PDB-3ish: Crystal structure of Helicobacter pylori thioredoxin reductase

ID or keywords:

Entry

Database: PDB / ID: 3ish

Title

Crystal structure of Helicobacter pylori thioredoxin reductase

Components

Thioredoxin reductase

Keywords

OXIDOREDUCTASE / Disulfide bond / FAD / Flavoprotein / NADP / Redox-active center

Function / homology

Function and homology information

thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / cytoplasm
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.43 Å

Authors

Sanders, D. / Obiero, J. / van Straaten, K.

Citation

Journal: To be Published
Title: Crystal structure of Helicobacter pylori thioredoxin reductase
Authors: Sanders, D. / Obiero, J. / van Straaten, K.

History

Deposition	Aug 25, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3ish.cif.gz	200 KB	Display	PDBx/mmCIF format
PDB format	pdb3ish.ent.gz	159.6 KB	Display	PDB format
PDBx/mmJSON format	3ish.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ish_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3ish_full_validation.pdf.gz	1.2 MB	Display
Data in XML	3ish_validation.xml.gz	45.5 KB	Display
Data in CIF	3ish_validation.cif.gz	63.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/3ish ftp://data.pdbj.org/pub/pdb/validation_reports/is/3ish	HTTPS FTP

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Related structure data

Related structure data	2a87S 2q0k 2q0l S: Starting model for refinement
Similar structure data	2q0k-d 4ccr-1 3d8x-d 5mjk-1 1trb-1 1cl0-1 2q0l-d 2a87-d 3itj-2 5m5j-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (2) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Thioredoxin reductase

B: Thioredoxin reductase

C: Thioredoxin reductase

hetero molecules

103 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thioredoxin reductase

B: Thioredoxin reductase

hetero molecules

defined by author&software
68.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Thioredoxin reductase

hetero molecules

C: Thioredoxin reductase

hetero molecules

defined by author&software
68.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.400, 89.400, 279.900
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
3	1	C

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	GLU	GLU	B	B	1 - 32	1 - 32
2	1	MET	MET	GLU	GLU	A	A	1 - 32	1 - 32
3	1	MET	MET	GLU	GLU	C	C	1 - 32	1 - 32
1	2	LYS	LYS	SER	SER	B	B	33 - 89	33 - 89
2	2	LYS	LYS	SER	SER	A	A	33 - 89	33 - 89
3	2	LYS	LYS	SER	SER	C	C	33 - 89	33 - 89
1	3	HIS	HIS	ILE	ILE	B	B	90 - 119	90 - 119
2	3	HIS	HIS	ILE	ILE	A	A	90 - 119	90 - 119
3	3	HIS	HIS	ILE	ILE	C	C	90 - 119	90 - 119
1	4	CYS	CYS	TYR	TYR	B	B	133 - 141	133 - 141
2	4	CYS	CYS	TYR	TYR	A	A	133 - 141	133 - 141
3	4	CYS	CYS	TYR	TYR	C	C	133 - 141	133 - 141
1	5	VAL	VAL	GLY	GLY	B	B	146 - 150	146 - 150
2	5	VAL	VAL	GLY	GLY	A	A	146 - 150	146 - 150
3	5	VAL	VAL	GLY	GLY	C	C	146 - 150	146 - 150
1	6	VAL	VAL	ARG	ARG	B	B	156 - 174	156 - 174
2	6	VAL	VAL	ARG	ARG	A	A	156 - 174	156 - 174
3	6	VAL	VAL	ARG	ARG	C	C	156 - 174	156 - 174
1	7	ILE	ILE	GLU	GLU	B	B	194 - 204	194 - 204
2	7	ILE	ILE	GLU	GLU	A	A	194 - 204	194 - 204
3	7	ILE	ILE	GLU	GLU	C	C	194 - 204	194 - 204
1	8	LYS	LYS	HIS	HIS	B	B	225 - 311	225 - 311
2	8	LYS	LYS	HIS	HIS	A	A	225 - 311	225 - 311
3	8	LYS	LYS	HIS	HIS	C	C	225 - 311	225 - 311

#1: Protein	Thioredoxin reductase / TRXR Mass: 33577.273 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0825 / Plasmid: pROK1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P56431
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.21 Å³/Da / Density % sol: 61.63 %
Crystal grow	Temperature: 277 K / pH: 5.6 Details: 2.0 M Ammonium sulfate,0.2M Ammonium Nitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007 / Details: MIRRORS
Radiation	Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.43→19.98 Å / Num. obs: 49803 / Observed criterion σ(I): -2 / Redundancy: 10.5 % / R_merge(I) obs: 0.068 / R_sym value: 0.068 / Net I/σ(I): 24.31

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Processing

Software

Name	Version	Classification
XDS		data scaling
MrBUMP	& molrep	phasing
REFMAC	5	refinement
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A87

2a87

Resolution: 2.43→19.98 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.905 / SU B: 13.923 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	2490	5 %	RANDOM
R_work	0.178	-	-	-
obs	0.181	47307	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 39.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.43→19.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7061	0	159	495	7715

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.026	0.022	7373
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.402	1.982	9978
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.217	5	930
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.265	24.751	301
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.942	15	1235
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.348	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.189	0.2	1098
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5480
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.263	0.2	3429
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	4873
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.232	0.2	505
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.223	0.2	82
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.248	0.2	24
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.246	1.5	4724
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.063	2	7341
X-RAY DIFFRACTION	r_scbond_it	3.401	3	3236
X-RAY DIFFRACTION	r_scangle_it	5.346	4.5	2637
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	B	996	tight positional	0.17	0.05
2	A	996	tight positional	0.23	0.05
3	C	996	tight positional	0.13	0.05
1	B	896	loose positional	0.7	5
2	A	896	loose positional	0.74	5
3	C	896	loose positional	0.66	5
1	B	996	tight thermal	0.4	0.5
2	A	996	tight thermal	0.34	0.5
3	C	996	tight thermal	0.55	0.5
1	B	896	loose thermal	3.37	10
2	A	896	loose thermal	2.9	10
3	C	896	loose thermal	4.17	10

LS refinement shell

Resolution: 2.43→2.49 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.299	176	-
R_work	0.212	3352	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0471	-0.0226	0.1209	0.0539	0.0225	0.461	-0.0077	0.0215	0.0031	0.0258	-0.0013	0.027	0.0446	0.0146	0.009	0.0013	-0.0313	0.0029	-0.0341	0.0063	-0.0007	-33.019	-8.2312	11.0152
2	0.2034	-0.0094	-0.0666	0.1645	0.0645	0.2273	0.0218	0.05	0.0291	0.0459	-0.0383	0.0016	-0.0019	-0.0153	0.0164	-0.0124	-0.0282	-0.017	-0.0445	0.0189	-0.0316	-33.3273	-0.853	3.9284

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 115
2	X-RAY DIFFRACTION	1	B	1 - 115
3	X-RAY DIFFRACTION	1	C	1 - 115
4	X-RAY DIFFRACTION	1	A	239 - 311
5	X-RAY DIFFRACTION	1	B	239 - 311
6	X-RAY DIFFRACTION	1	C	239 - 311
7	X-RAY DIFFRACTION	2	A	116 - 238
8	X-RAY DIFFRACTION	2	B	116 - 238
9	X-RAY DIFFRACTION	2	C	116 - 238

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