[English] 日本語
Yorodumi
- PDB-3hbk: Crystal structure of putative glycosyl hydrolase, was Domain of U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hbk
TitleCrystal structure of putative glycosyl hydrolase, was Domain of Unknown Function (DUF1080) (YP_001302580.1) from Parabacteroides distasonis ATCC 8503 at 2.36 A resolution
Componentsputative glycosyl hydrolase
KeywordsHYDROLASE / YP_001302580.1 / putative glycosyl hydrolase / was Domain of Unknown Function (DUF1080) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homology3-keto-disaccharide hydrolase / 3-keto-alpha-glucoside-1,2-lyase-like domain / Exo-inulinase; domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / Jelly Rolls / Sandwich / Mainly Beta / 3-keto-disaccharide hydrolase domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.36 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative glycosyl hydrolase, was Domain of Unknown Function (DUF1080) (YP_001302580.1) from Parabacteroides distasonis ATCC 8503 at 2.36 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 6, 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: putative glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6607
Polymers27,2201
Non-polymers4406
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.009, 61.009, 167.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein putative glycosyl hydrolase


Mass: 27219.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Gene: BDI_1195, YP_001302580.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LB94
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE SEQUENCE THIS CONSTRUCT (RESIDUE 29-268) WAS EXPRESSED WITH A PURIFICATION TAG ...SEQUENCE SEQUENCE THIS CONSTRUCT (RESIDUE 29-268) 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M Li2SO4, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97932,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979151
ReflectionResolution: 2.36→29.336 Å / Num. obs: 13756 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.809 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.77
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.36-2.440.9511.483282216192.8
2.44-2.540.7441.998862560199.8
2.54-2.660.522.6999525831100
2.66-2.80.3753.795602474199.9
2.8-2.970.2445.693632415199.7
2.97-3.20.1349.796802508199.9
3.2-3.520.07616.5959824751100
3.52-4.030.04525.796802505199.8
4.03-5.060.03432.796672497199.8
5.06-29.3360.03136.597792533199.2

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.36→29.336 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 14.445 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.226
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. SULFATE (SO4) AND ETHYLENE GLYCOL (EDO) HAVE BEEN MODELED FROM CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 685 5 %RANDOM
Rwork0.198 ---
obs0.2 13695 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.13 Å2 / Biso mean: 50.313 Å2 / Biso min: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.36→29.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 26 77 1884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211885
X-RAY DIFFRACTIONr_bond_other_d0.0020.021255
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9382555
X-RAY DIFFRACTIONr_angle_other_deg0.99433058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.865242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27224.94693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91115294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.164156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined0.1750.3300
X-RAY DIFFRACTIONr_nbd_other0.1770.31268
X-RAY DIFFRACTIONr_nbtor_refined0.1760.5872
X-RAY DIFFRACTIONr_nbtor_other0.0880.5918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.33
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1340.318
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.52
X-RAY DIFFRACTIONr_mcbond_it1.47931264
X-RAY DIFFRACTIONr_mcbond_other0.2743486
X-RAY DIFFRACTIONr_mcangle_it2.38451840
X-RAY DIFFRACTIONr_scbond_it4.2588820
X-RAY DIFFRACTIONr_scangle_it5.13111709
LS refinement shellResolution: 2.36→2.422 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 48 -
Rwork0.311 908 -
all-956 -
obs--97.75 %
Refinement TLS params.Method: refined / Origin x: 46.743 Å / Origin y: 11.312 Å / Origin z: 73.626 Å
111213212223313233
T-0.1238 Å20.013 Å2-0.0148 Å2--0.1998 Å20.0386 Å2---0.208 Å2
L4.8605 °2-1.2036 °21.7718 °2-1.3649 °2-1.0059 °2--4.5369 °2
S-0.0094 Å °0.0379 Å °0.095 Å °0.1167 Å °0.0506 Å °0.0716 Å °0.2296 Å °-0.0312 Å °-0.0412 Å °

+
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