[English] 日本語
Yorodumi
- PDB-3bkx: Crystal structure of cyclopropane-fatty-acyl-phospholipid synthas... -

+
Open data


ID or keywords:

Loading...

-
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 / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SAM-dependent methyltransferase
Similarity search - Component
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: SAD

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more