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Found 1 Document (1.389 seconds)

BMRB: 4958

2NBI

1H, 13C and 15N Sequence-specific Resonance Assignment of the PSCD4 Domain of Diatom cell wall Protein Pleuralin-1

Authors

Wenzler, M., Brunner, E., Kroger, N., Lehmann, G., Sumper, M., Kalbitzer, H.R., De Sanctis, S., Malloni, W.M.

Assembly

His6PSCD4

Entity

1. His6PSCD4 (polymer, Thiol state: not reported), 112 monomers, 11946.29 Da Detail

SYYHHHHHHT MMPSPEPSSQ PSDCGEVIEE CPIDACFLPK SDSARPPDCT AVGRPDCNVL PFPNNIGCPS CCPFECSPDN PMFTPSPDGS PPNCSPTMLP SPSPSAVTVP LT

Formula weight

11946.29 Da

Source organism

Cylindrotheca fusiformis

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 84.7 %, Completeness (bb): 90.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.7 % (1018 of 1202)	86.7 % (546 of 630)	80.8 % (386 of 478)	91.5 % (86 of 94)
Backbone	90.9 % (567 of 624)	92.6 % (189 of 204)	89.8 % (298 of 332)	90.9 % (80 of 88)
Sidechain	79.9 % (548 of 686)	83.8 % (357 of 426)	72.8 % (185 of 254)	100.0 % (6 of 6)
Aromatic	20.0 % (16 of 80)	40.0 % (16 of 40)	0.0 % (0 of 40)
Methyl	89.7 % (61 of 68)	94.1 % (32 of 34)	85.3 % (29 of 34)

1. pleuralin-1, formerly HEP200

SYYHHHHHHT MMPSPEPSSQ PSDCGEVIEE CPIDACFLPK SDSARPPDCT AVGRPDCNVL PFPNNIGCPS CCPFECSPDN PMFTPSPDGS PPNCSPTMLP SPSPSAVTVP LT

Show sample condition

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

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: -0.04 ppm, Outliers: 1 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: -0.04 ppm, Outliers: 1 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: 0.07 ppm, Outliers: 3 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: 0.0 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MK0, Strand ID: A Detail

Release date

2002-04-02

Citation 1

1H, 13C and 15N sequence-specific resonance assignment of the PSCD4 domain of diatom cell wall protein pleuralin-1 [etter]
Wenzler, M., Brunner, E., Kroger, N., Lehmann, G., Sumper, M., Kalbitzer, H.R.
J. Biomol. NMR (2001), 20, 191-192, PubMed 11495255 , DOI: , Abstract

Show more 2 citaions

Citation 2

Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension
Horton, R.M., Hunt, H.D., Ho, S.N., Pullen, J.K., Pease, L.R.
Gene (1989), 77, 61-68, PubMed 2744488 , DOI: , Abstract

Citation 3

Characterization of a 200-kDa diatom protein that is specifically associated with a silica-based substructure of the cell wall
Kroger, N., Lehmann, G., Rachel, R., Sumper, M.
Eur. J. Biochem. (1997), 250, 99-105, PubMed 9431996 , Abstract

Hide non-primary 2 citaions

Related entities 1. His6PSCD4, : 4 : 1 : 2 entities Detail

Experiments performed 8 experiments Detail

1 HNCA

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

2 CBCA(CO)NH

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

3 1H-15N-HSQC

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

4 1H-15N-NOESY HSQC

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

5 1H-15N-TOCSY HSQC

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

6 HNCO

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

7 HACACO

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

8 HCCH-TOCSY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	pleuralin-1, formerly HEP200			0.8 mM

Sample #2

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	pleuralin-1, formerly HEP200	[U-97% 15N]		0.8 mM

Sample #3

Temperature 298 (±1.5) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	pleuralin-1, formerly HEP200	[U-97% 13C; U-98% 15N]		0.8 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_4958_2nbi.nef
Input source #2: Coordindates	2nbi.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	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:101:CYS:SG	A:171:CYS:SG	unknown	unknown	2.059
A:108:CYS:SG	A:153:CYS:SG	unknown	unknown	2.023
A:113:CYS:SG	A:149:CYS:SG	unknown	unknown	2.009
A:126:CYS:SG	A:148:CYS:SG	unknown	unknown	2.045
A:134:CYS:SG	A:145:CYS:SG	unknown	unknown	2.037
A:193:CYS:SG	A:263:CYS:SG	unknown	unknown	2.033
A:200:CYS:SG	A:245:CYS:SG	unknown	unknown	2.009
A:205:CYS:SG	A:241:CYS:SG	unknown	unknown	2.01
A:218:CYS:SG	A:240:CYS:SG	unknown	unknown	2.016
A:226:CYS:SG	A:237:CYS:SG	unknown	unknown	2.023
A:291:CYS:SG	A:363:CYS:SG	unknown	unknown	2.032
A:298:CYS:SG	A:345:CYS:SG	unknown	unknown	2.023
A:303:CYS:SG	A:341:CYS:SG	unknown	unknown	2.038
A:316:CYS:SG	A:340:CYS:SG	unknown	unknown	2.02
A:326:CYS:SG	A:337:CYS:SG	unknown	unknown	2.027
A:380:CYS:SG	A:450:CYS:SG	unknown	unknown	2.027
A:387:CYS:SG	A:432:CYS:SG	unknown	unknown	2.008
A:392:CYS:SG	A:428:CYS:SG	unknown	unknown	2.029
A:405:CYS:SG	A:427:CYS:SG	unknown	unknown	2.015
A:413:CYS:SG	A:424:CYS:SG	unknown	unknown	2.028
A:495:CYS:SG	A:567:CYS:SG	unknown	unknown	2.019
A:502:CYS:SG	A:549:CYS:SG	unknown	unknown	2.042
A:507:CYS:SG	A:545:CYS:SG	unknown	unknown	2.036
A:520:CYS:SG	A:544:CYS:SG	unknown	unknown	2.025
A:530:CYS:SG	A:541:CYS:SG	unknown	unknown	2.034

