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Found 1 Document (0.821 seconds)

BMRB: 15431

2JU5

NMR assignment of the periplasmic oxidoreductase DsbH from Chlamydia

Authors

Ulmer, T.

Assembly

single polypeptide chain

Entity

1. single polypeptide chain (polymer, Thiol state: all disulfide bound), 144 monomers, 16456.50 Da Detail

ARRRASGENL QQTRPIAAAN LQWESYAEAL EHSKQDHKPI GLFFTGSDWC MWCIKMQDQI LQSSEFKHFA GVHLHMVEVD FPQKNHQPEE QRQKNQELKA QYKVTGFPEL VFIDAEGKQL ARMGFEPGGG AAYVSKVKSA LKLR

Formula weight

16456.5 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS50:SG	1:CYS53:SG

Source organism

Chlamydia pneumoniae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.6 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.6 % (1486 of 1735)	83.2 % (760 of 914)	87.9 % (582 of 662)	90.6 % (144 of 159)
Backbone	98.1 % (836 of 852)	98.6 % (288 of 292)	97.2 % (410 of 422)	100.0 % (138 of 138)
Sidechain	77.0 % (783 of 1017)	75.9 % (472 of 622)	81.6 % (305 of 374)	28.6 % (6 of 21)
Aromatic	32.9 % (54 of 164)	42.7 % (35 of 82)	20.3 % (16 of 79)	100.0 % (3 of 3)
Methyl	96.8 % (122 of 126)	96.8 % (61 of 63)	96.8 % (61 of 63)

1. DsbH

ARRRASGENL QQTRPIAAAN LQWESYAEAL EHSKQDHKPI GLFFTGSDWC MWCIKMQDQI LQSSEFKHFA GVHLHMVEVD FPQKNHQPEE QRQKNQELKA QYKVTGFPEL VFIDAEGKQL ARMGFEPGGG AAYVSKVKSA LKLR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.0, Details 50 mM NaH2PO4/Na2HPO4 pH 6.0, 0.02% w/v NaN3

#	Name	Isotope labeling	Concentration
1	DsbH	[U-99% 13C; U-99% 15N]	1.0 mM
2	NaH2PO4/Na2HPO4		50 mM
3	NaN3		0.02 % w/v
4	H2O		95 %
5	D2O		5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.77 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	4.77 ppm	internal	indirect	0.101329

Referencing offset: 0.1 ppm, Outliers: 5 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.77 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	4.77 ppm	internal	indirect	0.101329

Referencing offset: 0.1 ppm, Outliers: 5 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.77 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	4.77 ppm	internal	indirect	0.101329

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.77 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	4.77 ppm	internal	indirect	0.101329

Referencing offset: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JU5, Strand ID: A Detail

Release date

2007-11-15

Citation

NMR assignment of the periplasmic oxidoreductase DsbH from Chlamydia
Hung, K., Mac, T., Ulmer, T.S.
Biomol. NMR Assign. (2007), 1, 195-196, PubMed 19636863 , DOI 10.1007/s12104-007-9054-8 , Abstract

Related entities 1. single polypeptide chain, : 1 : 1 : 7 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15431_2ju5.nef
Input source #2: Coordindates	2ju5.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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:50:CYS:SG	A:53:CYS:SG	oxidized, CA 54.2, CB 41.5 ppm	reduced, CA 63.7, CB 31.8 ppm	2.015

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
MAHHHHHHSAARRRASGENLQQTRPIAAANLQWESYAEALEHSKQDHKPIGLFFTGSDWCMWCIKMQDQILQSSEFKHFAGVHLHMVEVDFPQKNHQPEE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAHHHHHHSAARRRASGENLQQTRPIAAANLQWESYAEALEHSKQDHKPIGLFFTGSDWCMWCIKMQDQILQSSEFKHFAGVHLHMVEVDFPQKNHQPEE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------100-------110-------120-------130-------140----
QRQKNQELKAQYKVTGFPELVFIDAEGKQLARMGFEPGGGAAYVSKVKSALKLR
||||||||||||||||||||||||||||||||||||||||||||||||||||||
QRQKNQELKAQYKVTGFPELVFIDAEGKQLARMGFEPGGGAAYVSKVKSALKLR
-------110-------120-------130-------140-------150----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	154	0	0	100.0

Content subtype: combined_15431_2ju5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1469		93.5 (chain: A, length: 154)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3766 (1)	noe	80.5 (chain: A, length: 154)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	257 (257)	.	80.5 (chain: A, length: 154)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 93.5%
- Total number of assignments
  - ¹H chemical shifts: 746
  - ¹³C chemical shifts: 582
  - ¹⁵N chemical shifts: 141
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
33	SER	HG	5.74

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	967	745	77.0
¹³C chemical shifts	706	582	82.4
¹⁵N chemical shifts	176	141	80.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	290	92.9
¹³C chemical shifts	308	275	89.3
¹⁵N chemical shifts	148	138	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	655	455	69.5
¹³C chemical shifts	398	307	77.1
¹⁵N chemical shifts	28	3	10.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	67	95.7
¹³C chemical shifts	70	67	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	33	35.1
¹³C chemical shifts	91	16	17.6
¹⁵N chemical shifts	3	3	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 80.5%
- Total number of restraints: 3659
- Weight of restraints: 1.0 (3659)
- Potential type of restraints: square-well-parabolic (3659)
- Range of distance target values: 2.25, 4.15 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 80.5%
- Total number of restraints: 257
- Total number of restraints per polymer type: 257
- Weight of restraints: 1.0 (257)
- Potential type of restraints: square-well-parabolic (257)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords oxidoreductase, protein

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Found 1 Document (0.821 seconds)

BMRB: 15431

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. single polypeptide chain, : 1 : 1 : 7 entities Detail

Experiments performed 6 experiments Detail

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NMR combined restraints 4 contents Detail