (50 of 128)	38.1 % (48 of 126)	100.0 % (2 of 2)
Methyl	98.8 % (160 of 162)	98.8 % (80 of 81)	98.8 % (80 of 81)

1. HR4660B

MGHHHHHHSH MAMQEGLSPN HLKKAKLMFF YTRYPSSNML KTYFSDVKFN RCITSQLIKW FSNFREFYYI QMEKYARQAI NDGVTSTEEL SITRDCELYR ALNMHYNKAN DFEVPERFLE VAQITLREFF NAIIAGKDVD PSWKKAIYKV ICKLDSEVPE IFKSPNCLQE LLHE

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.1 mM [U-100% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HR4660B	[U-100% 13C; U-100% 15N]	0.96 mM
2	sodium chloride	natural abundance	200 mM
3	DTT	natural abundance	10 mM
4	Calcium Chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	MES	natural abundance	20 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.2 mM [U-13C; U-15N; U-2H, 1H-LEU HD1,2 1H VAL-HG1,2 1H-ILE HD1] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	HR4660B	[U-13C; U-15N; U-2H]	0.2 mM
10	sodium chloride	natural abundance	200 mM
11	DTT	natural abundance	10 mM
12	Calcium Chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	MES	natural abundance	20 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.86 mM [5% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
17	HR4660B	[5% 13C; U-100% 15N]	0.86 mM
18	sodium chloride	natural abundance	200 mM
19	DTT	natural abundance	10 mM
20	Calcium Chloride	natural abundance	5 mM
21	sodium azide	natural abundance	0.02 %
22	MES	natural abundance	20 mM
23	H2O	natural abundance	95 %
24	D2O	natural abundance	5 %

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: 0.75 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.75 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	internal	direct	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	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2011-12-19

Related entities 1. HR4660B, : 1 : 21 entities Detail

Interaction partners 1. HR4660B, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.1 mM [U-100% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HR4660B	[U-100% 13C; U-100% 15N]	0.96 mM
2	sodium chloride	natural abundance	200 mM
3	DTT	natural abundance	10 mM
4	Calcium Chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	MES	natural abundance	20 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.1 mM [U-100% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HR4660B	[U-100% 13C; U-100% 15N]	0.96 mM
2	sodium chloride	natural abundance	200 mM
3	DTT	natural abundance	10 mM
4	Calcium Chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	MES	natural abundance	20 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.2 mM [U-13C; U-15N; U-2H, 1H-LEU HD1,2 1H VAL-HG1,2 1H-ILE HD1] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	HR4660B	[U-13C; U-15N; U-2H]	0.2 mM
10	sodium chloride	natural abundance	200 mM
11	DTT	natural abundance	10 mM
12	Calcium Chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	MES	natural abundance	20 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HR4660B	[U-13C; U-15N; U-2H]	0.2 mM
10	sodium chloride	natural abundance	200 mM
11	DTT	natural abundance	10 mM
12	Calcium Chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	MES	natural abundance	20 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HR4660B	[U-13C; U-15N; U-2H]	0.2 mM
10	sodium chloride	natural abundance	200 mM
11	DTT	natural abundance	10 mM
12	Calcium Chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	MES	natural abundance	20 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.1 mM [U-100% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HR4660B	[U-100% 13C; U-100% 15N]	0.96 mM
2	sodium chloride	natural abundance	200 mM
3	DTT	natural abundance	10 mM
4	Calcium Chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	MES	natural abundance	20 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.1 mM [U-100% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HR4660B	[U-100% 13C; U-100% 15N]	0.96 mM
2	sodium chloride	natural abundance	200 mM
3	DTT	natural abundance	10 mM
4	Calcium Chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	MES	natural abundance	20 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

8 3D 1H-13C-13C HSQC_NOESY_HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HR4660B	[U-13C; U-15N; U-2H]	0.2 mM
10	sodium chloride	natural abundance	200 mM
11	DTT	natural abundance	10 mM
12	Calcium Chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	MES	natural abundance	20 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.1 mM [U-100% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HR4660B	[U-100% 13C; U-100% 15N]	0.96 mM
2	sodium chloride	natural abundance	200 mM
3	DTT	natural abundance	10 mM
4	Calcium Chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	MES	natural abundance	20 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HR4660B	[U-13C; U-15N; U-2H]	0.2 mM
10	sodium chloride	natural abundance	200 mM
11	DTT	natural abundance	10 mM
12	Calcium Chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	MES	natural abundance	20 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

