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- PDB-4euy: Crystal structure of thioredoxin-like protein BCE_0499 from Bacil... -

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Basic information

Entry
Database: PDB / ID: 4euy
TitleCrystal structure of thioredoxin-like protein BCE_0499 from Bacillus cereus ATCC 10987
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyGlutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thioredoxin
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsShabalin, I.G. / Kagan, O. / Chruszcz, M. / Grabowski, M. / Savchenko, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of thioredoxin-like protein BCE_0499 from Bacillus cereus
Authors: Shabalin, I.G. / Kagan, O. / Chruszcz, M. / Grabowski, M. / Savchenko, A. / Joachimiak, A. / Minor, W.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,5321
Polymers12,5321
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.458, 73.458, 64.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-205-

HOH

Detailsbiological unit is the same as asym. unit

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Components

#1: Protein Uncharacterized protein


Mass: 12531.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_0499 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q73E61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 0.3M NaCl, 10mM Hepes pH 7.5, 0.5 mM TCEP, Precipitant: 20% PEG3350, 0.2M tri-Li Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2010 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 4254 / Num. obs: 4245 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 111 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Χ2: 1.224 / Net I/σ(I): 41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.9-2.9513.90.8143.12063.10.705100
2.95-314.30.7541880.714100
3-3.06140.5262320.739100
3.06-3.1214.40.4641880.7100
3.12-3.1914.10.3052120.741100
3.19-3.2714.20.2462010.77100
3.27-3.3514.10.1842150.705100
3.35-3.4413.80.1621970.94100
3.44-3.5413.60.1262070.962100
3.54-3.65140.1042100.885100
3.65-3.7813.70.0932100.923100
3.78-3.9313.60.0772151.106100
3.93-4.1113.70.062060.967100
4.11-4.3313.70.0532181.133100
4.33-4.613.90.0412081.34100
4.6-4.9513.50.0462171.407100
4.95-5.4513.50.0612111.75599.1
5.45-6.2313.10.0742212.219100
6.23-7.8312.60.0742303.137100
7.83-3011.30.0692532.67897.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
CCP4phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2987 / WRfactor Rwork: 0.2122 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / SU B: 30.558 / SU ML: 0.265 / SU R Cruickshank DPI: 0.4737 / SU Rfree: 0.3606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.361
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 194 4.6 %RANDOM
Rwork0.2195 ---
obs0.2227 4219 99.72 %-
all-4232 --
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: 204.62 Å2 / Biso mean: 104.5937 Å2 / Biso min: 63.12 Å2
Baniso -1Baniso -2Baniso -3
1--7.36 Å20 Å20 Å2
2---7.36 Å20 Å2
3---14.72 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms677 0 0 9 686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02686
X-RAY DIFFRACTIONr_bond_other_d0.0010.02444
X-RAY DIFFRACTIONr_angle_refined_deg1.831.996929
X-RAY DIFFRACTIONr_angle_other_deg0.9483.0041087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.719584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4725.16131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81615115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.012153
X-RAY DIFFRACTIONr_chiral_restr0.0780.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 19 -
Rwork0.306 234 -
all-253 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
115.2672-3.48321.85679.0996-1.00788.2256-0.3781-0.31470.4232-0.8578-0.02150.0127-1.13550.40450.39950.55690.0686-0.06830.3739-0.02780.207725.04315.79625.815
29.6922-1.6286-1.88028.76373.98910.6893-0.0654-0.2038-0.3704-0.29690.14940.2621-0.2685-0.2615-0.0840.55290.0712-0.03290.40950.05720.258622.17710.98327.257
323.25495.792715.8669.422210.338622.44460.26221.123-0.1356-1.1532-0.09330.0807-0.560.7371-0.16880.787-0.01-0.06070.64870.01330.288128.7336.77417.488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 45
2X-RAY DIFFRACTION2A46 - 88
3X-RAY DIFFRACTION3A89 - 103

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