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- PDB-4i2u: Crystal structure of the reduced glutaredoxin from Chlorella soro... -

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Basic information

Entry
Database: PDB / ID: 4i2u
TitleCrystal structure of the reduced glutaredoxin from Chlorella sorokiniana T-89 in complex with glutathione
Componentsglutaredoxin
KeywordsOXIDOREDUCTASE / cell redox homeostasis / Thioredoxin fold / Glutathione Binding
Function / homology
Function and homology information


Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutaredoxin
Similarity search - Component
Biological speciesChlorella sorokiniana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsNien, C.-Y. / Cheng, C.-Y. / Shaw, J.-F. / Chen, Y.-T. / Liu, J.-H.
CitationJournal: To be Published
Title: Crystal structure and functional analysis of glutaredoxin from Chlorella sorokiniana T-89
Authors: Nien, C.-Y. / Cheng, C.-Y. / Shaw, J.-F. / Chen, Y.-T. / Liu, J.-H.
History
DepositionNov 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8012
Polymers12,4931
Non-polymers3071
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.676, 51.310, 55.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein glutaredoxin


Mass: 12493.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella sorokiniana (plant) / Strain: T-89 / Gene: grx / Plasmid: pET-20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V9GZ94*PLUS
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5mM DTT, 30%(w/v) PEG 3000 , 0.1M CHES, pH 9., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2011 / Details: mirrors
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 24433 / Num. obs: 24365 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 30.615
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.925 / Num. unique all: 2371 / Rsym value: 0.312 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E7P

2e7p


Resolution: 1.3→24.463 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.9289 / SU ML: 0.12 / Isotropic thermal model: anisotropic / Cross valid method: PHENIX DEFAULT / σ(F): 1.36 / σ(I): 0 / Phase error: 12.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 1999 8.22 %RANDOM
Rwork0.1394 ---
all0.1416 24433 --
obs0.1416 24314 99.74 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.563 Å2 / ksol: 0.461 e/Å3
Displacement parametersBiso max: 49.54 Å2 / Biso mean: 13.3058 Å2 / Biso min: 4.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.7449 Å2-0 Å20 Å2
2---1.7998 Å20 Å2
3---2.5446 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 20 149 997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008871
X-RAY DIFFRACTIONf_angle_d1.2671172
X-RAY DIFFRACTIONf_dihedral_angle_d15.393333
X-RAY DIFFRACTIONf_chiral_restr0.068133
X-RAY DIFFRACTIONf_plane_restr0.006153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.33250.20281460.1985154699
1.3325-1.36860.21121330.1747155499
1.3686-1.40880.18841380.1589157399
1.4088-1.45430.15061340.14361576100
1.4543-1.50630.14991470.12991567100
1.5063-1.56660.15211420.12851567100
1.5666-1.63790.15661420.12411581100
1.6379-1.72420.1651370.1261595100
1.7242-1.83220.15071410.13021579100
1.8322-1.97360.13291520.12411609100
1.9736-2.17210.16371420.12611600100
2.1721-2.48610.15751400.12581604100
2.4861-3.13120.17431480.14771642100
3.1312-24.46690.18041570.14981722100
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)
10.45120.58190.4582.8039-0.81742.44130.01480.35470.0615-0.36370.0237-0.18650.08570.0679-0.0360.11850.00250.01350.1064-0.00160.068418.73734.34534.8984
20.7538-0.16740.02751.2052-0.2360.7137-0.01110.0095-0.02380.00240.02790.00190.0374-0.0291-0.02530.0601-0.004-0.01070.0644-0.0040.056312.489723.500910.0638
31.3337-0.7304-0.91620.51280.52590.7375-0.01310.0287-0.1090.0373-0.04850.09450.012-0.05130.04220.0805-0.0007-0.0010.0802-0.00570.08157.011819.172316.5272
41.4151-0.0808-1.43531.32740.96252.04240.10540.3210.0611-0.08680.20090.02660.0738-0.106-0.24780.1013-0-0.01280.1736-0.01630.12020.753626.994911.3327
51.34731.03230.09381.07020.0451.0881-0.0390.2053-0.0618-0.09090.0671-0.08070.07720.0758-0.03010.06670.0108-0.00130.087-0.00870.067620.822225.10397.0949
60.66550.42460.5241.124-0.26670.83610.001-0.0130.00430.0357-0.0053-0.07530.01280.0183-0.00430.0660.00150.00090.0691-0.00230.059516.653527.999416.1889
70.28390.3568-0.80160.5924-1.19372.7607-0.1051-0.2819-0.00040.16240.17890.02660.1845-0.0521-0.08030.11110.0150.00180.1183-0.00280.06698.695223.72424.99
81.3106-0.4751.81720.251-0.59852.6661-0.0221-0.23120.1110.16290.1507-0.00890.0327-0.0429-0.09830.09690.01510.00950.1212-0.00630.06343.745733.83722.7219
92.06650.24862.16024.59391.54812.6222-0.0383-0.34210.07060.3627-0.08830.40120.0454-0.33760.14590.13060.0170.01550.16640.00340.1372-4.46835.21519.629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:14)A2 - 14
2X-RAY DIFFRACTION2chain 'A' and (resseq 15:25)A15 - 25
3X-RAY DIFFRACTION3chain 'A' and (resseq 26:37)A26 - 37
4X-RAY DIFFRACTION4chain 'A' and (resseq 38:44)A38 - 44
5X-RAY DIFFRACTION5chain 'A' and (resseq 45:66)A45 - 66
6X-RAY DIFFRACTION6chain 'A' and (resseq 67:83)A67 - 83
7X-RAY DIFFRACTION7chain 'A' and (resseq 84:93)A84 - 93
8X-RAY DIFFRACTION8chain 'A' and (resseq 94:102)A94 - 102
9X-RAY DIFFRACTION9chain 'A' and (resseq 103:110)A103 - 110

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