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- PDB-4mja: Synechocystis sp. PCC 6803 glutaredoxin A-A75I -

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Basic information

Entry
Database: PDB / ID: 4mja
TitleSynechocystis sp. PCC 6803 glutaredoxin A-A75I
ComponentsProbable glutaredoxin ssr2061
KeywordsELECTRON TRANSPORT / glutaredoxin / oxidation/reduction / thioredoxin fold
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: 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable glutaredoxin ssr2061


Theoretical massNumber of molelcules
Total (without water)11,0641
Polymers11,0641
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.180, 38.320, 51.630
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: 11063.570 Da / Num. of mol.: 1 / Mutation: A75I
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.66 Å3/Da / Density % sol: 26 %
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: 1.232 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.232 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 5603 / Num. obs: 5603 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16

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Processing

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

3qmx


Resolution: 2→30.171 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 563 10.05 %random
Rwork0.2057 ---
obs0.2081 5603 98.99 %-
all-5603 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→30.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 0 62 835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03804
X-RAY DIFFRACTIONf_angle_d2.1321085
X-RAY DIFFRACTIONf_dihedral_angle_d17.079296
X-RAY DIFFRACTIONf_chiral_restr0.165112
X-RAY DIFFRACTIONf_plane_restr0.015144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.958-2.1550.27231350.2211249X-RAY DIFFRACTION100
2.155-2.46670.25391350.23841194X-RAY DIFFRACTION96
2.4667-3.10730.22311440.21161262X-RAY DIFFRACTION100
3.1073-30.17470.20961490.18391335X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.1028 Å / Origin y: 1.1064 Å / Origin z: -3.4893 Å
111213212223313233
T0.0867 Å20.0143 Å20.0047 Å2-0.1799 Å20.0084 Å2--0.1452 Å2
L0.6367 °20.5141 °20.7198 °2-0.659 °20.9275 °2--1.8998 °2
S0.0442 Å °-0.0646 Å °-0.0415 Å °0.0163 Å °-0.0664 Å °0.0558 Å °0.1187 Å °-0.0422 Å °0.045 Å °
Refinement TLS groupSelection details: (chain A and resid -10:88)

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