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- PDB-3txy: Structure of an Isochorismatase family protein (BTH_II2229) from ... -

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Basic information

Entry
Database: PDB / ID: 3txy
TitleStructure of an Isochorismatase family protein (BTH_II2229) from Burkholderia thailandensis
ComponentsIsochorismatase family protein family
KeywordsUNKNOWN FUNCTION / Isochorismatase family protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


: / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isochorismatase family protein family
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Isochorismatase family protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1352
Polymers21,0731
Non-polymers621
Water3,135174
1
A: Isochorismatase family protein family
hetero molecules

A: Isochorismatase family protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2704
Polymers42,1462
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3720 Å2
ΔGint-8 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.790, 61.790, 181.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-218-

HOH

31A-299-

HOH

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Components

#1: Protein Isochorismatase family protein family


Mass: 21072.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_II2229 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T332
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE IDENTITY OF THE RESIDUE AT THIS POSITION WAS VERIFIED BY SEQUENCING.

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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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium Malonate, 0.1 M BisTris propane, 20% PEG3350, Protein 55.9 mg/ml, Cryo protection 25% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→181.77 Å / Num. obs: 22855 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.875 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.4044.487441148487.6
1.74-1.790.3755.3312364147790
1.79-1.840.2886.9113212147691.8
1.84-1.90.2448.4213551148093.8
1.9-1.960.18311.1213598145195.7
1.96-2.030.14714.213858143397.4
2.03-2.110.12217.3713994142098.7
2.11-2.190.10722.3915821138199.6
2.19-2.290.09128.1417231132399.8
2.29-2.40.07931.61172431270100
2.4-2.530.07434.69173391209100
2.53-2.690.06640.2118182117299.8
2.69-2.870.05948.3319144108399.9
2.87-3.10.0556.0220290103199.7
3.1-3.40.04365.391832294399.8
3.4-3.80.03774.361620487399.7
3.8-4.390.03575.761417878799.5
4.39-5.380.03376.151188667099.1
5.38-7.60.03471.64942755098.9
7.60.03374.39480534294.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.79 Å
Translation2.5 Å45.79 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J2R

1j2r


Resolution: 1.7→40.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1891 / WRfactor Rwork: 0.1683 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9023 / SU B: 3.676 / SU ML: 0.062 / SU R Cruickshank DPI: 0.102 / SU Rfree: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1186 5.2 %RANDOM
Rwork0.1807 ---
obs0.1818 22845 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.41 Å2 / Biso mean: 15.9367 Å2 / Biso min: 6.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 4 174 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021449
X-RAY DIFFRACTIONr_bond_other_d0.0020.02910
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9581996
X-RAY DIFFRACTIONr_angle_other_deg0.95232248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37124.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3715208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.185157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 78 -
Rwork0.249 1235 -
all-1313 -
obs--86.15 %
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)
10.5190.11-0.02020.5268-0.00880.6408-0.0232-0.00250.06790.02620.0083-0.0465-0.13720.04410.01490.0695-0.0085-0.00210.0033-0.00150.059537.637815.089314.4317
20.46950.29650.33551.15980.56250.7964-0.04050.01810.0694-0.01910.01920.0887-0.13790.02060.02130.08920.0018-0.00610.01650.00580.065430.816117.016310.0422
31.0482-0.4312-0.07260.2630.42942.2232-0.02520.03840.00170.01570.03960.0070.01050.1759-0.01450.0635-0.0132-0.00420.0470.01410.074842.48148.34687.494
40.75950.0773-0.30570.82380.48081.5415-0.0027-0.04130.00320.08060.0004-0.02460.03220.11020.00220.06060.0039-0.02140.02020.00150.051940.89924.54319.8742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 72
2X-RAY DIFFRACTION2A73 - 114
3X-RAY DIFFRACTION3A115 - 132
4X-RAY DIFFRACTION4A133 - 191

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