[English] 日本語
Yorodumi
- PDB-3oyv: Crystal structure of an imelysin peptidase (BACOVA_03801) from Ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oyv
TitleCrystal structure of an imelysin peptidase (BACOVA_03801) from Bacteroides ovatus ATCC 8483 at 1.25 A resolution
ComponentsImelysin
KeywordsHYDROLASE / OUTER MEMBRANE PROTEIN / EXTRACELLULAR ACTIVE SITE / METAL BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyImelysin-like domain / Imelysin-like domain superfamily / Imelysin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Unknown ligand / Imelysin
Function and homology information
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Plos One / Year: 2011
Title: Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.
Authors: Xu, Q. / Rawlings, N.D. / Farr, C.L. / Chiu, H.J. / Grant, J.C. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / ...Authors: Xu, Q. / Rawlings, N.D. / Farr, C.L. / Chiu, H.J. / Grant, J.C. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Aug 10, 2011Group: Database references
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 27, 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: Imelysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1845
Polymers39,9641
Non-polymers2204
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.427, 47.921, 83.914
Angle α, β, γ (deg.)90.000, 124.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-731-

HOH

DetailsCRYSTAL PACKING SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING PROVIDES SUPPORTING EVIDENCE THAT A MONOMER IS A SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Imelysin


Mass: 39963.996 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: BACOVA_03801 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M120
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 25-384) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 25-384) 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.05M KH2PO4, 20.00% PEG-8000, No Buffer pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.85503,0.97934,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 12, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.855031
20.979341
30.979111
ReflectionResolution: 1.25→31.208 Å / Num. obs: 93405 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.53 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.79
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.25-1.290.5222.2242287550189.3
1.29-1.350.3943.13980410901199.8
1.35-1.410.3084337309176199.8
1.41-1.480.2295.2324268804199.8
1.48-1.570.1527.7341089210199.8
1.57-1.70.11210.23756710135199.8
1.7-1.870.07714.2345879317199.6
1.87-2.140.05320.4347429362199.5
2.14-2.690.03927.1346929377199.3
2.69-31.2080.03432.3348029571198.2

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.25→31.208 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.618 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.042
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CHLORIDE (CL), GLYCEROL (EDO) MODELED ARE PRESENT CRYSTALLIZATION/PURIFICATION/CRYO BUFFERS. 3. AN UNKNOWN LIGAND (UNL) IS MODELED ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CHLORIDE (CL), GLYCEROL (EDO) MODELED ARE PRESENT CRYSTALLIZATION/PURIFICATION/CRYO BUFFERS. 3. AN UNKNOWN LIGAND (UNL) IS MODELED INTO THE PUTATIVE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.163 4682 5 %RANDOM
Rwork0.1318 ---
obs0.1333 93405 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.97 Å2 / Biso mean: 17.0848 Å2 / Biso min: 3.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.74 Å2
2--1.14 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.25→31.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 19 533 3308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223219
X-RAY DIFFRACTIONr_bond_other_d0.0010.022096
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9454441
X-RAY DIFFRACTIONr_angle_other_deg0.9735217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3095447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85126.543162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30115546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.348158
X-RAY DIFFRACTIONr_chiral_restr0.090.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023762
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02601
X-RAY DIFFRACTIONr_mcbond_it2.34232003
X-RAY DIFFRACTIONr_mcbond_other2.0723791
X-RAY DIFFRACTIONr_mcangle_it3.17353266
X-RAY DIFFRACTIONr_scbond_it4.22581216
X-RAY DIFFRACTIONr_scangle_it5.843111140
X-RAY DIFFRACTIONr_rigid_bond_restr1.82735314
X-RAY DIFFRACTIONr_sphericity_free7.5873560
X-RAY DIFFRACTIONr_sphericity_bonded5.13435212
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 316 -
Rwork0.232 5798 -
all-6114 -
obs--88.21 %

+
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