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- PDB-5x5m: Crystal structure of a hydrolase encoded by lin2189 from Listeria... -

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Basic information

Entry
Database: PDB / ID: 5x5m
TitleCrystal structure of a hydrolase encoded by lin2189 from Listeria innocua
ComponentsLin2189 protein
KeywordsHYDROLASE/ANTIBIOTIC / hydrolase / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


GyrI-like cyclopropanoid cyclopropyl hydrolase Lin2189-like / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(+)-Yatakemycin / Lin2189 protein
Similarity search - Component
Biological speciesListeria innocua serovar 6a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.211 Å
AuthorsZhang, J.
CitationJournal: Nat Commun / Year: 2017
Title: GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection
Authors: Yuan, H. / Zhang, J. / Cai, Y. / Wu, S. / Yang, K. / Chan, H.C.S. / Huang, W. / Jin, W.B. / Li, Y. / Yin, Y. / Igarashi, Y. / Yuan, S. / Zhou, J. / Tang, G.L.
History
DepositionFeb 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin2189 protein
B: Lin2189 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2426
Polymers50,7262
Non-polymers1,5164
Water7,710428
1
A: Lin2189 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1213
Polymers25,3631
Non-polymers7582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area11020 Å2
MethodPISA
2
B: Lin2189 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1213
Polymers25,3631
Non-polymers7582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.630, 49.295, 80.361
Angle α, β, γ (deg.)90.00, 124.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21B-401-

HOH

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Components

#1: Protein Lin2189 protein


Mass: 25363.141 Da / Num. of mol.: 2 / Mutation: E157A/E185L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin2189 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q929T5
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-7YU / (+)-Yatakemycin


Mass: 679.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C35H29N5O8S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000, Glycerol, MES/imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 112031 / % possible obs: 96 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Net I/σ(I): 30.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data processing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B49

3b49


Resolution: 1.211→44.039 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 5605 5 %
Rwork0.1799 --
obs0.1807 112028 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.211→44.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 106 428 3912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063594
X-RAY DIFFRACTIONf_angle_d1.1464867
X-RAY DIFFRACTIONf_dihedral_angle_d24.6251397
X-RAY DIFFRACTIONf_chiral_restr0.083486
X-RAY DIFFRACTIONf_plane_restr0.005615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2112-1.2250.2391500.2223237X-RAY DIFFRACTION88
1.225-1.23940.20751650.21543460X-RAY DIFFRACTION94
1.2394-1.25450.23731840.21443462X-RAY DIFFRACTION94
1.2545-1.27040.22882020.21253458X-RAY DIFFRACTION94
1.2704-1.28710.24431840.20723466X-RAY DIFFRACTION96
1.2871-1.30480.22371760.2113510X-RAY DIFFRACTION95
1.3048-1.32340.22471910.20493518X-RAY DIFFRACTION96
1.3234-1.34320.20941850.19983443X-RAY DIFFRACTION94
1.3432-1.36410.21361960.19063420X-RAY DIFFRACTION94
1.3641-1.38650.19592060.19863500X-RAY DIFFRACTION96
1.3865-1.41040.22181850.1923578X-RAY DIFFRACTION96
1.4104-1.43610.21781820.19093562X-RAY DIFFRACTION97
1.4361-1.46370.20971890.18463555X-RAY DIFFRACTION97
1.4637-1.49360.20441930.183542X-RAY DIFFRACTION96
1.4936-1.5260.19541960.18043502X-RAY DIFFRACTION97
1.526-1.56150.22271940.17883512X-RAY DIFFRACTION95
1.5615-1.60060.21721920.17033424X-RAY DIFFRACTION93
1.6006-1.64390.1981830.17853576X-RAY DIFFRACTION97
1.6439-1.69230.18971810.1783627X-RAY DIFFRACTION98
1.6923-1.74690.20051730.183648X-RAY DIFFRACTION98
1.7469-1.80930.2031890.17893567X-RAY DIFFRACTION98
1.8093-1.88180.17911850.17653620X-RAY DIFFRACTION98
1.8818-1.96740.17621910.18013496X-RAY DIFFRACTION94
1.9674-2.07110.1721810.17183613X-RAY DIFFRACTION98
2.0711-2.20090.19122030.17613639X-RAY DIFFRACTION99
2.2009-2.37080.20591960.18773691X-RAY DIFFRACTION99
2.3708-2.60940.22051840.19373691X-RAY DIFFRACTION99
2.6094-2.98690.20111820.19043619X-RAY DIFFRACTION97
2.9869-3.76280.16682090.16693729X-RAY DIFFRACTION100
3.7628-44.06820.19591780.16523758X-RAY DIFFRACTION98

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