PDB-2g2q: The crystal structure of G4, the poxviral disulfide oxidoreductas...

ID or keywords:

Entry

Database: PDB / ID: 2g2q

Title

The crystal structure of G4, the poxviral disulfide oxidoreductase essential for cytoplasmic disulfide bond formation

Components

Glutaredoxin-2

Keywords

OXIDOREDUCTASE / Thioredoxin-fold /

Poxvirus /

Vaccinia Virus / Orthopox / G4

Function / homology

Function and homology information

: / host cell cytoplasm
Similarity search - Function

Biological species

Vaccinia virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.5 Å

Authors

Su, H.P. / Lin, D.Y. / Garboczi, D.N.

Citation

Journal: J.Virol. / Year: 2006
Title: The structure of G4, the poxvirus disulfide oxidoreductase essential for virus maturation and infectivity.
Authors: Su, H.P. / Lin, D.Y. / Garboczi, D.N.

History

Deposition	Feb 16, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 1, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2g2q.cif.gz	78.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2g2q.ent.gz	64 KB	Display	PDB format
PDBx/mmJSON format	2g2q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2q ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2q	HTTPS FTP

-
Related structure data

Similar structure data	2fqp-2 2yqd-d 4fap-d 1bv8-d 3owr-1 2jrs-d 3owr-4 1fqi-d 3owr-3 2idw-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) Search similar-shape structures by Omokage search (details) 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glutaredoxin-2

B: Glutaredoxin-2

C: Glutaredoxin-2

hetero molecules

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

1

A: Glutaredoxin-2

hetero molecules

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

2

B: Glutaredoxin-2

hetero molecules

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

3

C: Glutaredoxin-2

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

4

A: Glutaredoxin-2

B: Glutaredoxin-2

C: Glutaredoxin-2

hetero molecules

A: Glutaredoxin-2

B: Glutaredoxin-2

C: Glutaredoxin-2

hetero molecules

defined by software
85.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: Glutaredoxin-2

hetero molecules

B: Glutaredoxin-2

hetero molecules

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

6

C: Glutaredoxin-2

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

Unit cell

Length a, b, c (Å)	72.594, 72.594, 136.726
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	A
5	1	B
6	1	C
7	1	A
8	1	B
9	1	C

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MSE	PHE	A	A	1 - 40	1 - 40
2	1	MSE	PHE	B	B	1 - 40	1 - 40
3	1	MSE	PHE	C	C	1 - 40	1 - 40
4	2	GLY	LYS	A	A	60 - 90	60 - 90
5	2	GLY	LYS	B	B	60 - 90	60 - 90
6	2	GLY	LYS	C	C	60 - 90	60 - 90
7	3	VAL	THR	A	A	102 - 115	102 - 115
8	3	VAL	THR	B	B	102 - 115	102 - 115
9	3	VAL	THR	C	C	102 - 115	102 - 115

Details

The biological unit is likely a monomer. There are 3 biological units in the asymmetric unit (chains A, B, and C)

#1: Protein	Glutaredoxin-2 / Mass: 14142.767 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: Western Reserve / Gene: g4l / Plasmid: pNAN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: P68460
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.04 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100mM Citrate Buffer, 20% PEG 1500, 200mM LiSO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	19-ID	1	0.97702, 0.97948
SYNCHROTRON	APS	22-BM	2	0.97931

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Jul 4, 2004
MARRESEARCH	2	CCD	Aug 18, 2004

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97702	1
2	0.97948	1
3	0.97931	1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	Num. obs	% possible obs
5.4	1	7.6	72666	0.111	1	3.15	13383	99.1
7.7	2	7.7	104503	0.109	1.01	3.1	13560	99.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.78	50	1326	97	1	0.032	0.95	5.3
5.38	6.78	1339	98.9	1	0.075	1.019	5.4
4.7	5.38	1331	99.1	1	0.074	0.999	5.4
4.27	4.7	1354	99.3	1	0.079	0.973	5.5
3.97	4.27	1349	99.3	1	0.114	1.032	5.4
3.73	3.97	1312	99.5	1	0.131	1.031	5.5
3.55	3.73	1331	99.5	1	0.168	0.988	5.5
3.39	3.55	1330	99.6	1	0.283	1.003	5.4
3.26	3.39	1369	99.6	1	0.377	1.01	5.5
3.15	3.26	1342	99.7	1	0.501	1.04	5.5
6.67	50	1345	97.3	2	0.032	0.964	7.5
5.3	6.67	1345	98.9	2	0.074	0.988	7.6
4.63	5.3	1360	99.1	2	0.072	1.024	7.7
4.21	4.63	1362	99.3	2	0.079	0.97	7.7
3.91	4.21	1348	99.3	2	0.11	1.003	7.7
3.68	3.91	1364	99.5	2	0.126	1.031	7.7
3.49	3.68	1354	99.5	2	0.166	1.018	7.8
3.34	3.49	1360	99.6	2	0.263	1.041	7.7
3.21	3.34	1345	99.6	2	0.366	1.045	7.7
3.1	3.21	1377	99.9	2	0.473	1.042	7.8

