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- PDB-3efe: The crystal structure of the thiJ/pfpI family protein from Bacill... -

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Basic information

Entry
Database: PDB / ID: 3efe
TitleThe crystal structure of the thiJ/pfpI family protein from Bacillus anthracis
ComponentsThiJ/pfpI family protein
KeywordsCHAPERONE / thiJ/pfpI family protein / Bacillus anthracis / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ThiJ/pfpI family protein / ThiJ/pfpI family protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of the thiJ/pfpI family protein from Bacillus anthracis
Authors: Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W. / Joachimiak, A.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: ThiJ/pfpI family protein
B: ThiJ/pfpI family protein
C: ThiJ/pfpI family protein
D: ThiJ/pfpI family protein
E: ThiJ/pfpI family protein
F: ThiJ/pfpI family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,7977
Polymers142,7016
Non-polymers961
Water4,396244
1
A: ThiJ/pfpI family protein
D: ThiJ/pfpI family protein


Theoretical massNumber of molelcules
Total (without water)47,5672
Polymers47,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-20 kcal/mol
Surface area17350 Å2
MethodPISA
2
B: ThiJ/pfpI family protein
C: ThiJ/pfpI family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6633
Polymers47,5672
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-20 kcal/mol
Surface area17420 Å2
MethodPISA
3
E: ThiJ/pfpI family protein
F: ThiJ/pfpI family protein


Theoretical massNumber of molelcules
Total (without water)47,5672
Polymers47,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-21 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.129, 91.530, 167.206
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
ThiJ/pfpI family protein


Mass: 23783.445 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2475, BA_2657, GBAA2657 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81PY3, UniProt: A0A6H3AJL8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TARGET ID IDP01712 DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING.

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Heoes, 0.2M NH4(OAC0), 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2008 / 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: 2.3→83.62 Å / Num. all: 55865 / Num. obs: 54826 / % possible obs: 98.14 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.359 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.65 / Num. unique all: 4303 / % possible all: 83.29

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→83.62 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 16.854 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.374 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23661 2925 5.1 %RANDOM
Rwork0.19005 ---
obs0.19244 54826 98.14 %-
all-55865 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--0.79 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→83.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9842 0 5 244 10091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02210052
X-RAY DIFFRACTIONr_bond_other_d0.0020.026730
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.97213609
X-RAY DIFFRACTIONr_angle_other_deg1.209316575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.82251244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98125.182411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.976151812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.911524
X-RAY DIFFRACTIONr_chiral_restr0.1320.21548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021910
X-RAY DIFFRACTIONr_nbd_refined0.2390.22379
X-RAY DIFFRACTIONr_nbd_other0.220.27189
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24790
X-RAY DIFFRACTIONr_nbtor_other0.0980.25018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2354
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.29
X-RAY DIFFRACTIONr_mcbond_it1.2841.57933
X-RAY DIFFRACTIONr_mcbond_other0.2231.52531
X-RAY DIFFRACTIONr_mcangle_it1.598210014
X-RAY DIFFRACTIONr_scbond_it2.58134541
X-RAY DIFFRACTIONr_scangle_it3.6774.53595
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 187 -
Rwork0.282 3397 -
obs-3584 83.29 %
Refinement TLS params.Method: refined / Origin x: 83.497 Å / Origin y: 3.89 Å / Origin z: 25.68 Å
111213212223313233
T-0.1676 Å2-0.0208 Å20.0292 Å2-0.0689 Å2-0.05 Å2---0.2033 Å2
L0.2354 °2-0.0255 °20.0075 °2-0.3992 °2-0.0829 °2--0.4166 °2
S-0.0422 Å °-0.0056 Å °0.0637 Å °0.04 Å °-0.0236 Å °0.1128 Å °0.096 Å °-0.0351 Å °0.0658 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 209
2X-RAY DIFFRACTION1B-1 - 210
3X-RAY DIFFRACTION1C4 - 209
4X-RAY DIFFRACTION1D2 - 210
5X-RAY DIFFRACTION1E3 - 210
6X-RAY DIFFRACTION1F3 - 209

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