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

--90------100-------110-------120-------130-------140-------150-------160-------170-------180-------
QPSDLNPSSQPSECADVLEECPIDECFLPYSDASRPPSCLSFGRPDCDVLPTPQNINCPRCCATECRPDNPMFTPSPDGSPPICSPTMLPTNQPTPPEPS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QPSDLNPSSQPSECADVLEECPIDECFLPYSDASRPPSCLSFGRPDCDVLPTPQNINCPRCCATECRPDNPMFTPSPDGSPPICSPTMLPTNQPTPPEPS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------
SAPSDCGEVIEECPLDTCFLPTSDPARPPDCTAVGRPDCDVLPFPNNLGCPACCPFECSPDNPMFTPSPDGSPPNCSPTMLPTPQPSTPTVITSPAPSSQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SAPSDCGEVIEECPLDTCFLPTSDPARPPDCTAVGRPDCDVLPFPNNLGCPACCPFECSPDNPMFTPSPDGSPPNCSPTMLPTPQPSTPTVITSPAPSSQ
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------
PSQCAEVIEQCPIDECFLPYGDSSRPLDCTDPAVNRPDCDVLPTPQNINCPACCAFECRPDNPMFTPSPDGSPPICSPTMMPSPEPSSQPSDCGEVIEEC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PSQCAEVIEQCPIDECFLPYGDSSRPLDCTDPAVNRPDCDVLPTPQNINCPACCAFECRPDNPMFTPSPDGSPPICSPTMMPSPEPSSQPSDCGEVIEEC
-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300

390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------
PIDACFLPKSDSARPPDCTAVGRPDCNVLPFPNNIGCPSCCPFECSPDNPMFTPSPDGSPPNCSPTMLPSPSPSAVTVPLTPAPSSAPTRQPSSQPTGPQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PIDACFLPKSDSARPPDCTAVGRPDCNVLPFPNNIGCPSCCPFECSPDNPMFTPSPDGSPPNCSPTMLPSPSPSAVTVPLTPAPSSAPTRQPSSQPTGPQ
-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400

490-------500-------510-------520-------530-------540-------550-------560-------570-------580-
PSSQPSECADVLELCPYDTCFLPFDDSSRPPDCTDPSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPMFSPSPDGSPPVCSPTMMPSPLPSPTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PSSQPSECADVLELCPYDTCFLPFDDSSRPPDCTDPSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPMFSPSPDGSPPVCSPTMMPSPLPSPTE
-------410-------420-------430-------440-------450-------460-------470-------480-------490----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	494	0	0	100.0

Content subtype: combined_4958_2nbi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	system_His6PSCD4	OK	25		No information
1	Assigned chemical shifts	shift_set_1	Error	1012		20.2 (chain: A, length: 494)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	7645 (1)	noe	79.1 (chain: A, length: 494)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	118 (1)	hbond	24.1 (chain: A, length: 494)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	445 (445)	.	67.6 (chain: A, length: 494)

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 494, Sequence coverage: 20.2%
- Total number of assignments
  - ¹³C chemical shifts: 391
  - ¹H chemical shifts: 535
  - ¹⁵N chemical shifts: 86
- Completeness of assignments
- 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

Covalent bonds

Saveframe: system_His6PSCD4
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 494, Sequence coverage: 79.1%
- Total number of restraints: 7640
- Weight of restraints: 1.0 (7640)
- Potential type of restraints: lower-bound-parabolic (9), square-well-parabolic (7631)
- Range of distance target values: 1.78, 80.0 (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
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 494, Sequence coverage: 24.1%
  - Total number of restraints: 118
  - Weight of restraints: 1.0 (118)
  - Potential type of restraints: square-well-parabolic (118)
  - Range of distance target values: 1.76, 2.9 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 494, Sequence coverage: 67.6%
- Total number of restraints: 445
- Total number of restraints per polymer type: 445
- Weight of restraints: 1.0 (445)
- Potential type of restraints: square-well-parabolic (445)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords diatom cell wall, NMR assignments, pleuralin, PSCD

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Found 1 Document (1.389 seconds)

BMRB: 4958

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. His6PSCD4, : 4 : 1 : 2 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 5 contents Detail