BMRBj - BMREntryMaster

Found 1 Document (0.546 seconds)

BMRB: 34257

6G81

Solution structure of the Ni metallochaperone HypA from Helicobacter pylori

Authors

Spronk, C.A.E.M., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Hu, H., Maroney, M., Ciurli, S.

Assembly

Hydrogenase maturation factor HypA

Entity

1. Hydrogenase maturation factor HypA, entity 1 (polymer, Thiol state: free and other bound), 117 monomers, 13202.09 Da Detail

MHEYSVVSSL IALCEEHAKK NQAHKIERVV VGIGERSAMD KSLFVSAFET FREESLVCKD AILDIVDEKV ELECKDCSHV FKPNALDYGV CEKCHSKNVI ITQGNEMRLL SLEMLAE

2. Hydrogenase maturation factor HypA, entity ZN (non-polymer), 65.409 Da

Total weight

13267.499 Da

Max. entity weight

13202.09 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS74:SG	2:ZN1:ZN
2	disulfide	sing	1:CYS77:SG	2:ZN1:ZN
3	disulfide	sing	1:CYS91:SG	2:ZN1:ZN
4	disulfide	sing	1:CYS94:SG	2:ZN1:ZN

Source organism

Helicobacter pylori J99

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.4 %, Completeness (bb): 97.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.4 % (1291 of 1353)	94.3 % (661 of 701)	97.4 % (516 of 530)	93.4 % (114 of 122)
Backbone	97.9 % (685 of 700)	97.0 % (230 of 237)	98.3 % (341 of 347)	98.3 % (114 of 116)
Sidechain	93.5 % (716 of 766)	92.9 % (431 of 464)	96.3 % (285 of 296)	0.0 % (0 of 6)
Aromatic	85.5 % (65 of 76)	86.8 % (33 of 38)	84.2 % (32 of 38)
Methyl	100.0 % (140 of 140)	100.0 % (70 of 70)	100.0 % (70 of 70)

1. entity 1

MHEYSVVSSL IALCEEHAKK NQAHKIERVV VGIGERSAMD KSLFVSAFET FREESLVCKD AILDIVDEKV ELECKDCSHV FKPNALDYGV CEKCHSKNVI ITQGNEMRLL SLEMLAE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

LACS Plot; CA

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

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.06 ppm, Outliers: 5 Detail

LACS Plot; CO

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

Referencing offset: 0.35 ppm, Outliers: 3 Detail

Release date

2018-07-16

Citation

Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools
Spronk, C., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Basak, P., Blum, F.C., Johnson, R.C., Hu, H., Merrell, D.S., Maroney, M., Ciurli, S.
J. Biol. Inorg. Chem. (2018), 23, 1309-1330, PubMed 30264175 , DOI 10.1007/s00775-018-1616-y , Abstract

Related entities 1. Hydrogenase maturation factor HypA, entity 1, : 1 : 2 : 79 entities Detail

Interaction partners 1. Hydrogenase maturation factor HypA, entity 1, : 19 interactors Detail

More details for 19 interactors identified by 2 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

2 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

3 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

6 3D HN(CA)CO

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

8 3D HBHANH

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

9 2D 1H-13C HSQC aromatic

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

10 2D (HB)CB(CGCD)HD

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

11 2D (HB)CB(CGCDCE)HE

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

12 3D HBCB(CGCD)HD

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

13 3D HBCB(CGCDCE)HE

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

14 3D 1H-13C NOESY aromatic

Instrument

Agilent DDR2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

15 4D 13C(ali)-HMQC-NOESY-13C(aro)-HSQC

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

16 3D 1H-15N NOESY

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

17 4D 13C(ali)-HMQC-NOESY-13C(ali)-HMQC

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

18 4D 13C-HMQC-NOESY-15N-HSQC

Instrument

Agilent DDR2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HypA	[U-13C; U-15N]	1 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	TCEP	natural abundance	1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34257_6g81.nef
Input source #2: Coordindates	6g81.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)
1:74:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:77:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:91:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:94: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--------60--------70--------80--------90-------100
MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI

-------110-------
ITQGNEMRLLSLEMLAE
|||||||||||||||||
ITQGNEMRLLSLEMLAE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	117	0	0	100.0

Content subtype: combined_34257_6g81.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_chemical_shifts_1	Warning	1295		100.0 (chain: A, length: 117)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	3484 (1)	noe	100.0 (chain: A, length: 117)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	191 (191)	.	96.6 (chain: A, length: 117)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 665
  - ¹³C chemical shifts: 516
  - ¹⁵N chemical shifts: 114
- 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	701	665	94.9
¹³C chemical shifts	530	516	97.4
¹⁵N chemical shifts	126	114	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	237	233	98.3
¹³C chemical shifts	234	231	98.7
¹⁵N chemical shifts	116	114	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	464	432	93.1
¹³C chemical shifts	296	285	96.3
¹⁵N chemical shifts	10	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	74	100.0
¹³C chemical shifts	74	74	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	32	84.2
¹³C chemical shifts	38	32	84.2

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 100.0%
- Total number of restraints: 3374
- Weight of restraints: 1.0 (3374)
- Potential type of restraints: square-well-parabolic (3374)
- Range of distance target values: 1.13, 4.0 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 96.6%
- Total number of restraints: 191
- Total number of restraints per polymer type: 191
- Weight of restraints: 1.0 (191)
- Potential type of restraints: square-well-parabolic (191)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords METAL BINDING PROTEIN, metallochaperone metal-binding Nickel hydrogenase

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Found 1 Document (0.546 seconds)

BMRB: 34257

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Hydrogenase maturation factor HypA, entity 1, : 1 : 2 : 79 entities Detail

Interaction partners 1. Hydrogenase maturation factor HypA, entity 1, : 19 interactors Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 4 contents Detail