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- PDB-2o12: Mycobacterium tuberculosis Chorismate synthase in complex with FMN -

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Basic information

Entry
Database: PDB / ID: 2o12
TitleMycobacterium tuberculosis Chorismate synthase in complex with FMN
ComponentsChorismate synthase
KeywordsLYASE / Shikimate pathway / M. tuberculosis / Chorismate synthase
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 / FLAVIN MONONUCLEOTIDE / Chorismate synthase / Chorismate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.72 Å
AuthorsBruning, M. / Bartunik, H.D.
CitationJournal: To be Published
Title: Complexes of Chorismate synthase from M. tuberculosis
Authors: Bruning, M. / Bourenkov, G.P. / Strizhov, N.I. / Bartunik, H.D.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4128
Polymers42,6731
Non-polymers7397
Water9,206511
1
A: Chorismate synthase
hetero molecules

A: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,82416
Polymers85,3472
Non-polymers1,47714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area12120 Å2
ΔGint-97 kcal/mol
Surface area28630 Å2
MethodPISA
2
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)173,64732
Polymers170,6934
Non-polymers2,95428
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 area34870 Å2
ΔGint-227 kcal/mol
Surface area46620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.445, 133.445, 158.619
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-843-

HOH

21A-882-

HOH

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Components

#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: aroF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: P63611, UniProt: P9WPY1*PLUS, chorismate synthase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 4.77 Å3/Da / Density % sol: 74.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 4.8 M NH4-Acetate, 0.1 M Na-Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2005 / Details: Au-coated planar; toroidal mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.72→20 Å / Num. all: 88402 / Num. obs: 88273 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.6
Reflection shellResolution: 1.72→1.74 Å / Redundancy: 7 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3488 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.72→19.74 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.401 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18783 4415 5 %RANDOM
Rwork0.1645 ---
obs0.1657 83603 99.63 %-
all-83913 --
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: 23.079 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: 1.72→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 49 511 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213088
X-RAY DIFFRACTIONr_bond_other_d0.0010.022928
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9814225
X-RAY DIFFRACTIONr_angle_other_deg0.88436748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41121.866134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5615490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7781542
X-RAY DIFFRACTIONr_chiral_restr0.0810.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02643
X-RAY DIFFRACTIONr_nbd_refined0.2170.2640
X-RAY DIFFRACTIONr_nbd_other0.190.23083
X-RAY DIFFRACTIONr_nbtor_refined0.170.21534
X-RAY DIFFRACTIONr_nbtor_other0.0810.21929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2342
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.247
X-RAY DIFFRACTIONr_mcbond_it3.08281998
X-RAY DIFFRACTIONr_mcbond_other0.9198820
X-RAY DIFFRACTIONr_mcangle_it4.433123195
X-RAY DIFFRACTIONr_scbond_it6.02161141
X-RAY DIFFRACTIONr_scangle_it8.393241014
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 313 -
Rwork0.271 6079 -
obs--99.86 %

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