11 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.86 mM [5% 13C; U-100% 15N] HR4660B, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
17	HR4660B	[5% 13C; U-100% 15N]	0.86 mM
18	sodium chloride	natural abundance	200 mM
19	DTT	natural abundance	10 mM
20	Calcium Chloride	natural abundance	5 mM
21	sodium azide	natural abundance	0.02 %
22	MES	natural abundance	20 mM
23	H2O	natural abundance	95 %
24	D2O	natural abundance	5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18112_2lmd.nef
Input source #2: Coordindates	2lmd.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
MGHHHHHHSHMAMQEGLSPNHLKKAKLMFFYTRYPSSNMLKTYFSDVKFNRCITSQLIKWFSNFREFYYIQMEKYARQAINDGVTSTEELSITRDCELYR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMAMQEGLSPNHLKKAKLMFFYTRYPSSNMLKTYFSDVKFNRCITSQLIKWFSNFREFYYIQMEKYARQAINDGVTSTEELSITRDCELYR

-------110-------120-------130-------140-------150-------160-------170----
ALNMHYNKANDFEVPERFLEVAQITLREFFNAIIAGKDVDPSWKKAIYKVICKLDSEVPEIFKSPNCLQELLHE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ALNMHYNKANDFEVPERFLEVAQITLREFFNAIIAGKDVDPSWKKAIYKVICKLDSEVPEIFKSPNCLQELLHE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	174	0	0	100.0

Content subtype: combined_18112_2lmd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1198		90.8 (chain: A, length: 174)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1488 (1)	noe	86.2 (chain: A, length: 174)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	150 (1)	hbond	56.9 (chain: A, length: 174)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	164 (164)	.	60.9 (chain: A, length: 174)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	97 (97)	.	55.7 (chain: A, length: 174)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 90.8%
- Total number of assignments
  - ¹H chemical shifts: 522
  - ¹³C chemical shifts: 530
  - ¹⁵N chemical shifts: 146
- 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	1127	522	46.3
¹³C chemical shifts	844	530	62.8
¹⁵N chemical shifts	194	146	75.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	346	251	72.5
¹³C chemical shifts	348	289	83.0
¹⁵N chemical shifts	168	144	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	781	271	34.7
¹³C chemical shifts	496	241	48.6
¹⁵N chemical shifts	26	2	7.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	84	95.5
¹³C chemical shifts	88	84	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	128	50	39.1
¹³C chemical shifts	126	48	38.1
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 86.2%
- Total number of restraints: 1488
- Weight of restraints: 1.0 (1488)
- Potential type of restraints: square-well-parabolic (1488)
- Range of distance target values: 2.35, 4.07 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 56.9%
  - Total number of restraints: 150
  - Weight of restraints: 1.0 (150)
  - Potential type of restraints: square-well-parabolic (150)
  - Range of distance target values: 1.9, 2.85 (Å)
  - Histogram of 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: 174, Sequence coverage: 60.9%
- Total number of restraints: 164
- Total number of restraints per polymer type: 164
- Weight of restraints: 1.0 (164)
- Potential type of restraints: square-well-parabolic (164)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 55.7%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MGHHHHHHSHMAMQEGLSPNHLKKAKLMFFYTRYPSSNMLKTYFSDVKFNRCITSQLIKWFSNFREFYYIQMEKYARQAINDGVTSTEELSITRDCELYR
           ||   |              | | |  ||   ||| ||        |  ||  |  ||||||||||| |||||||  |||  |  | ||
...........AM...L..............T.Y.S..ML...FSD.KF........I..FS..R..YYIQMEKYARQ.INDGVTS..ELS..R..E.YR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150-------160-------170----
ALNMHYNKANDFEVPERFLEVAQITLREFFNAIIAGKDVDPSWKKAIYKVICKLDSEVPEIFKSPNCLQELLHE
|| || ||||| || || || |||||||| |||||||||| |||||||||  | |||| |  |  ||||  || 
AL.MH.NKAND.EV.ER.LE.AQITLREF.NAIIAGKDVD.SWKKAIYKV..K.DSEV.E..K..NCLQ..LH 
-------110-------120-------130-------140-------150-------160-------170---

Total number of restraints: 97
Potential type of restraints: undefined (97)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, PSI-2, Structural Genomics, Target HR4660B

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Found 1 Document (1.899 seconds)

BMRB: 18112

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR4660B, : 1 : 21 entities Detail

Interaction partners 1. HR4660B, : 4 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 6 contents Detail