[English] 日本語
Yorodumi
- PDB-4qvs: 2.1 Angstrom resolution crystal structure of S-layer domain-conta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qvs
Title2.1 Angstrom resolution crystal structure of S-layer domain-containing protein (residues 221-444) from Clostridium thermocellum ATCC 27405
ComponentsS-layer domain-containing protein
KeywordsUNKNOWN FUNCTION / Human Microbiome / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homology
Function and homology information


S-layer / cellulose binding / carbohydrate metabolic process / membrane
Similarity search - Function
Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / LamG-like jellyroll fold / LamG-like jellyroll fold domain / : / Concanavalin A-like lectin/glucanases superfamily / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Cellulose binding domain ...Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / LamG-like jellyroll fold / LamG-like jellyroll fold domain / : / Concanavalin A-like lectin/glucanases superfamily / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
S-layer domain-containing protein
Similarity search - Component
Biological speciesRuminiclostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.1 Angstrom resolution crystal structure of S-layer domain-containing protein (residues 221-444) from Clostridium thermocellum ATCC 27405
Authors: Halavaty, A.S. / Wawrzak, Z. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-layer domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0223
Polymers24,9641
Non-polymers582
Water79344
1
A: S-layer domain-containing protein
hetero molecules

A: S-layer domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0446
Polymers49,9272
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area16780 Å2
ΔGint-149 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.958, 74.813, 98.398
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
11A-603-

HOH

-
Components

#1: Protein S-layer domain-containing protein


Mass: 24963.666 Da / Num. of mol.: 1 / Fragment: UNP residues 221-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum ATCC 27405 (bacteria)
Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2506 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A3DIC9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein: 9.35 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, crystallization: The PEGs II Suite G11 (83): 0.5 M Lithium chloride, 0.1 M Tris pH 8.5. 28% (w/v) PEG 6000, cyo: well ...Details: protein: 9.35 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, crystallization: The PEGs II Suite G11 (83): 0.5 M Lithium chloride, 0.1 M Tris pH 8.5. 28% (w/v) PEG 6000, cyo: well solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2014 / Details: Beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 14480 / Num. obs: 14480 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 43.56
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Num. unique all: 668 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0029refinement
xia2data reduction
MOSFLMdata reduction
pointlessdata scaling
Aimlessdata scaling
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→27.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.957 / SU ML: 0.162 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24878 721 5 %RANDOM
Rwork0.20802 ---
obs0.20994 13697 99.01 %-
all-13697 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.661 Å2
Baniso -1Baniso -2Baniso -3
1--5.6 Å20 Å2-0 Å2
2---0.74 Å2-0 Å2
3---6.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 2 44 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021725
X-RAY DIFFRACTIONr_bond_other_d0.0010.021525
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9422340
X-RAY DIFFRACTIONr_angle_other_deg0.83333518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3265217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24625.11984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69315251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1154
X-RAY DIFFRACTIONr_chiral_restr0.1090.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 47 -
Rwork0.319 968 -
obs-968 95.75 %
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)
11.86440.47470.42661.3275-0.89051.07770.0465-0.29510.19720.2173-0.11490.0245-0.2017-0.03840.06840.3095-0.00690.01940.1329-0.03250.02298.995522.905181.8999
22.02030.0013-0.09722.40970.27071.12340.0144-0.1943-0.30790.135-0.0215-0.20110.10670.04040.00710.29920.0068-0.02270.15710.04470.065516.28865.795582.4876
34.855-1.14032.74361.7001-0.55182.94750.00720.36540.1665-0.45540.0424-0.3695-0.2866-0.1293-0.04960.3161-0.01060.10730.20270.0340.099420.8405-8.4474107.7386
41.8757-0.2453-0.54872.46510.28370.7886-0.01470.20660.1318-0.1182-0.064-0.01150.0798-0.04380.07870.30470.00980.01130.16470.020.031214.8677-12.2684113.5942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A221 - 285
2X-RAY DIFFRACTION2A286 - 345
3X-RAY DIFFRACTION3A346 - 389
4X-RAY DIFFRACTION4A390 - 438

+
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