[English] 日本語
Yorodumi
- PDB-3taw: Crystal structure of a putative glycoside hydrolase (BDI_3141) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3taw
TitleCrystal structure of a putative glycoside hydrolase (BDI_3141) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
ComponentsHypothetical glycoside hydrolase
KeywordsHYDROLASE / 5-bladed beta-propeller / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Unknown ligand / Uncharacterized protein
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical glycoside hydrolase (BDI_3141) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,80919
Polymers39,8601
Non-polymers94918
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.361, 56.361, 231.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Hypothetical glycoside hydrolase


Mass: 39859.828 Da / Num. of mol.: 1 / Fragment: sequence database residues 32-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3141 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LGN3

-
Non-polymers , 5 types, 345 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

-
Details

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 GLY 0 FOLLOWED BY RESIDUES 32-386 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 3350, 0.2M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97907
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 5, 2011
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.7→28.97 Å / Num. all: 42521 / Num. obs: 42521 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 17.622 Å2 / Rsym value: 0.124 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7412.90.8920.93943030470.892100
1.74-1.7914.40.71.14314229890.7100
1.79-1.8414.40.571.44224429300.57100
1.84-1.914.40.4511.74106328460.451100
1.9-1.9614.50.352.23979227480.35100
1.96-2.0314.50.2922.63881726840.292100
2.03-2.1114.40.2423.23713125750.242100
2.11-2.1914.50.2013.83587224800.201100
2.19-2.2914.50.1824.13471724010.182100
2.29-2.414.40.1614.63292322850.161100
2.4-2.5314.40.145.23170822040.14100
2.53-2.6914.30.1275.63013721020.127100
2.69-2.8714.30.1195.72793219560.119100
2.87-3.114.20.1162619818390.11100
3.1-3.414.20.0857.62416517030.085100
3.4-3.8140.078.62201615730.07100
3.8-4.3913.80.0639.41921313910.063100
4.39-5.3813.70.069.71638011990.06100
5.38-7.613.10.0679.1127029690.067100
7.6-28.9711.60.0688.169346000.06898.4

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.6.0116refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.97 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.872 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.084
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM TLS REFINEMENT. 4.MAGNESIUM FROM THE CRYSTALLIZATION AND 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5.UNKNOWN LIGANDS (UNL) WAS MODELED INTO THE PUTATIVE ACTIVE SITE. THE POSITIONINGS OF THE UNL'S ARE SIMILAR TO THE POSITIONING OF FRUCTOSE INTO THE ACTIVE SITE ON A RELATED STRUCTURE, AN INVERTASE FROM SCHWANNOCYMES OCCIDENTALIS (PDB ID 3KF3). 6. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 7. ASN A82 IS A RAMACHANDRAN OUTLIER IN MOLPROBITY EVEN THOUGH ITS POSITIONING IS SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 2138 5 %RANDOM
Rwork0.149 ---
obs0.1502 42405 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.08 Å2 / Biso mean: 19.109 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 69 327 3149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222970
X-RAY DIFFRACTIONr_bond_other_d0.0010.022059
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9714026
X-RAY DIFFRACTIONr_angle_other_deg0.86335017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8675373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53324.71138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9515477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2561513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 148 -
Rwork0.235 2560 -
all-2708 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 6.5353 Å / Origin y: 25.3691 Å / Origin z: 72.5084 Å
111213212223313233
T0.0125 Å2-0.009 Å2-0.0073 Å2-0.043 Å20.0255 Å2--0.024 Å2
L0.7388 °20.2998 °2-0.2191 °2-0.5828 °2-0.1402 °2--0.5119 °2
S-0.0273 Å °0.0518 Å °0.0333 Å °-0.0299 Å °0.05 Å °0.0227 Å °-0.0296 Å °-0.0073 Å °-0.0227 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://pdbjlvh1.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