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- PDB-3hz4: Crystal Structure of Thioredoxin from Methanosarcina mazei -

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Basic information

Entry
Database: PDB / ID: 3hz4
TitleCrystal Structure of Thioredoxin from Methanosarcina mazei
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / NYSGXRC / PSI-II / reduced form / thioredoxin / 11215h / Protein structure Initiative / structural genomics / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


protein-disulfide reductase activity / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / 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: 2.3 Å
AuthorsSyed Ibrahim, B. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Thioredoxin from Methanosarcina mazei
Authors: Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7035
Polymers32,5172
Non-polymers1863
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-2 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.068, 82.068, 93.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Thioredoxin


Mass: 16258.526 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: MM_2079 / Plasmid: TOP10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8PV92
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% Peg 3350, 0.1M Bis Tris pH 5.5, 0.2M LiSo4, 0.1M EDTA, 20% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2009 / Details: Mirrors
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: -h,-k,l / Fraction: 0.38
ReflectionResolution: 2.3→50 Å / Num. all: 18041 / Num. obs: 18041 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.5 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 21 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 9.6 / Num. unique all: 1639 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.592 / SU ML: 0.139 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The data is hemihedral twinning with twinning operator (-h, -k, l) and corresponding twinned fraction: 0.38.
RfactorNum. reflection% reflectionSelection details
Rfree0.24659 927 5.1 %RANDOM
Rwork0.19053 ---
obs0.19335 17112 94.83 %-
all-18040 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.4 Å20 Å2
2--0.81 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 12 99 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222001
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.942707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4265238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38224.25594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.37115325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.226158
X-RAY DIFFRACTIONr_chiral_restr0.1930.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021550
X-RAY DIFFRACTIONr_nbd_refined0.2430.2872
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4290.215
X-RAY DIFFRACTIONr_mcbond_it1.6591.51225
X-RAY DIFFRACTIONr_mcangle_it2.21521951
X-RAY DIFFRACTIONr_scbond_it3.8123908
X-RAY DIFFRACTIONr_scangle_it5.7634.5756
LS refinement shellResolution: 2.257→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 63 -
Rwork0.251 1106 -
obs--85.39 %

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