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- PDB-3oqh: Crystal structure of B. licheniformis CDPS yvmC-BLIC -

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Basic information

Entry
Database: PDB / ID: 3oqh
TitleCrystal structure of B. licheniformis CDPS yvmC-BLIC
ComponentsPutative uncharacterized protein yvmC
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: 1.901 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 1.3Mar 20, 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

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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)59,4183
Polymers59,3262
Non-polymers921
Water8,557475
1
A: Putative uncharacterized protein yvmC


Theoretical massNumber of molelcules
Total (without water)29,6631
Polymers29,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein yvmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7552
Polymers29,6631
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.719, 54.911, 101.523
Angle α, β, γ (deg.)90.000, 130.660, 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.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.69 Å3/Da / Density % sol: 54.21 % / Mosaicity: 0.192 °
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: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 15.07 / Number: 184550 / Rmerge(I) obs: 0.092 / Χ2: 1 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 49609 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.610.0310.8633.7
3.254.0999.510.0471.0843.6
2.843.2599.610.0861.2723.7
2.582.8499.710.1131.0063.7
2.392.5899.910.1450.8793.7
2.252.3999.910.1940.8863.7
2.142.2510010.2540.9183.7
2.052.1410010.3350.9863.7
1.972.0510010.4871.0213.7
1.91.9710010.6921.0733.7
ReflectionResolution: 1.9→50 Å / Num. obs: 49609 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.092 / Χ2: 0.998 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.70.69249221.0731100
1.97-2.053.70.48749551.0211100
2.05-2.143.70.33549230.9861100
2.14-2.253.70.25449240.9181100
2.25-2.393.70.19449510.886199.9
2.39-2.583.70.14549710.879199.9
2.58-2.843.70.11349351.006199.7
2.84-3.253.70.08649611.272199.6
3.25-4.093.60.04749731.084199.5
4.09-503.70.03150940.863199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.99 Å37.41 Å
Translation1.99 Å37.41 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→37.413 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8764 / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1864 3.97 %
Rwork0.18 --
obs0.1811 46979 94.3 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.839 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 72.13 Å2 / Biso mean: 23.4339 Å2 / Biso min: 9.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.0781 Å20 Å2-1.8917 Å2
2--1.8262 Å20 Å2
3----1.7481 Å2
Refinement stepCycle: LAST / Resolution: 1.901→37.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 6 475 3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073619
X-RAY DIFFRACTIONf_angle_d0.9774894
X-RAY DIFFRACTIONf_chiral_restr0.071536
X-RAY DIFFRACTIONf_plane_restr0.004644
X-RAY DIFFRACTIONf_dihedral_angle_d12.5761341
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 (%)
1.9012-1.96920.25481560.22623871402782
1.9692-2.0480.25791740.20734220439489
2.048-2.14120.22021750.18624429460494
2.1412-2.25410.20831920.17454489468194
2.2541-2.39530.2081840.17274565474996
2.3953-2.58020.20061890.17784571476096
2.5802-2.83980.21521920.18474616480897
2.8398-3.25050.20871970.18144680487798
3.2505-4.09450.18121940.15944787498199
4.0945-37.42060.19642110.1854887509899

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