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- PDB-3os6: Crystal structure of putative 2,3-dihydroxybenzoate-specific isoc... -

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Basic information

Entry
Database: PDB / ID: 3os6
TitleCrystal structure of putative 2,3-dihydroxybenzoate-specific isochorismate synthase, DhbC from Bacillus anthracis.
ComponentsIsochorismate synthase DhbC
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / isochorismate synthase DhbC
Function / homology
Function and homology information


isochorismate synthase / isochorismate synthase activity / biosynthetic process
Similarity search - Function
Isochorismate synthase / Anthranilate synthase / Anthranilate synthase / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
isochorismate synthase / isochorismate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsDomagalski, M.J. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of isochorismate synthase DhbC from Bacillus anthracis.
Authors: Domagalski, M.J. / Tkaczuk, K.L. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Cymborowski, M. / Grabowski, M. / Savchenko, A. / Minor, W.
History
DepositionSep 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Apr 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Isochorismate synthase DhbC
B: Isochorismate synthase DhbC
C: Isochorismate synthase DhbC
D: Isochorismate synthase DhbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,28140
Polymers179,9794
Non-polymers6,30236
Water13,745763
1
A: Isochorismate synthase DhbC
B: Isochorismate synthase DhbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,14420
Polymers89,9892
Non-polymers3,15518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-210 kcal/mol
Surface area30460 Å2
MethodPISA
2
C: Isochorismate synthase DhbC
D: Isochorismate synthase DhbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,13620
Polymers89,9892
Non-polymers3,14718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-192 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.389, 201.389, 201.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A9 - 392
2114B9 - 392
3114C9 - 392
4114D9 - 392

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Components

#1: Protein
Isochorismate synthase DhbC


Mass: 44994.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS2205, BA_2369, dhbC, GBAA2369, GBAA_2369 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q81QQ0, UniProt: A0A6H3A7J7*PLUS, isochorismate synthase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2M NH4Sulph, 2% PEG400, Hepes 0.1M pH 7.5, Bis-Tris 50mM pH 5.5, 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: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 105217 / Num. obs: 105217 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.613 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
ARP/wARPmodel building
CCP4model building
REFMAC5.6.0070refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.644 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.193
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21152 4978 5 %RANDOM
Rwork0.17134 ---
obs0.17334 94245 93.8 %-
all-94245 --
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 mean: 44.406 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11550 0 214 763 12527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02212049
X-RAY DIFFRACTIONr_bond_other_d0.0010.028175
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.99316347
X-RAY DIFFRACTIONr_angle_other_deg0.969320071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56351503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06824.542513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.927152072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8211573
X-RAY DIFFRACTIONr_chiral_restr0.0920.21844
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022191
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4703 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.460.5
2BMEDIUM POSITIONAL0.450.5
3CMEDIUM POSITIONAL0.440.5
4DMEDIUM POSITIONAL0.450.5
1AMEDIUM THERMAL8.452
2BMEDIUM THERMAL8.212
3CMEDIUM THERMAL8.072
4DMEDIUM THERMAL7.972
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 225 -
Rwork0.229 4037 -
obs--54.78 %
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)
11.6166-0.22010.12540.17140.05430.1006-0.01990.3601-0.22420.03660.0615-0.0587-0.02970.0515-0.04160.0716-0.02420.00880.2811-0.19820.19412.886242.22978.033
20.96390.26850.1110.580.4290.33110.01610.02120.00850.00260.0297-0.03020.0170.0182-0.04580.1552-0.0416-0.04510.1043-0.01210.0935-41.144632.967177.2041
30.3140.4303-0.11620.6059-0.2580.9592-0.04010.0139-0.0184-0.03090.0251-0.0051-0.0099-0.02370.0150.0972-0.01610.04480.10640.04470.148326.759883.378591.4521
40.10450.0703-0.06950.18450.25531.7046-0.0330.03720.0267-0.06140.0547-0.03930.2294-0.355-0.02170.1939-0.1949-0.00290.27190.02610.075127.847992.624447.4844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 392
2X-RAY DIFFRACTION2B10 - 392
3X-RAY DIFFRACTION3C10 - 392
4X-RAY DIFFRACTION4D9 - 392

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