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- PDB-2qhf: Mycobacterium tuberculosis Chorismate synthase in complex with NCA -

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Basic information

Entry
Database: PDB / ID: 2qhf
TitleMycobacterium tuberculosis Chorismate synthase in complex with NCA
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 / NICOTINAMIDE / Chorismate synthase / Chorismate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBruning, M. / Bourenkov, G.P. / Strizhov, N.I. / Bartunik, H.D.
CitationJournal: To be Published
Title: Mycobacterium tuberculosis Chorismate synthase in complex with NCA
Authors: Bruning, M. / Bourenkov, G.P. / Strizhov, N.I. / Bartunik, H.D.
History
DepositionJul 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,70718
Polymers42,6731
Non-polymers1,03417
Water8,521473
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)174,83072
Polymers170,6934
Non-polymers4,13768
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area40380 Å2
ΔGint-222 kcal/mol
Surface area46310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.589, 132.589, 159.565
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-505-

ACT

21A-505-

ACT

31A-886-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chorismate synthase / 5-enolpyruvylshikimate-3-phosphate phospholyase


Mass: 42673.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: aroC, aroF / Plasmid: pET24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P63611, UniProt: P9WPY1*PLUS, chorismate synthase

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Non-polymers , 6 types, 490 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 4.84 Å3/Da / Density % sol: 74.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 4.8 M NH4-Acetate, 0.1 M Na-Acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 98095 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.3
Reflection shellResolution: 1.65→1.67 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3904 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QXO

1qxo


Resolution: 1.65→19.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.203 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18649 4977 5.1 %RANDOM
Rwork0.16391 ---
obs0.16508 93091 98.83 %-
all-98095 --
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: 22.497 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 68 473 3416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223148
X-RAY DIFFRACTIONr_bond_other_d0.0020.022997
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.984300
X-RAY DIFFRACTIONr_angle_other_deg0.83636913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4175443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80322.279136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57615502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9961540
X-RAY DIFFRACTIONr_chiral_restr0.0790.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
X-RAY DIFFRACTIONr_nbd_refined0.2170.2623
X-RAY DIFFRACTIONr_nbd_other0.2070.23007
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21580
X-RAY DIFFRACTIONr_nbtor_other0.0840.21811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2300
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.2165
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.242
X-RAY DIFFRACTIONr_mcbond_it2.72182062
X-RAY DIFFRACTIONr_mcbond_other0.8228835
X-RAY DIFFRACTIONr_mcangle_it4.018123278
X-RAY DIFFRACTIONr_scbond_it5.189161107
X-RAY DIFFRACTIONr_scangle_it7.32924998
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 376 -
Rwork0.252 6784 -
obs--99.32 %

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