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- PDB-3emx: Crystal structure of thioredoxin from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 3emx
TitleCrystal structure of thioredoxin from Aeropyrum pernix
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Miller, S. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of thioredoxin from Aeropyrum pernix
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Miller, S. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)30,5372
Polymers30,5372
Non-polymers00
Water86548
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)15,2691
Polymers15,2691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)15,2691
Polymers15,2691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.229, 54.852, 159.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thioredoxin


Mass: 15268.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE0641, APE_0641 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YED4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.87 Å3/Da / Density % sol: 34.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Hepes pH 7.5, 1.4M sodium tri-citrate, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.25→30.817 Å / Num. all: 11259 / Num. obs: 11236 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 16.5
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.8 / Num. measured all: 8131 / Num. unique all: 1629 / Rsym value: 0.45 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.816 / SU B: 7.65 / SU ML: 0.188 / SU R Cruickshank DPI: 0.386 / SU Rfree: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.386 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 552 4.9 %RANDOM
Rwork0.195 ---
obs0.198 11217 99.92 %-
all-11226 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.35 Å2 / Biso mean: 25.857 Å2 / Biso min: 10.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.18 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 0 48 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221991
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9772704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74823.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78315348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211470
X-RAY DIFFRACTIONr_mcbond_it0.5731.51235
X-RAY DIFFRACTIONr_mcangle_it1.13921992
X-RAY DIFFRACTIONr_scbond_it1.9393756
X-RAY DIFFRACTIONr_scangle_it3.3624.5711
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 41 -
Rwork0.249 750 -
all-791 -
obs-750 99.75 %

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