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- PDB-3oqp: Crystal structure of a putative isochorismatase (Bxe_A0706) from ... -

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Basic information

Entry
Database: PDB / ID: 3oqp
TitleCrystal structure of a putative isochorismatase (Bxe_A0706) from BURKHOLDERIA XENOVORANS LB400 at 1.22 A resolution
ComponentsPutative isochorismatase
KeywordsHYDROLASE / CATALYTIC TRIAD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
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 hydrolase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.22 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative isochorismatase (Bxe_A0706) from BURKHOLDERIA XENOVORANS LB400 at 1.22 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 12, 2014Group: Non-polymer description
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative isochorismatase
B: Putative isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5635
Polymers45,1392
Non-polymers4243
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-23 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.369, 103.135, 45.062
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number4
Space group name H-MP1211
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative isochorismatase


Mass: 22569.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxeno_A3690, Bxe_A0706 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13UL1
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.9 Å3/Da / Density % sol: 35.27 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 20.0% polyethylene glycol 3000, 0.15M sodium chloride, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97937,0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 10, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979371
30.978981
ReflectionResolution: 1.22→29.574 Å / Num. obs: 99282 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.39 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.22-1.260.4441.7249941681292.1
1.26-1.310.3662.1275461850693.2
1.31-1.370.2952.5283471898194.4
1.37-1.450.223.3311082080695.1
1.45-1.540.1484.9280891874796.2
1.54-1.660.0986.8285551910096.4
1.66-1.820.0689.5274881832896.7
1.82-2.090.0414.7293621958696.6
2.09-2.630.02720.9281861881295.9
2.630.0227.9280351860194

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.22→29.574 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.965 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.042
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. PEG-200 (PG4) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 4954 5 %RANDOM
Rwork0.14 ---
obs0.1413 99237 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.43 Å2 / Biso mean: 15.4416 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å21.7 Å2
2---2.11 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.22→29.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 15 481 3615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213432
X-RAY DIFFRACTIONr_bond_other_d0.0010.022229
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.9354720
X-RAY DIFFRACTIONr_angle_other_deg1.02835435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.235469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85423.185157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64415499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9091530
X-RAY DIFFRACTIONr_chiral_restr0.1110.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02737
X-RAY DIFFRACTIONr_mcbond_it1.8271.52208
X-RAY DIFFRACTIONr_mcbond_other1.2411.5885
X-RAY DIFFRACTIONr_mcangle_it2.47823577
X-RAY DIFFRACTIONr_scbond_it3.32231224
X-RAY DIFFRACTIONr_scangle_it4.5814.51132
X-RAY DIFFRACTIONr_rigid_bond_restr1.68935659
X-RAY DIFFRACTIONr_sphericity_free9.7133490
X-RAY DIFFRACTIONr_sphericity_bonded6.29535566
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 366 -
Rwork0.249 6970 -
all-7336 -
obs--99.07 %

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