[English] 日本語
Yorodumi
- PDB-3ib5: Crystal structure of Sex pheromone precursor (YP_536235.1) from L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ib5
TitleCrystal structure of Sex pheromone precursor (YP_536235.1) from LACTOBACILLUS SALIVARIUS SUBSP. SALIVARIUS UCC118 at 1.35 A resolution
ComponentsSex pheromone precursor
KeywordsHORMONE / YP_536235.1 / Sex pheromone precursor / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Lipoprotein / CamS sex pheromone cAM373 precursor
Function / homology
Function and homology information


sex pheromone staph- cam373 precursor fold / sex pheromone staph- cam373 precursor domain / CamS sex pheromone cAM373 / CamS sex pheromone cAM373 precursor / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / DI(HYDROXYETHYL)ETHER / Lipoprotein, pheromone
Similarity search - Component
Biological speciesLactobacillus salivarius UCC118 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Sex pheromone precursor (YP_536235.1) from LACTOBACILLUS SALIVARIUS SUBSP. SALIVARIUS UCC118 at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sex pheromone precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0697
Polymers38,6911
Non-polymers3796
Water9,458525
1
A: Sex pheromone precursor
hetero molecules

A: Sex pheromone precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,13914
Polymers77,3822
Non-polymers75712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6680 Å2
ΔGint-9 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.175, 82.175, 108.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Sex pheromone precursor / Lipoprotein / pheromone


Mass: 38690.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus salivarius UCC118 (bacteria)
Gene: LSL_1347, YP_536235.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1WSH7

-
Non-polymers , 5 types, 531 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 35-381) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 35-381) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2000M MgNO3, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97858,0.97797
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978581
30.977971
ReflectionResolution: 1.35→28.061 Å / Num. obs: 81765 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 15.512 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.49
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.35-1.40.8291.57572311550896.6
1.4-1.450.6212.1522551401399.9
1.45-1.520.4283621531662499.9
1.52-1.60.2894.4584941555099.9
1.6-1.70.2096590221560099.9
1.7-1.830.1398.9587901548599.9
1.83-2.020.08314.2611421605699.9
2.02-2.310.05321.2589621544099.9
2.31-2.910.0427.2598051556099.9
2.91-28.0610.03136597811558899.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→28.061 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.712 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.054
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. NITRATE(NO3), MAGNESIUM(MG), POLYETHYLENE GLYCOL (PEG), AND ETHYLENE GLYCOL (EDO) MODELED ARE PRESENT IN CRYSTALLIZATION OR CRYO CONDITIONS. 4. FOLLOWING REGIONS HAVE POORLY DEFINED DENSITY: A44-50,A158-163,A179-190,A252-255 AND A367-374. MODEL AT THESE REGIONS MAY NOT BE ACCURATE.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 4095 5 %RANDOM
Rwork0.15 ---
obs0.151 81678 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.64 Å2 / Biso mean: 20.495 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.35→28.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 21 549 3607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223166
X-RAY DIFFRACTIONr_bond_other_d0.0010.022164
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9574347
X-RAY DIFFRACTIONr_angle_other_deg0.91535388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29626.118152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24415583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.985157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023696
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
X-RAY DIFFRACTIONr_mcbond_it1.6411.51928
X-RAY DIFFRACTIONr_mcbond_other0.7841.5792
X-RAY DIFFRACTIONr_mcangle_it2.56823167
X-RAY DIFFRACTIONr_scbond_it3.0331238
X-RAY DIFFRACTIONr_scangle_it4.4334.51134
X-RAY DIFFRACTIONr_rigid_bond_restr1.45535330
X-RAY DIFFRACTIONr_sphericity_free8.4253545
X-RAY DIFFRACTIONr_sphericity_bonded4.43535226
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 282 -
Rwork0.227 5623 -
all-5905 -
obs--99.06 %

+
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