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

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Basic information

Entry
Database: PDB / ID: 2g2q
TitleThe crystal structure of G4, the poxviral disulfide oxidoreductase essential for cytoplasmic disulfide bond formation
ComponentsGlutaredoxin-2
KeywordsOXIDOREDUCTASE / Thioredoxin-fold / Poxvirus / Vaccinia Virus / Orthopox / G4
Function / homologyGlutaredoxin-like / Glutaredoxin-like domain (DUF836) / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / host cell cytoplasm / 3-Layer(aba) Sandwich / Alpha Beta / Glutaredoxin-2
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSu, H.P. / Lin, D.Y. / Garboczi, D.N.
CitationJournal: 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
DepositionFeb 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaredoxin-2
B: Glutaredoxin-2
C: Glutaredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6205
Polymers42,4283
Non-polymers1922
Water1,44180
1
A: Glutaredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2392
Polymers14,1431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2392
Polymers14,1431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaredoxin-2


Theoretical massNumber of molelcules
Total (without water)14,1431
Polymers14,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Glutaredoxin-2
B: Glutaredoxin-2
C: Glutaredoxin-2
hetero molecules

A: Glutaredoxin-2
B: Glutaredoxin-2
C: Glutaredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,24110
Polymers84,8576
Non-polymers3844
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area18300 Å2
ΔGint-200 kcal/mol
Surface area30210 Å2
MethodPISA
5
A: Glutaredoxin-2
hetero molecules

B: Glutaredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4784
Polymers28,2862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4870 Å2
ΔGint-71 kcal/mol
Surface area11780 Å2
MethodPISA
6
C: Glutaredoxin-2

C: Glutaredoxin-2


Theoretical massNumber of molelcules
Total (without water)28,2862
Polymers28,2862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3950 Å2
ΔGint-36 kcal/mol
Surface area11250 Å2
MethodPISA
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 number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEPHEPHEAA1 - 401 - 40
21MSEMSEPHEPHEBB1 - 401 - 40
31MSEMSEPHEPHECC1 - 401 - 40
42GLYGLYLYSLYSAA60 - 9060 - 90
52GLYGLYLYSLYSBB60 - 9060 - 90
62GLYGLYLYSLYSCC60 - 9060 - 90
73VALVALTHRTHRAA102 - 115102 - 115
83VALVALTHRTHRBB102 - 115102 - 115
93VALVALTHRTHRCC102 - 115102 - 115
DetailsThe biological unit is likely a monomer. There are 3 biological units in the asymmetric unit (chains A, B, and C)

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Components

#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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.04 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 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

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97702, 0.97948
SYNCHROTRONAPS 22-BM20.97931
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 4, 2004
MARRESEARCH2CCDAug 18, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.977021
20.979481
30.979311
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
5.417.6726660.11113.151338399.1
7.727.71045030.1091.013.11356099.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785013269710.0320.955.3
5.386.78133998.910.0751.0195.4
4.75.38133199.110.0740.9995.4
4.274.7135499.310.0790.9735.5
3.974.27134999.310.1141.0325.4
3.733.97131299.510.1311.0315.5
3.553.73133199.510.1680.9885.5
3.393.55133099.610.2831.0035.4
3.263.39136999.610.3771.015.5
3.153.26134299.710.5011.045.5
6.6750134597.320.0320.9647.5
5.36.67134598.920.0740.9887.6
4.635.3136099.120.0721.0247.7
4.214.63136299.320.0790.977.7
3.914.21134899.320.111.0037.7
3.683.91136499.520.1261.0317.7
3.493.68135499.520.1661.0187.8
3.343.49136099.620.2631.0417.7
3.213.34134599.620.3661.0457.7
3.13.21137799.920.4731.0427.8
ReflectionResolution: 2.5→50 Å / Num. obs: 23962 / % possible obs: 99.1 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.082 / Χ2: 1.031 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2.5-2.591007.80.4424301.0561,2
2.59-2.691007.80.31323851.0481,2
2.69-2.8299.97.90.24224011.0351,2
2.82-2.9699.97.80.17924061.0241,2
2.96-3.1599.87.80.12624321.0181,2
3.15-3.3999.57.90.09823931.041,2
3.39-3.7399.37.90.06923991.0181,2
3.73-4.2798.67.90.05924050.981,2
4.27-5.3898.380.06923631.051,2
5.38-509680.04723481.041,2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1wavelength10.97710.81-2.5
2wavelength20.979513.83-10.2
Phasing MAD clust
IDExpt-ID
1wavelength
2wavelength
Phasing dmFOM : 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 acentricFOM centricReflectionReflection acentricReflection centric
8.8-19.960.760.840.66341192149
5.5-8.80.650.690.521037751286
4.4-5.50.610.650.4812811012269
3.9-4.40.510.530.3712541024230
3.3-3.90.370.380.322291870359
3.1-3.30.220.220.1813061120186

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.05phasing
RESOLVE2.05phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
MAR345data collection
RefinementMethod to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 754 5.8 %RANDOM
Rwork0.225 ---
all0.229 13092 --
obs0.229 23962 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 10 80 2842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222815
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9733802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27525.882119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98415521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.437152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022043
X-RAY DIFFRACTIONr_nbd_refined0.2140.21108
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.2186
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.220
X-RAY DIFFRACTIONr_mcbond_it0.6471.51771
X-RAY DIFFRACTIONr_mcangle_it1.10622794
X-RAY DIFFRACTIONr_scbond_it1.40331188
X-RAY DIFFRACTIONr_scangle_it2.1044.51008
Refine LS restraints NCS

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

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.260.5
2BMEDIUM POSITIONAL0.410.5
3CMEDIUM POSITIONAL0.40.5
1ALOOSE POSITIONAL0.835
2BLOOSE POSITIONAL0.825
3CLOOSE POSITIONAL0.935
1AMEDIUM THERMAL0.732
2BMEDIUM THERMAL0.82
3CMEDIUM THERMAL0.512
1ALOOSE THERMAL1.4110
2BLOOSE THERMAL1.6310
3CLOOSE THERMAL1.6310
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 56 -
Rwork0.241 871 -
obs-927 99.04 %
Refinement TLS params.

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

IDL11 (°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)
14.4755-0.78310.29643.4383-1.58572.5526-0.072-0.34360.10890.23150.07040.1393-0.0551-0.2020.0016-0.1380.00680.0136-0.12830.0624-0.01431.24329.46250.441
22.53360.7877-1.64453.2597-1.04982.27280.0834-0.2151-0.2570.0915-0.1592-0.3969-0.0340.26720.0759-0.145-0.01850.0233-0.16630.02840.033150.21145.41128.18
35.0716-1.951-3.54082.46852.66417.95630.45850.35590.5453-0.165-0.2667-0.1609-0.9029-0.0124-0.19190.20080.20250.1347-0.02750.12430.215421.6658.88838.137
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC

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