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- PDB-7p5r: Racemic protein crystal structure of lacticin Q from Lactococcus ... -

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Basic information

Entry
Database: PDB / ID: 7p5r
TitleRacemic protein crystal structure of lacticin Q from Lactococcus lactis
Components
  • D-Lacticin Q
  • Lacticin Q
KeywordsANTIMICROBIAL PROTEIN / Racemic protein / D-protein / Bacteriocin
Function / homologyBacteriocin class II, aureocin-like / Aureocin-like type II bacteriocin / FORMIC ACID / Lacticin Q
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsLander, A.J. / Li, X. / Baumann, P. / Rizkallah, P. / Luk, L.Y.P. / Jin, Y.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L027240/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T015799/1 United Kingdom
Leverhulme TrustRPG-2017-195 United Kingdom
Royal SocietyRG170187 United Kingdom
Engineering and Physical Sciences Research Council2107414 United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Roles of inter- and intramolecular tryptophan interactions in membrane-active proteins revealed by racemic protein crystallography.
Authors: Lander, A.J. / Mercado, L.D. / Li, X. / Taily, I.M. / Findlay, B.L. / Jin, Y. / Luk, L.Y.P.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Lacticin Q
BBB: Lacticin Q
DDD: D-Lacticin Q
CCC: D-Lacticin Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,93011
Polymers23,6084
Non-polymers3227
Water3,369187
1
AAA: Lacticin Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9522
Polymers5,9061
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Lacticin Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0444
Polymers5,9061
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
DDD: D-Lacticin Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9903
Polymers5,8981
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
CCC: D-Lacticin Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9442
Polymers5,8981
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.210, 27.830, 70.450
Angle α, β, γ (deg.)95.030, 90.430, 115.410
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lacticin Q


Mass: 5906.080 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: QU 5 / Source: (synth.) Lactococcus lactis (lactic acid bacteria) / References: UniProt: A4UVR2
#2: Protein D-Lacticin Q


Mass: 5898.024 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: QU 5 / Source: (synth.) Lactococcus lactis (lactic acid bacteria)
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.81 Å3/Da / Density % sol: 31.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: A racemic mixture of L-lacticin Q and D-lacticin Q at 27 mg/mL concentration was mixed 1:1 with 4.0M sodium formate precipitant condition pH 7.0 in a 1 microlitre sitting drop. Crystals were ...Details: A racemic mixture of L-lacticin Q and D-lacticin Q at 27 mg/mL concentration was mixed 1:1 with 4.0M sodium formate precipitant condition pH 7.0 in a 1 microlitre sitting drop. Crystals were submerged in 2.0M Lithium sulfate cryoprotectant and flash frozen in liquid nitrogen during harvesting.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8156 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8156 Å / Relative weight: 1
ReflectionResolution: 0.96→35.05 Å / Num. obs: 93924 / % possible obs: 93 % / Redundancy: 3.5 % / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 0.96→0.98 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4211 / CC1/2: 0.67 / % possible all: 84.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless1.11.21data scaling
Fragon0.2.6phasing
Coot0.9.5model building
SHELXE2019/1model building
XDSdata reduction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal helix fragments

Resolution: 0.96→35.05 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.065 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.03
RfactorNum. reflection% reflection
Rfree0.2053 4686 4.989 %
Rwork0.1823 89236 -
all0.183 --
obs-93922 92.978 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20.374 Å2-0.818 Å2
2---0.053 Å2-0.852 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 0.96→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 21 189 1882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121795
X-RAY DIFFRACTIONr_bond_other_d0.0080.0171844
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.5972431
X-RAY DIFFRACTIONr_angle_other_deg1.3191.5894251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9235232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg51.7022630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06115171
X-RAY DIFFRACTIONr_chiral_restr0.1020.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022052
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02388
X-RAY DIFFRACTIONr_nbd_refined0.2440.2466
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.21630
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2101
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3120.235
X-RAY DIFFRACTIONr_nbd_other0.350.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.231
X-RAY DIFFRACTIONr_mcbond_it1.3561.157877
X-RAY DIFFRACTIONr_mcbond_other1.3571.158878
X-RAY DIFFRACTIONr_mcangle_it1.7321.7421099
X-RAY DIFFRACTIONr_mcangle_other1.7331.7421100
X-RAY DIFFRACTIONr_scbond_it2.2551.427918
X-RAY DIFFRACTIONr_scbond_other2.2521.428917
X-RAY DIFFRACTIONr_scangle_it2.542.0241323
X-RAY DIFFRACTIONr_scangle_other2.542.0251324
X-RAY DIFFRACTIONr_lrange_it2.61615.8822120
X-RAY DIFFRACTIONr_lrange_other2.54615.5262077
X-RAY DIFFRACTIONr_rigid_bond_restr5.43633639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.9850.3262960.3315982X-RAY DIFFRACTION84.3024
0.985-1.0120.2793170.2826066X-RAY DIFFRACTION87.3905
1.012-1.0410.2433120.2425997X-RAY DIFFRACTION89.2236
1.041-1.0730.2012860.2076044X-RAY DIFFRACTION91.3552
1.073-1.1080.1863520.1835831X-RAY DIFFRACTION92.6153
1.108-1.1470.1753140.1695668X-RAY DIFFRACTION93.0761
1.147-1.1910.2032960.1555482X-RAY DIFFRACTION93.4196
1.191-1.2390.1942600.1455328X-RAY DIFFRACTION93.9002
1.239-1.2940.1732650.1395191X-RAY DIFFRACTION94.2966
1.294-1.3570.1682720.1334952X-RAY DIFFRACTION94.9818
1.357-1.4310.1752590.1444723X-RAY DIFFRACTION95.4223
1.431-1.5180.1822480.1394478X-RAY DIFFRACTION95.4747
1.518-1.6220.2041920.1484276X-RAY DIFFRACTION96.0447
1.622-1.7520.1872270.163923X-RAY DIFFRACTION96.5565
1.752-1.9190.2222030.1793605X-RAY DIFFRACTION96.5762
1.919-2.1460.221450.1793367X-RAY DIFFRACTION97.0166
2.146-2.4770.2141600.1842898X-RAY DIFFRACTION97.1719
2.477-3.0330.2191200.1972515X-RAY DIFFRACTION97.7737
3.033-4.2860.1991010.1921899X-RAY DIFFRACTION97.6086

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