[English] 日本語
Yorodumi
- PDB-4qhw: Crystal structure of a putative two-domain sugar hydrolase (BACCA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qhw
TitleCrystal structure of a putative two-domain sugar hydrolase (BACCAC_02064) from Bacteroides caccae ATCC 43185 at 1.35 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / galactose-binding domain-like fold / concanavalin A-like fold / PF11958 family / DUF3472 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF3472 / Domain of unknown function DUF5077 / Domain of unknown function (DUF3472) / Domain of unknown function (DUF5077) / DI(HYDROXYETHYL)ETHER / DUF5077 domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACCAC_02064) from Bacteroides caccae ATCC 43185 at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,45520
Polymers45,9661
Non-polymers1,48919
Water12,430690
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.055, 117.803, 113.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-792-

HOH

21A-865-

HOH

31A-880-

HOH

41A-1011-

HOH

51A-1288-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 45966.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_02064 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZGP5

-
Non-polymers , 5 types, 709 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 19-418 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M ammonium sulfate, 2.0% polyethylene glycol 400, 0.1M sodium HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2014
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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.35→29.812 Å / Num. all: 127336 / Num. obs: 127336 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rsym value: 0.11 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.392.60.5011.52262688300.50197.4
1.39-1.423.50.4611.63175291260.461100
1.42-1.466.10.4641.65396589180.464100
1.46-1.516.10.37725232186280.377100
1.51-1.566.10.3052.45145684530.305100
1.56-1.616.10.2592.84937880930.259100
1.61-1.676.10.223.34802878470.22100
1.67-1.746.10.1953.64651175710.195100
1.74-1.826.20.17144461872360.171100
1.82-1.916.20.1484.54268169360.148100
1.91-2.016.20.1334.94079365940.133100
2.01-2.136.20.1255.13887162820.125100
2.13-2.286.20.1245.13653659030.124100
2.28-2.466.20.1225.23402954920.122100
2.46-2.76.20.1085.93153550750.108100
2.7-3.026.20.0966.62851745920.096100
3.02-3.496.20.0867.22535941020.086100
3.49-4.276.10.0857.62105734600.08599.9
4.27-6.045.90.0798.21596226980.07999.6
6.04-29.8125.70.0828.1852815000.08296.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.8.0069refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→29.812 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0.05 / SU B: 1.262 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.034
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. ETHYLENE GLYCOL (EDO), SULFATE (SO4), CHLORIDE (CL), AND PEG (PEG) MODELED WERE PRESENT IN PURIFICATION/CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1336 6399 5 %RANDOM
Rwork0.106 120908 --
obs0.1074 127307 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.5 Å2 / Biso mean: 20.6094 Å2 / Biso min: 6.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20 Å2
2--0.08 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 88 690 4008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223608
X-RAY DIFFRACTIONr_bond_other_d0.0020.023348
X-RAY DIFFRACTIONr_angle_refined_deg2.2631.9564896
X-RAY DIFFRACTIONr_angle_other_deg1.12137771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28524.033181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16715627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3491521
X-RAY DIFFRACTIONr_chiral_restr0.1340.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214125
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02882
X-RAY DIFFRACTIONr_mcbond_it1.9141.3731665
X-RAY DIFFRACTIONr_mcbond_other1.8611.3731664
X-RAY DIFFRACTIONr_mcangle_it2.1722.0772096
X-RAY DIFFRACTIONr_rigid_bond_restr6.35436955
X-RAY DIFFRACTIONr_sphericity_free31.1185439
X-RAY DIFFRACTIONr_sphericity_bonded13.20657115
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 496 -
Rwork0.262 8647 -
all-9143 -
obs--97.88 %

+
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