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- PDB-2x9q: Structure of the Mycobacterium tuberculosis protein, Rv2275, demo... -

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Basic information

Entry
Database: PDB / ID: 2x9q
TitleStructure of the Mycobacterium tuberculosis protein, Rv2275, demonstrates that cyclodipeptide synthetases are related to type I tRNA-Synthetases.
ComponentsCYCLODIPEPTIDE SYNTHETASE
KeywordsLIGASE
Function / homology
Function and homology information


cyclo(L-tyrosyl-L-tyrosyl) synthase / ligase activity, forming carbon-oxygen bonds / aminoacyltransferase activity
Similarity search - Function
Cyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclo(L-tyrosyl-L-tyrosyl) synthase / Cyclo(L-tyrosyl-L-tyrosyl) synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsVetting, M.W. / Hegde, S.S. / Blanchard, J.S.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: The Structure and Mechanism of the Mycobacterium Tuberculosis Cyclodityrosine Synthetase.
Authors: Vetting, M.W. / Hegde, S.S. / Blanchard, J.S.
History
DepositionMar 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLODIPEPTIDE SYNTHETASE
B: CYCLODIPEPTIDE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)63,8042
Polymers63,8042
Non-polymers00
Water4,756264
1
A: CYCLODIPEPTIDE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)31,9021
Polymers31,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYCLODIPEPTIDE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)31,9021
Polymers31,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.090, 75.060, 140.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9028, -0.1225, -0.4122), (-0.1256, -0.9919, 0.01964), (-0.4113, 0.03403, -0.9109)
Vector: 38.26, 8.569, 173.4)

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Components

#1: Protein CYCLODIPEPTIDE SYNTHETASE


Mass: 31901.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q50688, UniProt: P9WPF9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.99 Å3/Da / Density % sol: 58.8 % / Description: NONE
Crystal growpH: 8.75
Details: 12-15% (W/V) PEG 8000, 1M LICL, 100 MM TRIS/BICINE, PH 8.75

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→39 Å / Num. obs: 49827 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.6 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.02→70.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.903 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-48, A212-A216, A285-289, B1-B48, B209- B222, B285-B289 ARE DISORDERED RESIDUE WITH MINIMAL SIDE CHAIN DENSITY AT TERMINI MAY BE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-48, A212-A216, A285-289, B1-B48, B209- B222, B285-B289 ARE DISORDERED RESIDUE WITH MINIMAL SIDE CHAIN DENSITY AT TERMINI MAY BE MODELED AS ALANINES OR GLYCINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.21047 2525 5.1 %RANDOM
Rwork0.17983 ---
obs0.18142 47238 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.091 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---1.52 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.02→70.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 0 264 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9584884
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27722.833180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81515598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5411542
X-RAY DIFFRACTIONr_chiral_restr0.1630.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212781
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4031.52252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49223616
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.24431354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.6434.51268
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.015→2.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 193 -
Rwork0.226 3284 -
obs--95.31 %

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