[English] 日本語
Yorodumi
- PDB-3iv0: Crystal structure of SusD homolog (NP_809186.1) from BACTEROIDES ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iv0
TitleCrystal structure of SusD homolog (NP_809186.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / NP_809186.1 / SusD homolog / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / RagB / SusD and hypothetical proteins / unknown function
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of SusD homolog (NP_809186.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 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: 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 / 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 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: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9777
Polymers55,6321
Non-polymers3466
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.650, 74.370, 67.375
Angle α, β, γ (deg.)90.000, 111.640, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein SusD homolog


Mass: 55631.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_0273, NP_809186.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AB38
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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. THE CLONED CONSTRUCT CONTAINS RESIDUES 24-503 OF THE FULL LENGTH PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2000M NaNO3, 20.0000% PEG-3350, No Buffer pH 6.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97848,0.97787
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 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
20.978481
30.977871
ReflectionResolution: 1.35→29.656 Å / Num. obs: 87986 / % possible obs: 86.8 % / Redundancy: 4 % / Biso Wilson estimate: 12.865 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.3920.2592.61337766680.25991.1
1.39-1.422.20.2323.11439266100.23290.8
1.42-1.464.10.3042.32614764240.30490.4
1.46-1.514.10.242.92578962650.2490.3
1.51-1.564.10.2013.52456459440.20189.4
1.56-1.614.20.1694.22423157820.16989.1
1.61-1.674.20.1434.92332555470.14388.5
1.67-1.744.30.1255.62253552970.12588
1.74-1.824.30.116.12161050420.1187.1
1.82-1.914.30.0976.82055147470.09786.7
1.91-2.014.40.0877.51975945280.08785.8
2.01-2.134.40.0797.91864342200.07985
2.13-2.284.50.0718.81756539280.07184.2
2.28-2.464.50.063101640536240.06383.4
2.46-2.74.60.062101509432930.06282.2
2.7-3.024.70.05810.71374429470.05881.2
3.02-3.494.70.05810.81201925580.05879.9
3.49-4.274.70.04912.8990521300.04978.5
4.27-6.044.60.04912.9740416070.04976.4
6.04-29.674.30.05611.835438250.05669.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→29.656 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 0.773 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.CHLORIDE ANION FROM CRYSTALLIZATION AND ETHYLENE GLYCOL FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY. 4.RESIDUE 191 IS CHEMICALLY MODIFIED TO S-HYDROXYCYSTINE WITH ELECTRON DENSITY SUPPORT.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 4361 5 %RANDOM
Rwork0.146 ---
obs0.147 87959 86.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.68 Å2 / Biso mean: 17.65 Å2 / Biso min: 3.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.19 Å2
2---0.42 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 21 610 4518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224012
X-RAY DIFFRACTIONr_bond_other_d0.0010.022695
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9445462
X-RAY DIFFRACTIONr_angle_other_deg0.85936521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0915.039509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39623.819199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63915652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.621529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02890
X-RAY DIFFRACTIONr_nbd_refined0.2680.3963
X-RAY DIFFRACTIONr_nbd_other0.2160.33164
X-RAY DIFFRACTIONr_nbtor_refined0.1960.52088
X-RAY DIFFRACTIONr_nbtor_other0.0920.51985
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5780
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0850.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.551
X-RAY DIFFRACTIONr_mcbond_it1.52232507
X-RAY DIFFRACTIONr_mcbond_other0.3743988
X-RAY DIFFRACTIONr_mcangle_it2.23953955
X-RAY DIFFRACTIONr_scbond_it3.65481745
X-RAY DIFFRACTIONr_scangle_it4.978111507
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 336 -
Rwork0.217 6470 -
all-6806 -
obs--91.17 %

+
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