[English] 日本語
Yorodumi
- PDB-4js7: Crystal structure of D78N mutant apo form of clavibacter michigan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4js7
TitleCrystal structure of D78N mutant apo form of clavibacter michiganensis expansin
Componentscellulose binding protein
KeywordsSUGAR BINDING PROTEIN / Cellulose binding protein
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide binding / polysaccharide catabolic process
Similarity search - Function
: / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Cellulose binding domain ...: / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Barwin-like endoglucanases / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClavibacter michiganensis subsp. michiganensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsYennawar, N.H. / Yennawar, H.P. / Georgelis, N. / Cosgrove, D.J.
CitationJournal: To be Published
Title: Crystal structure of wild type and d78n mutant Clavibacter michiganensis expansin, in apo form and in complex with oligosaccharides
Authors: Yennawar, N.H. / Yennawar, H.P. / Georgelis, N. / Cosgrove, D.J.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Sep 20, 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 / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cellulose binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8882
Polymers21,7921
Non-polymers961
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.758, 69.556, 81.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein cellulose binding protein


Mass: 21791.609 Da / Num. of mol.: 1 / Fragment: unp residues 546-746 / Mutation: D78N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clavibacter michiganensis subsp. michiganensis (bacteria)
Strain: NCPPB 382 / Gene: celA, pCM1_0020 / Production host: Escherichia coli (E. coli) / References: UniProt: A5CLK3, cellulase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Lithium sulfate, .1M bis-tris, 25%PEG3350 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: varimax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 12259 / Num. obs: 12259 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.038
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.140.064197
2.14-2.181100
2.18-2.221100
2.22-2.261100
2.26-2.311100
2.31-2.361100
2.36-2.421100
2.42-2.491100
2.49-2.561100
2.56-2.651100
2.65-2.741100
2.74-2.85199.8
2.85-2.981100
2.98-3.141100
3.14-3.331100
3.33-3.591100
3.59-3.95199.2
3.95-4.52195.6
4.52-5.68197.8
5.68-25193.8

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJO

4jjo


Resolution: 2.101→21.334 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 15.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 1211 9.99 %random
Rwork0.1523 ---
obs0.1548 12119 98.32 %-
all-12259 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→21.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 5 292 1828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031575
X-RAY DIFFRACTIONf_angle_d0.7992148
X-RAY DIFFRACTIONf_dihedral_angle_d13.235564
X-RAY DIFFRACTIONf_chiral_restr0.051236
X-RAY DIFFRACTIONf_plane_restr0.003283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1005-2.18450.19211260.14911141X-RAY DIFFRACTION96
2.1845-2.28390.15551340.14341192X-RAY DIFFRACTION99
2.2839-2.40410.20461330.1591212X-RAY DIFFRACTION99
2.4041-2.55450.18881340.15371205X-RAY DIFFRACTION99
2.5545-2.75140.20561340.15841200X-RAY DIFFRACTION99
2.7514-3.02760.20031350.1631215X-RAY DIFFRACTION99
3.0276-3.4640.18741340.16021223X-RAY DIFFRACTION100
3.464-4.35820.14591380.13521239X-RAY DIFFRACTION98
4.3582-21.33490.15761430.15521281X-RAY DIFFRACTION97
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)
10.15490.1357-0.05820.17470.04410.14280.05260.05110.0824-0.1254-0.04430.0409-0.0253-0.04750.02920.09450.02480.01160.08650.01430.1438-6.31615.6236-7.2509
20.41950.1616-0.00490.20290.27850.49560.0015-0.019-0.05660.0016-0.0277-0.00710.0208-0.0111-0.00060.10210.00570.0040.09460.00130.0997-4.82419.8046-8.161
30.260.02920.01180.2791-0.16550.147-0.11350.1659-0.2021-0.04920.1423-0.0382-0.01230.09340.0120.1858-0.02650.02760.1792-0.04250.203-1.15685.0886-29.6367
40.2185-0.09920.00040.06550.01760.017-0.08890.10860.1835-0.18650.2197-0.0141-0.0980.06890.01560.3146-0.0815-0.00210.20980.01440.1676-1.941915.4275-37.3022
50.2083-0.1210.12160.1266-0.03770.0575-0.11520.0938-0.0605-0.13020.09610.0781-0.1132-0.0219-0.07790.1459-0.05230.01820.1329-0.03310.1251-4.16116.386-33.3847
60.1493-0.16770.25720.2317-0.16090.9466-0.13950.172-0.0448-0.01150.06130.0582-0.1418-0.16530.02620.1662-0.04930.00270.1172-0.00540.1171.138419.172-28.3271
70.1813-0.0132-0.15440.51550.19350.1860.0128-0.1278-0.13470.2770.0729-0.2888-0.00830.290.01260.1638-0.06390.01770.1993-0.01830.15138.945910.8394-26.218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 147 )
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 181 )
7X-RAY DIFFRACTION7chain 'A' and (resid 182 through 202 )

+
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