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- PDB-5z9o: The crystal structure of Cyclopropane-fatty-acyl-phospholipid syn... -

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Basic information

Entry
Database: PDB / ID: 5z9o
TitleThe crystal structure of Cyclopropane-fatty-acyl-phospholipid synthase from Lactobacillus acidophilus
ComponentsCyclopropane-fatty-acyl-phospholipid synthase
KeywordsTRANSFERASE / Cyclopropane-fatty-acyl-phospholipid synthase / phosphatidyl ethanolamine / bicarbonate ion / carbocation mechanism / LIPID BINDING PROTEIN
Function / homology
Function and homology information


cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / lipid biosynthetic process / methylation
Similarity search - Function
Mycolic acid cyclopropane synthase / Mycolic acid cyclopropane synthetase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
CARBONATE ION / Chem-EPH / Cyclopropane-fatty-acyl-phospholipid synthase
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPan, C.L. / Ma, Y.L. / Wang, Q.H.
Funding support China, 2items
OrganizationGrant numberCountry
Hubei Natural Science Foundation of China2015ZFB763 China
the research fund from JCUTZR201410 China
CitationJournal: J.Biochem. / Year: 2019
Title: Crystal structure of bacterial cyclopropane-fatty-acyl-phospholipid synthase with phospholipid.
Authors: Ma, Y. / Pan, C. / Wang, Q.
History
DepositionFeb 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 1.2Nov 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclopropane-fatty-acyl-phospholipid synthase
B: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6006
Polymers92,0602
Non-polymers1,5404
Water4,720262
1
A: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8003
Polymers46,0301
Non-polymers7702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8003
Polymers46,0301
Non-polymers7702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.982, 120.982, 163.487
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 0 / Auth seq-ID: 4 - 389 / Label seq-ID: 4 - 389

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cyclopropane-fatty-acyl-phospholipid synthase /


Mass: 46030.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM) (bacteria)
Strain: ATCC 700396 / NCK56 / N2 / NCFM / Gene: LBA1274 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5FJM0, cyclopropane-fatty-acyl-phospholipid synthase
#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 709.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 1.5 M ammonium sulfate, 0.1 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dehydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→88.21 Å / Num. obs: 37057 / % possible obs: 99.94 % / Redundancy: 4.3 % / Net I/σ(I): 5.2
Reflection shellResolution: 2.703→2.773 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PHASERphasing
PDBSETdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L1E

1l1e


Resolution: 2.7→44.106 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.335 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21258 1852 5 %RANDOM
Rwork0.17515 ---
obs0.17696 35208 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.138 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.7→44.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 102 262 6376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196245
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9688399
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7685741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4124.916297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.984151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7491524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214707
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7264.5812976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.8726.8583713
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7374.953269
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined34.75464.6889748
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24562 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.703→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 136 -
Rwork0.272 2570 -
obs--99.27 %

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