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- PDB-2xhg: Crystal Structure of the Epimerization Domain from the Initiation... -

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Basic information

Entry
Database: PDB / ID: 2xhg
TitleCrystal Structure of the Epimerization Domain from the Initiation Module of Tyrocidine Biosynthesis
ComponentsTYROCIDINE SYNTHETASE A
KeywordsISOMERASE / NONRIBOSOMAL PEPTIDE SYNTHESIS / COFACTOR-INDEPENDENT EPIMERIZATION
Function / homology
Function and homology information


lipid biosynthetic process / ligase activity
Similarity search - Function
Nonribosomal peptide synthetase, condensation domain / Non-ribosomal peptide synthase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrocidine synthetase a
Similarity search - Component
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsSamel, S.-A. / Heine, A. / Marahiel, M.A. / Essen, L.-O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the Epimerization Domain of Tyrocidine Synthetase A
Authors: Samel, S.-A. / Czodrowski, P. / Essen, L.-O.
History
DepositionJun 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references / Non-polymer description ...Database references / Non-polymer description / Source and taxonomy / Version format compliance
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: TYROCIDINE SYNTHETASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4617
Polymers52,9771
Non-polymers4836
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.710, 74.590, 124.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYROCIDINE SYNTHETASE A


Mass: 52977.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EPIMERIZATION DOMAIN LACKS HELICAL SEGMENT AT C-TERMINUS THAT WAS PROPOSED TO MEDIATE MUTUAL RECOGNITION OF SUCCESSIVE SYNTHETASES.
Source: (gene. exp.) BREVIBACILLUS BREVIS (bacteria) / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: G1K3P2*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGLYCEROL (GOL): GLYCEROL MOLECULES DERIVED FROM CRYO BUFFER

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.29 % / Description: NONE
Crystal growDetails: 0.1 M POTASSIUM PHOSPHATE, 20% PEG 8000, (20 % GLYCEROL).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.03946
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03946 Å / Relative weight: 1
ReflectionResolution: 1.5→47.84 Å / Num. obs: 72029 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.649 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 1061 1.5 %RANDOM
Rwork0.15958 ---
obs0.15987 70891 99.84 %-
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: 12.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 31 441 4106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213831
X-RAY DIFFRACTIONr_bond_other_d0.0010.022521
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9445223
X-RAY DIFFRACTIONr_angle_other_deg0.83336186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3455484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59825.078193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32315635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9851515
X-RAY DIFFRACTIONr_chiral_restr0.0710.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
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_it2.00822314
X-RAY DIFFRACTIONr_mcbond_other0.5862939
X-RAY DIFFRACTIONr_mcangle_it3.20633743
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.90521517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.51531466
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 72 -
Rwork0.256 5164 -
obs--99.96 %
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)
10.7423-0.23650.01730.86050.03910.6084-0.005-0.0166-0.010.0175-0.01080.08690.009-0.06030.01580.001-0.00240.00330.0274-0.00450.0127-21.5539-1.628723.5485
20.2063-0.03020.11240.6067-0.07940.75-0.01580.06020.0389-0.11960.01250.01670.01680.05220.00330.0629-0.010.00140.0650.00680.0549-10.30980.0088-1.1893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 195
2X-RAY DIFFRACTION1A374 - 405
3X-RAY DIFFRACTION2A196 - 373
4X-RAY DIFFRACTION2A406 - 460

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