[English] 日本語
Yorodumi
- PDB-3qwt: The crystal structure of a possible member of GH105 family from S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qwt
TitleThe crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
ComponentsPutative GH105 family protein
KeywordsUNKNOWN FUNCTION / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomic s / MCSG / Hydrolase / GH105 / Midwest Center for Structural Genomics / alpha/alpha toroid
Function / homology
Function and homology information


Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Paratyphi A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.183 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Authors: Tan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative GH105 family protein
B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,66315
Polymers179,6504
Non-polymers1,01311
Water6,413356
1
A: Putative GH105 family protein
B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules

A: Putative GH105 family protein
B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,32630
Polymers359,3008
Non-polymers2,02622
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area32700 Å2
ΔGint-56 kcal/mol
Surface area101260 Å2
MethodPISA
2
A: Putative GH105 family protein
hetero molecules

B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,66315
Polymers179,6504
Non-polymers1,01311
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-x,y,-z+1/21
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-16 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.026, 159.361, 179.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-405-

HOH

DetailsExperimentally Unknown. It is possilbe the molecule forms dimer. The chains A and B form a dimer. The chain C and its symmetry-related moleucle, by an operator -x,y,-z+1/2, form a dimer. The chain D and its symmtry-related molecule, by an operator, -x,y,-z+1/2, form a dimer.

-
Components

#1: Protein
Putative GH105 family protein


Mass: 44912.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Paratyphi A (bacteria)
Gene: SPA0958 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5PMY7, UniProt: A0A0H2WND1*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M NaCl, 0.1M Tris.HCl, 25% (w/v) PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942, 0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979511
ReflectionResolution: 2.18→40 Å / Num. all: 87941 / Num. obs: 87941 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 20.7
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.02 / Num. unique all: 4188 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.183→39.84 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 4255 5.01 %random
Rwork0.1824 ---
all0.1851 84868 --
obs0.1851 84868 94.54 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.937 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7133 Å2-0 Å2-0 Å2
2---1.317 Å20 Å2
3----2.3963 Å2
Refinement stepCycle: LAST / Resolution: 2.183→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12396 0 66 356 12818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812820
X-RAY DIFFRACTIONf_angle_d1.11717412
X-RAY DIFFRACTIONf_dihedral_angle_d15.7384616
X-RAY DIFFRACTIONf_chiral_restr0.0731816
X-RAY DIFFRACTIONf_plane_restr0.0052228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1829-2.26090.30243670.25146897X-RAY DIFFRACTION82
2.2609-2.35140.34863510.24897390X-RAY DIFFRACTION87
2.3514-2.45840.31734200.23377676X-RAY DIFFRACTION91
2.4584-2.5880.32034480.23057872X-RAY DIFFRACTION93
2.588-2.75020.31184200.22448161X-RAY DIFFRACTION96
2.7502-2.96240.26384430.2098317X-RAY DIFFRACTION98
2.9624-3.26040.26664140.20868484X-RAY DIFFRACTION99
3.2604-3.73190.22424640.18058507X-RAY DIFFRACTION100
3.7319-4.70060.17364790.13218542X-RAY DIFFRACTION100
4.7006-39.84690.19894490.14978767X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62280.0843-0.44750.50670.13940.4774-0.1255-0.38920.0450.2250.1547-0.05110.22480.2696-0.02120.22430.1867-0.06320.3437-0.00990.067117.960828.732379.1237
20.50580.2939-0.2940.2409-0.08530.9186-0.0788-0.02840.1084-0.01060.0958-0.10830.08920.3936-0.00860.03510.1675-0.030.2064-0.01780.150738.621833.491841.6826
30.85410.011-0.4280.2540.00060.7488-0.28880.152-0.17590.02550.0824-0.03520.727-0.04970.19350.64370.0180.10950.1019-0.06060.120512.4529-1.362327.2024
40.63170.20730.0290.37090.02390.4556-0.03080.12520.3409-0.0660.0768-0.0319-0.02930.025-0.03260.026-0.0292-0.00960.08640.07670.20998.278463.531524.9004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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