Reflection

Resolution: 2.5→50 Å / Num. obs: 23962 / % possible obs: 99.1 % / Redundancy: 7.9 % / R_merge(I) obs: 0.082 / Χ²: 1.031 / Net I/σ(I): 13.5

Reflection shell

Resolution (Å)	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID
2.5-2.59	100	7.8	0.44	2430	1.056	1,2
2.59-2.69	100	7.8	0.313	2385	1.048	1,2
2.69-2.82	99.9	7.9	0.242	2401	1.035	1,2
2.82-2.96	99.9	7.8	0.179	2406	1.024	1,2
2.96-3.15	99.8	7.8	0.126	2432	1.018	1,2
3.15-3.39	99.5	7.9	0.098	2393	1.04	1,2
3.39-3.73	99.3	7.9	0.069	2399	1.018	1,2
3.73-4.27	98.6	7.9	0.059	2405	0.98	1,2
4.27-5.38	98.3	8	0.069	2363	1.05	1,2
5.38-50	96	8	0.047	2348	1.04	1,2

-
Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	wavelength	1	0.977	10.81	-2.5
2	wavelength	2	0.9795	13.83	-10.2

Phasing MAD clust

ID	Expt-ID
1	wavelength
2	wavelength

Phasing dm

FOM : 0.46 / FOM acentric: 0.48 / FOM centric: 0.41 / Reflection: 7448 / Reflection acentric: 5969 / Reflection centric: 1479

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.8-19.96	0.76	0.84	0.66	341	192	149
5.5-8.8	0.65	0.69	0.52	1037	751	286
4.4-5.5	0.61	0.65	0.48	1281	1012	269
3.9-4.4	0.51	0.53	0.37	1254	1024	230
3.3-3.9	0.37	0.38	0.3	2229	1870	359
3.1-3.3	0.22	0.22	0.18	1306	1120	186

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.05	phasing
RESOLVE	2.05	phasing
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction
HKL-2000		data reduction
MAR345		data collection

Refinement

Method to determine structure:

MAD / Resolution: 2.5→25 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.871 / SU B: 22.811 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.992 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FRIEDEL PAIRS WERE USED FOR PHASING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.291	754	5.8 %	RANDOM
R_work	0.225	-	-	-
all	0.229	13092	-	-
obs	0.229	23962	98.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 34.702 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.86 Å²	0 Å²	0 Å²
2-	-	0.86 Å²	0 Å²
3-	-	-	-1.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2752	0	10	80	2842

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	2815
X-RAY DIFFRACTION	r_angle_refined_deg	1.281	1.973	3802
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.311	5	340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.275	25.882	119
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.984	15	521
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	26.437	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	437
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2043
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1108
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	1919
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	104
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.218	0.2	186
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.152	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	0.647	1.5	1771
X-RAY DIFFRACTION	r_mcangle_it	1.106	2	2794
X-RAY DIFFRACTION	r_scbond_it	1.403	3	1188
X-RAY DIFFRACTION	r_scangle_it	2.104	4.5	1008

Refine LS restraints NCS

Ens-ID: 1 / Number: 340 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	MEDIUM POSITIONAL	0.26	0.5
2	B	MEDIUM POSITIONAL	0.41	0.5
3	C	MEDIUM POSITIONAL	0.4	0.5
1	A	LOOSE POSITIONAL	0.83	5
2	B	LOOSE POSITIONAL	0.82	5
3	C	LOOSE POSITIONAL	0.93	5
1	A	MEDIUM THERMAL	0.73	2
2	B	MEDIUM THERMAL	0.8	2
3	C	MEDIUM THERMAL	0.51	2
1	A	LOOSE THERMAL	1.41	10
2	B	LOOSE THERMAL	1.63	10
3	C	LOOSE THERMAL	1.63	10

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	56	-
R_work	0.241	871	-
obs	-	927	99.04 %

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	4.4755	-0.7831	0.2964	3.4383	-1.5857	2.5526	-0.072	-0.3436	0.1089	0.2315	0.0704	0.1393	-0.0551	-0.202	0.0016	-0.138	0.0068	0.0136	-0.1283	0.0624	-0.014	31.243	29.462	50.441
2	2.5336	0.7877	-1.6445	3.2597	-1.0498	2.2728	0.0834	-0.2151	-0.257	0.0915	-0.1592	-0.3969	-0.034	0.2672	0.0759	-0.145	-0.0185	0.0233	-0.1663	0.0284	0.0331	50.211	45.411	28.18
3	5.0716	-1.951	-3.5408	2.4685	2.6641	7.9563	0.4585	0.3559	0.5453	-0.165	-0.2667	-0.1609	-0.9029	-0.0124	-0.1919	0.2008	0.2025	0.1347	-0.0275	0.1243	0.2154	21.66	58.888	38.137

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 119 / Label seq-ID: 1 - 119

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	2	B	B
3	3	C	C

-
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