[English] 日本語
Yorodumi
- PDB-5klc: Structure of CBM_E1, a novel carbohydrate-binding module found by... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5klc
TitleStructure of CBM_E1, a novel carbohydrate-binding module found by sugar cane soil metagenome
ComponentsCarbohydrate binding module E1
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein / metagenomics / cellulose / biofuels
Function / homologyCarbohydrate binding module E1
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.746 Å
AuthorsLiberato, M.V. / Campos, B.M. / Zeri, A.C.M. / Squina, F.M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties.
Authors: Campos, B.M. / Liberato, M.V. / Alvarez, T.M. / Zanphorlin, L.M. / Ematsu, G.C. / Barud, H. / Polikarpov, I. / Ruller, R. / Gilbert, H.J. / Zeri, A.C. / Squina, F.M.
History
DepositionJun 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbohydrate binding module E1


Theoretical massNumber of molelcules
Total (without water)10,0121
Polymers10,0121
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.391, 26.514, 99.294
Angle α, β, γ (deg.)90.000, 92.780, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-589-

HOH

-
Components

#1: Protein Carbohydrate binding module E1


Mass: 10011.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R5P8X1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2 M ammonium sulfate, 0.2 M lithium sulfate and 0.1 M CAPS, pH 10.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.74→27.62 Å / Num. obs: 7638 / % possible obs: 98.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.74-1.785.50.9721.9181
9.06-27.625.90.03429.8197.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.2data scaling
PHASER2.5.7phasing
PHENIX1.10.1refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KLF

5klf


Resolution: 1.746→26.922 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.24
RfactorNum. reflection% reflection
Rfree0.2073 412 5.4 %
Rwork0.1539 --
obs0.1566 7635 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.25 Å2 / Biso mean: 17.0854 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 1.746→26.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 0 116 792
Biso mean---29.64 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006690
X-RAY DIFFRACTIONf_angle_d0.815937
X-RAY DIFFRACTIONf_chiral_restr0.059103
X-RAY DIFFRACTIONf_plane_restr0.004121
X-RAY DIFFRACTIONf_dihedral_angle_d7.846393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7464-1.99910.27941340.18592336247098
1.9991-2.51830.1841730.147923732546100
2.5183-26.92480.2011050.147825142619100
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)
11.4162-0.10350.38912.0687-0.78931.982-0.03150.163-0.01190.1210.03080.0622-0.06970.00950.00480.1421-0.01720.00570.1415-0.02140.1044-5.3022-7.6245-20.3094
22.6653-2.10641.79924.1887-0.13771.86420.03070.2852-0.2466-0.08760.00750.07760.11660.20120.06490.0990.02360.00220.14180.02760.13522.0824-2.7958-18.3776
32.70971.80090.06056.674-2.71444.57930.0490.0388-0.0823-0.25330.00670.1070.4681-0.0914-0.06410.1246-0.0151-0.01650.1085-0.01920.1381-7.6913-10.6979-16.083
43.52880.18370.441.6429-0.73282.89110.106-0.1898-0.06910.0377-0.0350.21170.3208-0.1464-0.0750.1639-0.02870.00520.11760.0150.1096-6.0013-10.5825-6.2028
53.32250.08340.81274.3214-1.41172.83740.03440.1990.03690.0044-0.2403-0.181-0.13810.16810.17110.1418-0.0345-0.01920.14460.020.11986.9348-1.3257-7.2491
62.78530.17590.60352.5124-0.94512.3953-0.0357-0.0620.1280.13160.00850.0569-0.1555-0.10010.06270.11320.0017-0.00170.0996-0.00870.1055-5.3893-1.374-7.91
74.62762.24981.05513.0932-0.4251.8732-0.0501-0.11490.0757-0.05530.11520.26860.1233-0.12-0.0890.09460.01830.00870.126-0.00940.1209-9.4688-5.0587-13.6178
84.13794.9952-3.02068.3783-5.91755.2783-0.05230.1146-0.08380.00170.015-0.01510.14340.21970.01460.09290.0204-0.00030.10560.01230.14791.7227-6.6631-10.1613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 335 through 352 )A335 - 352
2X-RAY DIFFRACTION2chain 'A' and (resid 353 through 359 )A353 - 359
3X-RAY DIFFRACTION3chain 'A' and (resid 360 through 365 )A360 - 365
4X-RAY DIFFRACTION4chain 'A' and (resid 366 through 374 )A366 - 374
5X-RAY DIFFRACTION5chain 'A' and (resid 375 through 379 )A375 - 379
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 401 )A380 - 401
7X-RAY DIFFRACTION7chain 'A' and (resid 402 through 416 )A402 - 416
8X-RAY DIFFRACTION8chain 'A' and (resid 417 through 427 )A417 - 427

+
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