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- PDB-3oqv: AlbC, a cyclodipeptide synthase from Streptomyces noursei -

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Basic information

Entry
Database: PDB / ID: 3oqv
TitleAlbC, a cyclodipeptide synthase from Streptomyces noursei
ComponentsAlbC
KeywordsPROTEIN BINDING / ROSSMANN FOLD / Cyclodipeptide Synthase / aminoacyl-tRNA
Function / homology
Function and homology information


cyclo(L-leucyl-L-phenylalanyl) synthase / aminoacyltransferase activity / antibacterial peptide biosynthetic process
Similarity search - Function
Cyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DITHIANE DIOL / PHOSPHATE ION / Cyclo(L-leucyl-L-phenylalanyl) synthase
Similarity search - Component
Biological speciesStreptomyces noursei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSauguet, L. / Ledu, M.H. / Charbonnier, J.B. / Gondry, M.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis.
Authors: Sauguet, L. / Moutiez, M. / Li, Y. / Belin, P. / Seguin, J. / Le Du, M.H. / Thai, R. / Masson, C. / Fonvielle, M. / Pernodet, J.L. / Charbonnier, J.B. / Gondry, M.
History
DepositionSep 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: AlbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2485
Polymers27,8111
Non-polymers4374
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.170, 97.170, 45.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein AlbC


Mass: 27811.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces noursei (bacteria) / Gene: albC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GED7
#2: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 290 K
Details: 1.7 M Na/K Phosphate, 100 mM DTT, pH pH 6, batch method under oil, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792, 0.9794, 0.9757
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97571
ReflectionResolution: 1.9→41.2 Å / Num. obs: 15963 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 6.9 / Rsym value: 0.615 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→41.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.743 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23647 849 5 %RANDOM
Rwork0.18587 ---
obs0.18841 15963 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 23 107 1740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211668
X-RAY DIFFRACTIONr_angle_refined_deg0.7931.9652260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3295211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.91622.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2641521
X-RAY DIFFRACTIONr_chiral_restr0.0640.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211278
X-RAY DIFFRACTIONr_mcbond_it1.6481.51053
X-RAY DIFFRACTIONr_mcangle_it2.68221674
X-RAY DIFFRACTIONr_scbond_it4.3493615
X-RAY DIFFRACTIONr_scangle_it6.9184.5586
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 57 -
Rwork0.275 1166 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -17.54 Å / Origin y: -34.934 Å / Origin z: -0.265 Å
111213212223313233
T0.0543 Å20.0457 Å2-0.0084 Å2-0.048 Å2-0.0071 Å2--0.0345 Å2
L0.693 °20.0305 °2-0.0967 °2-1.2706 °2-0.2245 °2--0.9161 °2
S-0.0394 Å °0.0116 Å °0.0368 Å °-0.0623 Å °0.0266 Å °0.0191 Å °0.0698 Å °0.0187 Å °0.0127 Å °

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