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- PDB-3bkx: Crystal structure of cyclopropane-fatty-acyl-phospholipid synthas... -

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Basic information

Entry
Database: PDB / ID: 3bkx
TitleCrystal structure of cyclopropane-fatty-acyl-phospholipid synthase-like protein (YP_807781.1) from Lactobacillus casei ATCC 334 at 1.85 A resolution
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / YP_807781.1 / Cyclopropane-fatty-acyl-phospholipid synthase-like protein / Methyltransferase domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyMethyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / SAM-dependent methyltransferase
Function and homology information
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of cyclopropane-fatty-acyl-phospholipid synthase-like protein (YP_807781.1) from Lactobacillus casei ATCC 334 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1013
Polymers60,0662
Non-polymers351
Water8,863492
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.136, 42.381, 154.014
Angle α, β, γ (deg.)90.000, 103.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 30032.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: ATCC 334 / Gene: YP_807781.1, LSEI_2619 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q034N3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: NANODROP, 0.2M NH4OAc, 30.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.85→40.825 Å / Num. obs: 45283 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 13.78 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.954.60.6111.32925064000.61197.2
1.95-2.075.30.4661.73280262000.46699.7
2.07-2.215.30.3532.23102858680.35399.8
2.21-2.395.30.2722.92897854650.27299.8
2.39-2.625.30.2193.52696350810.21999.9
2.62-2.935.30.1485.22412045480.14899.9
2.93-3.385.30.0948.12146740490.094100
3.38-4.145.30.06211.51814634260.062100
4.14-5.855.20.05512.51410327220.055100
5.85-40.8254.90.04613.8748915240.04699.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0062refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→40.825 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.961 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.151
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RAMACHANDRAN OUTLIER A115G IS SUPPORTED BY CLEARLY DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2285 5 %RANDOM
Rwork0.185 ---
obs0.188 45282 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-1 Å2
2--0.64 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 1 492 4645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214314
X-RAY DIFFRACTIONr_bond_other_d0.0010.022717
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9435921
X-RAY DIFFRACTIONr_angle_other_deg1.01136679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.20924.497189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08915665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7481523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214904
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02835
X-RAY DIFFRACTIONr_mcbond_it0.7971.52759
X-RAY DIFFRACTIONr_mcbond_other0.2131.51119
X-RAY DIFFRACTIONr_mcangle_it1.36924433
X-RAY DIFFRACTIONr_scbond_it2.33831555
X-RAY DIFFRACTIONr_scangle_it3.4574.51477
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 165 -
Rwork0.294 2985 -
all-3150 -
obs--94.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.48850.08030.36850.33250.10661.463-0.02120.0185-0.002-0.00230.0259-0.0244-0.02810.0078-0.0047-0.0489-0.00610.00360.001-0.004-0.030227.08451.68577.9176
20.41530.11380.56630.05380.25031.1729-0.0576-0.04870.04810.02020.0028-0.0128-0.0275-0.1120.0547-0.0342-0.0049-0.00290.0017-0.0038-0.015929.51915.116528.3432
30.3680.0358-0.06610.6955-0.00430.9840.01110.026-0.03070.0493-0.0209-0.0180.04770.00860.0098-0.0094-0.0128-0.0045-0.04770.0027-0.013350.59332.425265.9308
40.6380.29360.65450.67430.20250.9638-0.0112-0.06680.0285-0.0676-0.01860.064-0.0484-0.07940.0297-0.0068-0.01330.0071-0.0315-0.0046-0.021342.46927.914247.5341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1302 - 131
2X-RAY DIFFRACTION2AA131 - 274132 - 275
3X-RAY DIFFRACTION3BB1 - 1302 - 131
4X-RAY DIFFRACTION4BB131 - 274132 - 275

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