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- PDB-4bai: Mycobacterium tuberculosis Chorismate synthase before exposure to... -

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Basic information

Entry
Database: PDB / ID: 4bai
TitleMycobacterium tuberculosis Chorismate synthase before exposure to 266 nm UV laser
ComponentsCHORISMATE SYNTHASE
KeywordsLYASE
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / Chorismate via Shikimate Pathway / oxidoreductase activity, acting on NAD(P)H / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NAD binding / FMN binding / cytosol
Similarity search - Function
Chorismate synthase signature 3. / Chorismate synthase, AroC fold / Chorismate synthase AroC / Chorismate synthase signature 2. / Chorismate synthase / Chorismate synthase, conserved site / Chorismate synthase AroC superfamily / Chorismate synthase / Chorismate synthase signature 1. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chorismate synthase / Chorismate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsPereira, P.J.B. / Royant, A. / Panjikar, S. / de Sanctis, D.
CitationJournal: J. Struct. Biol. / Year: 2013
Title: In-house UV radiation-damage-induced phasing of selenomethionine-labeled protein structures.
Authors: Pereira, P.J. / Royant, A. / Panjikar, S. / de Sanctis, D.
History
DepositionSep 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Refinement description
Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _software.name
Revision 1.2Jun 6, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _software.version
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CHORISMATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3073
Polymers43,1891
Non-polymers1182
Water1,982110
1
A: CHORISMATE SYNTHASE
hetero molecules

A: CHORISMATE SYNTHASE
hetero molecules

A: CHORISMATE SYNTHASE
hetero molecules

A: CHORISMATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,22912
Polymers172,7564
Non-polymers4728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area28680 Å2
ΔGint-114.4 kcal/mol
Surface area46920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.820, 131.820, 160.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-3-

ARG

21A-2037-

HOH

31A-2107-

HOH

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Components

#1: Protein CHORISMATE SYNTHASE / / 5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE PHOSPHOLYASE


Mass: 43189.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P63611, UniProt: P9WPY1*PLUS, chorismate synthase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 4.5 Å3/Da / Density % sol: 76 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 4.5
Details: 4.8 M NH4-ACETATE, 0.1 M NA-ACETATE, PH 4.5, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION GEMINI / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: AGILENT / Detector: CCD / Date: Nov 25, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 34968 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 26.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.25 / % possible all: 72.2

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.3→14.81 Å / SU ML: 0.23 / σ(F): 0.95 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 3316 5.1 %
Rwork0.1816 --
obs0.1828 34935 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 23.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 8 110 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082827
X-RAY DIFFRACTIONf_angle_d1.053837
X-RAY DIFFRACTIONf_dihedral_angle_d13.511031
X-RAY DIFFRACTIONf_chiral_restr0.069440
X-RAY DIFFRACTIONf_plane_restr0.005516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.33280.25231030.23851784X-RAY DIFFRACTION65
2.3328-2.36750.2491010.23181856X-RAY DIFFRACTION68
2.3675-2.40430.2391400.2211981X-RAY DIFFRACTION74
2.4043-2.44360.26851290.22362163X-RAY DIFFRACTION79
2.4436-2.48550.23711090.20822361X-RAY DIFFRACTION86
2.4855-2.53050.23431320.19922669X-RAY DIFFRACTION97
2.5305-2.57890.23731380.20872639X-RAY DIFFRACTION98
2.5789-2.63130.24461630.2042749X-RAY DIFFRACTION100
2.6313-2.68810.24261220.19862751X-RAY DIFFRACTION100
2.6881-2.75030.23681370.20262712X-RAY DIFFRACTION100
2.7503-2.81860.24351720.19062704X-RAY DIFFRACTION100
2.8186-2.89430.2281280.20262731X-RAY DIFFRACTION100
2.8943-2.97880.24691540.19782724X-RAY DIFFRACTION100
2.9788-3.07410.22441420.20142732X-RAY DIFFRACTION100
3.0741-3.18290.23871260.19812738X-RAY DIFFRACTION100
3.1829-3.3090.20311390.19172744X-RAY DIFFRACTION100
3.309-3.45780.17831520.17732721X-RAY DIFFRACTION99
3.4578-3.63750.2351530.17132668X-RAY DIFFRACTION98
3.6375-3.86160.18021610.15752625X-RAY DIFFRACTION97
3.8616-4.15370.14871730.14282601X-RAY DIFFRACTION96
4.1537-4.56060.16211140.14522654X-RAY DIFFRACTION96
4.5606-5.19540.1671380.15062675X-RAY DIFFRACTION98
5.1954-6.45420.18391360.19382645X-RAY DIFFRACTION97
6.4542-14.81010.17151540.17172512X-RAY DIFFRACTION92

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