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- PDB-3nzn: The crystal structure of the Glutaredoxin from Methanosarcina maz... -

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Basic information

Entry
Database: PDB / ID: 3nzn
TitleThe crystal structure of the Glutaredoxin from Methanosarcina mazei Go1
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / Structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Rossmann Fold / Glutaredoxin
Function / homology
Function and homology information


Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsZhang, R. / Wu, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the Glutaredoxin from Methanosarcina mazei Go1
Authors: Zhang, R. / Wu, R. / Freeman, L. / Joachimiak, A.
History
DepositionJul 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Glutaredoxin
B: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8937
Polymers23,4172
Non-polymers4765
Water4,756264
1
A: Glutaredoxin
hetero molecules

A: Glutaredoxin
hetero molecules

B: Glutaredoxin

B: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)47,78614
Polymers46,8334
Non-polymers95310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_655-x+1,y,-z1
Buried area5380 Å2
ΔGint-116 kcal/mol
Surface area20620 Å2
MethodPISA
2
A: Glutaredoxin
B: Glutaredoxin
hetero molecules

A: Glutaredoxin
B: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,78614
Polymers46,8334
Non-polymers95310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5990 Å2
ΔGint-110 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.423, 31.542, 57.935
Angle α, β, γ (deg.)90.00, 109.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-209-

HOH

21B-221-

HOH

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Components

#1: Protein Glutaredoxin


Mass: 11708.267 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: MM_3271 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8PS17
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M (NH4)2SO4, 20% PEG3350, 0.1M Na-hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.1→51.69 Å / Num. all: 72315 / Num. obs: 63391 / % possible obs: 87.66 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.24
Reflection shellResolution: 1.1→1.129 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1 / Num. unique all: 5273 / % possible all: 35.67

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.1→51.69 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.398 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.039 / Phase error: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18928 3410 5.1 %RANDOM
Rwork0.14678 ---
obs0.14907 63391 87.66 %-
all-72315 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å21.46 Å2
2---0.05 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.1→51.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 26 264 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0221700
X-RAY DIFFRACTIONr_bond_other_d0.0020.021180
X-RAY DIFFRACTIONr_angle_refined_deg2.6371.982285
X-RAY DIFFRACTIONr_angle_other_deg1.2532868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.05624.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83715314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.11512
X-RAY DIFFRACTIONr_chiral_restr0.1640.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02346
X-RAY DIFFRACTIONr_mcbond_it2.481.51014
X-RAY DIFFRACTIONr_mcbond_other1.2591.5424
X-RAY DIFFRACTIONr_mcangle_it3.55921638
X-RAY DIFFRACTIONr_scbond_it5.9313686
X-RAY DIFFRACTIONr_scangle_it8.464.5647
X-RAY DIFFRACTIONr_rigid_bond_restr2.66532880
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 104 -
Rwork0.339 1881 -
obs-1985 35.67 %

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