PDB-2h1g: ResA C74A/C77A

ID or keywords:

Entry

Database: PDB / ID: 2h1g

Title

ResA C74A/C77A

Components

Thiol-disulfide oxidoreductase resA

Keywords

OXIDOREDUCTASE / ResA /

double mutant / C77A / C74A / ResA C74A/C77A /

Thioredoxin

Function / homology

Function and homology information

cytochrome complex assembly / disulfide oxidoreductase activity /

antioxidant activity /

plasma membrane
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Lewin, A. / Crow, A. / Oubrie, A. / Le Brun, N.E.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Molecular Basis for Specificity of the Extracytoplasmic Thioredoxin ResA.
Authors: Lewin, A. / Crow, A. / Oubrie, A. / Le Brun, N.E.

History

Deposition	May 16, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2h1g.cif.gz	65.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2h1g.ent.gz	48.2 KB	Display	PDB format
PDBx/mmJSON format	2h1g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/2h1g ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h1g	HTTPS FTP

-
Related structure data

Related structure data	2h19C 2h1aC 2h1bC 2h1dC 1su9S 1st9 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1st9-1 1su9-2 2h1a-1 2f9s-2 1su9-1 2h1d-2 2h1d-1 2h1b-3 3c73-1 2h1b-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (2) #91 - Jul 2007 Thymine Dimers similarity (2)

Deposited unit

A: Thiol-disulfide oxidoreductase resA

B: Thiol-disulfide oxidoreductase resA

31.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thiol-disulfide oxidoreductase resA

defined by author
15.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Thiol-disulfide oxidoreductase resA

defined by author
15.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	47.031, 59.522, 109.562
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	LYS	LYS	1	A	A	40 - 53	4 - 17
2	1	1	SER	SER	LYS	LYS	1	B	B	40 - 53	4 - 17
3	2	1	ARG	ARG	ARG	ARG	3	A	A	54	18
4	2	1	ARG	ARG	ARG	ARG	3	B	B	54	18
5	3	1	ILE	ILE	LYS	LYS	1	A	A	55 - 78	19 - 42
6	3	1	ILE	ILE	LYS	LYS	1	B	B	55 - 78	19 - 42
7	4	1	LYS	LYS	LYS	LYS	3	A	A	79	43
8	4	1	LYS	LYS	LYS	LYS	3	B	B	79	43
9	5	1	GLU	GLU	LYS	LYS	1	A	A	80 - 89	44 - 53
10	5	1	GLU	GLU	LYS	LYS	1	B	B	80 - 89	44 - 53
11	6	1	HIS	HIS	HIS	HIS	3	A	A	90	54
12	6	1	HIS	HIS	HIS	HIS	3	B	B	90	54
13	7	1	PHE	PHE	VAL	VAL	1	A	A	91 - 110	55 - 74
14	7	1	PHE	PHE	VAL	VAL	1	B	B	91 - 110	55 - 74
15	8	1	HIS	HIS	HIS	HIS	5	A	A	111	75
16	8	1	HIS	HIS	HIS	HIS	5	B	B	111	75
17	9	1	ASN	ASN	VAL	VAL	1	A	A	112 - 137	76 - 101
18	9	1	ASN	ASN	VAL	VAL	1	B	B	112 - 137	76 - 101
19	10	1	PRO	PRO	PRO	PRO	1	A	A	141 - 174	105 - 138
20	10	1	PRO	PRO	PRO	PRO	1	B	B	141 - 174	105 - 138
1	1	2	SER	SER	LYS	LYS	1	B	B	40 - 53	4 - 17
2	1	2	SER	SER	LYS	LYS	1	A	A	40 - 53	4 - 17
3	2	2	ARG	ARG	ARG	ARG	3	B	B	54	18
4	2	2	ARG	ARG	ARG	ARG	3	A	A	54	18
5	3	2	ILE	ILE	LYS	LYS	1	B	B	55 - 78	19 - 42
6	3	2	ILE	ILE	LYS	LYS	1	A	A	55 - 78	19 - 42
7	4	2	LYS	LYS	LYS	LYS	3	B	B	79	43
8	4	2	LYS	LYS	LYS	LYS	3	A	A	79	43
9	5	2	GLU	GLU	LYS	LYS	1	B	B	80 - 89	44 - 53
10	5	2	GLU	GLU	LYS	LYS	1	A	A	80 - 89	44 - 53
11	6	2	HIS	HIS	HIS	HIS	3	B	B	90	54
12	6	2	HIS	HIS	HIS	HIS	3	A	A	90	54
13	7	2	PHE	PHE	VAL	VAL	1	B	B	91 - 110	55 - 74
14	7	2	PHE	PHE	VAL	VAL	1	A	A	91 - 110	55 - 74
15	8	2	HIS	HIS	HIS	HIS	5	B	B	111	75
16	8	2	HIS	HIS	HIS	HIS	5	A	A	111	75
17	9	2	ASN	ASN	VAL	VAL	1	B	B	112 - 137	76 - 101
18	9	2	ASN	ASN	VAL	VAL	1	A	A	112 - 137	76 - 101
19	10	2	PRO	PRO	PRO	PRO	1	B	B	141 - 174	105 - 138
20	10	2	PRO	PRO	PRO	PRO	1	A	A	141 - 174	105 - 138

