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- PDB-3oqi: Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex w... -

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Basic information

Entry
Database: PDB / ID: 3oqi
TitleCrystal structure of B. licheniformis CDPS yvmC-BLIC in complex with CHES
Components(Putative uncharacterized protein yvmC) x 2
KeywordsLIGASE / tRNA / ROSSMANN FOLD
Function / homology
Function and homology information


cyclo(L-leucyl-L-leucyl) synthase / pigment biosynthetic process / 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-leucyl-L-leucyl) synthase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.701 Å
AuthorsBonnefond, L. / Arai, T. / Suzuki, T. / Ishitani, R. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
Authors: Bonnefond, L. / Arai, T. / Sakaguchi, Y. / Suzuki, T. / Ishitani, R. / Nureki, O.
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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: Putative uncharacterized protein yvmC
B: Putative uncharacterized protein yvmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4639
Polymers59,3582
Non-polymers1,1057
Water7,440413
1
A: Putative uncharacterized protein yvmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1694
Polymers29,6631
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein yvmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2945
Polymers29,6951
Non-polymers5994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.946, 55.011, 102.299
Angle α, β, γ (deg.)90.000, 130.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative uncharacterized protein yvmC / YvmC


Mass: 29662.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NdeI/XhoI restriction sites / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: ATCC 14580 / Gene: BL00817, BLi03566, yvmC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: Q65EX3
#2: Protein Putative uncharacterized protein yvmC / YvmC


Mass: 29694.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NdeI/XhoI restriction sites / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: ATCC 14580 / Gene: BL00817, BLi03566, yvmC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: Q65EX3
#3: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.72 Å3/Da / Density % sol: 54.71 % / Mosaicity: 0.282 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 20% PEG 8000, pH 9.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.5 % / Av σ(I) over netI: 29.72 / Number: 529353 / Rmerge(I) obs: 0.085 / Χ2: 1.18 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 70129 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665099.810.0331.1187.4
2.913.6610010.072.2697.5
2.542.9110010.0831.5757.6
2.312.5410010.0880.987.6
2.142.3110010.1130.9367.6
2.022.1410010.150.9087.6
1.912.0210010.2080.9157.6
1.831.9110010.3060.9917.6
1.761.8310010.4141.0227.5
1.71.7610010.5661.0937.5
ReflectionResolution: 1.7→50 Å / Num. obs: 70129 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.085 / Χ2: 1.181 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.767.50.56670061.0931100
1.76-1.837.50.41469591.0221100
1.83-1.917.60.30669210.9911100
1.91-2.027.60.20870000.9151100
2.02-2.147.60.1569640.9081100
2.14-2.317.60.11370220.9361100
2.31-2.547.60.08869850.981100
2.54-2.917.60.08370291.5751100
2.91-3.667.50.0770692.2691100
3.66-507.40.03371741.118199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å32.35 Å
Translation2.5 Å32.35 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.2.4phasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.701→32.354 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9061 / SU ML: 0.19 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1836 1925 2.84 %
Rwork0.1653 --
obs0.1658 67798 96.59 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.142 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 73.68 Å2 / Biso mean: 17.7777 Å2 / Biso min: 5.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.4089 Å20 Å2-1.05 Å2
2--1.4739 Å20 Å2
3----1.065 Å2
Refinement stepCycle: LAST / Resolution: 1.701→32.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 70 413 4011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063702
X-RAY DIFFRACTIONf_angle_d1.064998
X-RAY DIFFRACTIONf_chiral_restr0.075538
X-RAY DIFFRACTIONf_plane_restr0.004645
X-RAY DIFFRACTIONf_dihedral_angle_d16.3761390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7011-1.76190.20091800.18656102628290
1.7619-1.83240.20821800.17716244642492
1.8324-1.91580.20191790.1646321650094
1.9158-2.01680.18021960.15696558675496
2.0168-2.14310.17341860.15956630681698
2.1431-2.30850.1842000.16366711691198
2.3085-2.54080.18221960.16346699689599
2.5408-2.90820.19252030.1696785698899
2.9082-3.66320.16852030.158968537056100
3.6632-32.35940.18292020.168369707172100

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