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- PDB-3fk8: The crystal structure of disulphide isomerase from Xylella fastid... -

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Basic information

Entry
Database: PDB / ID: 3fk8
TitleThe crystal structure of disulphide isomerase from Xylella fastidiosa Temecula1
ComponentsDisulphide isomerase
KeywordsISOMERASE / APC61824.1 / disulphide isomerase / Xylella fastidiosa Temecula1 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Thioredoxin-like / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Disulphide isomerase
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsTan, K. / Sather, A. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of disulphide isomerase from Xylella fastidiosa Temecula1
Authors: Tan, K. / Sather, A. / Shackelford, G. / Joachimiak, A.
History
DepositionDec 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Apr 9, 2014Group: Data collection
Revision 1.3Nov 20, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disulphide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9625
Polymers14,7781
Non-polymers1844
Water2,756153
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.325, 50.236, 65.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsauthors state that biological unit is experimentally unknown, and is predicted to be monomeric.

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Components

#1: Protein Disulphide isomerase


Mass: 14777.548 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: Temecula1 / Gene: PD_1033, Xylella fastidiosa / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q87CN2
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 0.2M Trimethylamine N-oxide, 20% PEG MME 2000, pH 8.5, 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: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.3→27.54 Å / Num. all: 29212 / Num. obs: 29212 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 32.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.76 / Num. unique all: 1426 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→27.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.555 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17916 1486 5.1 %RANDOM
Rwork0.15421 ---
all0.15543 27672 --
obs0.15543 27672 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.859 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 12 153 1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221157
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9561576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83623.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72715217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.835159
X-RAY DIFFRACTIONr_chiral_restr0.1050.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021882
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8611.5712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.76721149
X-RAY DIFFRACTIONr_scbond_it3.4863445
X-RAY DIFFRACTIONr_scangle_it5.0384.5417
X-RAY DIFFRACTIONr_rigid_bond_restr1.86431157
X-RAY DIFFRACTIONr_sphericity_free7.7363157
X-RAY DIFFRACTIONr_sphericity_bonded5.55731128
LS refinement shellResolution: 1.302→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 121 -
Rwork0.274 1930 -
obs-2051 95.98 %

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