NCS ensembles :

ID
1
2

#1: Protein	Thiol-disulfide oxidoreductase resA Mass: 15878.000 Da / Num. of mol.: 2 / Mutation: C77A, C74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: resA / Production host: Escherichia coli (E. coli) / References: UniProt: P35160
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49.03 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20 % - 27 % PEG 4,000, 0.1 M MES pH 5.6, 0.1 M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0688 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2006
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0688 Å / Relative weight: 1
Reflection	Resolution: 3.1→55.048 Å / Num. all: 5722 / Num. obs: 5722 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / R_merge(I) obs: 0.127 / R_sym value: 0.127 / Net I/σ(I): 4.6
Reflection shell	Resolution: 3.1→3.27 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.296 / Mean I/σ(I) obs: 2.2 / Num. measured all: 4118 / Num. unique all: 761 / R_sym value: 0.296 / % possible all: 91.9

-
Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3.2 Å	36.9 Å

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ProDC		data collection
MOSFLM		data reduction
CCP4	(SCALA)	data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1su9

1su9

Resolution: 3.1→37.16 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.848 / SU B: 21.411 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.263	298	5.2 %	Free set copied from 1SU9 and extended as necessary.
R_work	0.185	-	-	-
all	0.189	5695	-	-
obs	0.238	5695	95.65 %	-

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: 13.01 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	0 Å²	0 Å²
2-	-	0.14 Å²	0 Å²
3-	-	-	-0.46 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→37.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2153	0	0	13	2166

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	2207
X-RAY DIFFRACTION	r_angle_refined_deg	2.044	1.953	2994
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.952	5	271
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.033	25.464	97
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.832	15	376
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.763	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	331
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1664
X-RAY DIFFRACTION	r_nbd_refined	0.24	0.2	1002
X-RAY DIFFRACTION	r_nbtor_refined	0.333	0.2	1505
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	62
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.186	0.2	28
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.076	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0.856	1.5	1387
X-RAY DIFFRACTION	r_mcangle_it	1.503	2	2212
X-RAY DIFFRACTION	r_scbond_it	2.253	3	926
X-RAY DIFFRACTION	r_scangle_it	3.913	4.5	782

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1019	TIGHT POSITIONAL	0.09	0.05
1	A	4	MEDIUM POSITIONAL	0.1	0.5
1	A	24	LOOSE POSITIONAL	1.46	5
1	A	1019	TIGHT THERMAL	0.11	0.5
1	A	4	MEDIUM THERMAL	0.23	2
1	A	24	LOOSE THERMAL	6.83	10
2	B	1019	TIGHT POSITIONAL	0.09	0.05
2	B	4	MEDIUM POSITIONAL	0.1	0.5
2	B	24	LOOSE POSITIONAL	1.46	5
2	B	1019	TIGHT THERMAL	0.11	0.5
2	B	4	MEDIUM THERMAL	0.23	2
2	B	24	LOOSE THERMAL	6.83	10

LS refinement shell

Resolution: 3.102→3.182 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	18	-
R_work	0.242	364	-
obs	-	382	89.25 %

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi