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- PDB-4mje: Synechocystis sp. PCC 6803 glutaredoxin A-R27L -

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Basic information

Entry
Database: PDB / ID: 4mje
TitleSynechocystis sp. PCC 6803 glutaredoxin A-R27L
ComponentsProbable glutaredoxin ssr2061
KeywordsELECTRON TRANSPORT / thioredoxin motif / oxidation/reduction
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm
Similarity search - Function
Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin ...Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable glutaredoxin ssr2061
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSutton, R.B. / Knaff, D.B.
CitationJournal: Front Plant Sci / Year: 2013
Title: Utility of Synechocystis sp. PCC 6803 glutaredoxin A as a platform to study high-resolution mutagenesis of proteins.
Authors: Knaff, D.B. / Sutton, R.B.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Other
Revision 1.3Sep 20, 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_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_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: Probable glutaredoxin ssr2061
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1703
Polymers10,9771
Non-polymers1922
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.290, 39.100, 50.630
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 Probable glutaredoxin ssr2061


Mass: 10977.454 Da / Num. of mol.: 1 / Fragment: Glutaredoxin A / Mutation: R27L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: ssr2061 / Plasmid: pQE3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73492
#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.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 1.68 Å3/Da / Density % sol: 26.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M Ammonium Sulfate, 1% PEG400, 10mM HEPES, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 23433 / Num. obs: 23433 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.8
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3qmx

3qmx


Resolution: 1.2→26.985 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 1977 8.44 %random
Rwork0.1787 ---
obs0.1802 23433 98.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→26.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 10 106 883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009806
X-RAY DIFFRACTIONf_angle_d1.2711090
X-RAY DIFFRACTIONf_dihedral_angle_d12.661291
X-RAY DIFFRACTIONf_chiral_restr0.079113
X-RAY DIFFRACTIONf_plane_restr0.006142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.32371490.31921532X-RAY DIFFRACTION99
1.23-1.26330.21481400.20751510X-RAY DIFFRACTION100
1.2633-1.30040.32771230.27971534X-RAY DIFFRACTION99
1.3004-1.34240.25481570.20591509X-RAY DIFFRACTION99
1.3424-1.39040.18121300.17471535X-RAY DIFFRACTION100
1.3904-1.44610.19661470.1671535X-RAY DIFFRACTION100
1.4461-1.51190.18081420.17481523X-RAY DIFFRACTION100
1.5119-1.59160.18471430.14841547X-RAY DIFFRACTION100
1.5916-1.69130.16041450.1461550X-RAY DIFFRACTION100
1.6913-1.82180.16551400.14511541X-RAY DIFFRACTION100
1.8218-2.00510.21971360.18931520X-RAY DIFFRACTION96
2.0051-2.29510.20811380.1821507X-RAY DIFFRACTION96
2.2951-2.89110.17581390.16671521X-RAY DIFFRACTION95
2.8911-26.9920.17391480.16371592X-RAY DIFFRACTION95
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)
12.73761.48493.10470.81531.74094.0864-0.1160.09430.4399-0.43220.1778-0.6224-0.58660.5399-0.03660.1373-0.01540.04570.097-0.00140.230330.4707-4.05621.8297
21.08920.78590.79732.50820.27254.72190.1250.01810.0057-0.00490.03430.1027-0.0256-0.0951-0.14020.0835-0.0111-0.00340.07190.00410.064926.9231-11.917711.7941
33.1102-2.09532.24831.5474-1.52261.7232-0.109-0.27360.571-0.04570.12360.269-0.622-0.4263-0.07680.22220.0794-0.040.23340.00070.279523.5714-3.256.977
41.8545-0.8372-0.36831.38960.19460.9925-0.0113-0.02350.0024-0.00690.0081-0.06630.02250.0029-0.00580.0262-0.00560.00040.0295-0.00480.02513.39417.12831.7334
52.4104-2.271.72672.5909-2.24022.6481-0.0495-0.1293-0.15880.10820.11710.1141-0.0188-0.157-0.0610.0405-0.0016-0.00040.03820.00630.0511-1.88753.49528.9861
60.9911-0.2881-0.27180.9893-0.07761.35060.09740.13780.0356-0.0899-0.0804-0.0169-0.02340.0073-0.00760.03840.00330.01020.0626-0.00390.04165.30579.4436-2.1317
71.6493-1.02250.33880.7665-0.36412.00610.14330.3332-0.203-0.0917-0.0870.13630.0664-0.1077-0.04870.05080.0024-0.01010.0817-0.01760.05740.99552.3856-5.3003
81.28761.0303-1.25810.9324-0.86611.909-0.01120.0849-0.0847-0.02880.0470.01550.104-0.0661-0.03590.0539-0.0094-0.00840.0378-0.00590.05630.7846-4.46632.0238
95.6077-1.4148-1.75354.4267-0.41964.7196-0.03350.0091-0.3421-0.0595-0.0143-0.5170.02430.4876-0.05110.08260.01190.01410.08750.00780.12716.1885-9.91528.1702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 10 )
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 15 )
4X-RAY DIFFRACTION4chain 'A' and (resid 16 through 26 )
5X-RAY DIFFRACTION5chain 'A' and (resid 27 through 39 )
6X-RAY DIFFRACTION6chain 'A' and (resid 40 through 61 )
7X-RAY DIFFRACTION7chain 'A' and (resid 62 through 73 )
8X-RAY DIFFRACTION8chain 'A' and (resid 74 through 89 )
9X-RAY DIFFRACTION9chain 'A' and (resid 90 through 99 )

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