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- PDB-3feu: Crystal Structure of DsbA-like thioredoxin domain VF_A0457 from V... -

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Basic information

Entry
Database: PDB / ID: 3feu
TitleCrystal Structure of DsbA-like thioredoxin domain VF_A0457 from Vibrio fischeri
Componentsputative Lipoprotein
KeywordsOXIDOREDUCTASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Lipoprotein / unknown function
Function / homology
Function and homology information


Thioredoxin / Thioredoxin-like fold / Thiol:disulphide interchange protein DsbA/DsbL / : / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipoprotein, putative
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.758 Å
AuthorsKim, Y. / Sather, A. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of DsbA-like thioredoxin domain VF_A0457 from Vibrio fischeri
Authors: Kim, Y. / Sather, A. / Shackelford, G. / Joachimiak, A.
History
DepositionDec 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8062
Polymers20,7821
Non-polymers241
Water3,063170
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.807, 55.737, 62.521
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 putative Lipoprotein


Mass: 20781.918 Da / Num. of mol.: 1 / Fragment: residues 30-211
Source method: isolated from a genetically manipulated source
Details: N-terminal 6-His tag with TEV protease cleavage site
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: VF_A0457 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q5E0B9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyehtlyene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→41.59 Å / Num. all: 17131 / Num. obs: 17131 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 26.75 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.05 / Num. unique all: 768 / % possible all: 90.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.4.0078refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.758→41.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.699 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 844 5 %RANDOM
Rwork0.188 ---
all0.191 15926 --
obs0.191 15926 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.103 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---2.29 Å20 Å2
3---3.52 Å2
Refinement stepCycle: LAST / Resolution: 1.758→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 1 170 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211596
X-RAY DIFFRACTIONr_bond_other_d0.0020.021040
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.9472182
X-RAY DIFFRACTIONr_angle_other_deg0.98132569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5215214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43625.92681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02915274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.519155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211904
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.51004
X-RAY DIFFRACTIONr_mcbond_other0.2771.5403
X-RAY DIFFRACTIONr_mcangle_it1.65221637
X-RAY DIFFRACTIONr_scbond_it2.6553592
X-RAY DIFFRACTIONr_scangle_it4.0584.5545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.758→1.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 49 -
Rwork0.327 977 -
obs-1081 84.03 %
Refinement TLS params.Method: refined / Origin x: 44.5185 Å / Origin y: 45.2287 Å / Origin z: 7.6555 Å
111213212223313233
T0.0122 Å20.0003 Å2-0.016 Å2-0.0499 Å2-0.0032 Å2--0.0491 Å2
L0.3974 °20.2606 °2-0.0343 °2-2.1479 °2-1.21 °2--1.9805 °2
S-0.0488 Å °0.0533 Å °-0.0814 Å °0.159 Å °-0.0027 Å °-0.1748 Å °-0.1678 Å °0.0371 Å °0.0515 Å °

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