[English] 日本語
Yorodumi
- PDB-6xsu: GH5-4 broad specificity endoglucanase from Ruminococcus flavefaciens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xsu
TitleGH5-4 broad specificity endoglucanase from Ruminococcus flavefaciens
ComponentsGH5-4 broad specificity endoglucanase
KeywordsHYDROLASE / Cellulase / xylanase / manganese / GH5 / endoglucanase
Function / homologyETHANOL
Function and homology information
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBingman, C.A. / Smith, R.W. / Glasgow, E.M. / Fox, B.G.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DEFC0207ER64494 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH 5 T32 GM008349 Biotechnology Training Program United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis.
Authors: Glasgow, E.M. / Kemna, E.I. / Bingman, C.A. / Ing, N. / Deng, K. / Bianchetti, C.M. / Takasuka, T.E. / Northen, T.R. / Fox, B.G.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GH5-4 broad specificity endoglucanase
B: GH5-4 broad specificity endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0646
Polymers79,8792
Non-polymers1844
Water16,232901
1
A: GH5-4 broad specificity endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9862
Polymers39,9401
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH5-4 broad specificity endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0784
Polymers39,9401
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.232, 78.303, 82.415
Angle α, β, γ (deg.)90.000, 92.075, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein GH5-4 broad specificity endoglucanase


Mass: 39939.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 901 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 microliter of protein at XXXX was combined with 1 microliter of reservoir solution consisting of 31%w/v PEG3350, 0.2 M NaCl, 0.1M bistris pH 5.5. Sample was cryoproected by brief exposure to ethanol vapor.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2015
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.41→56.75 Å / Num. obs: 118191 / % possible obs: 96.23 % / Redundancy: 4 % / Biso Wilson estimate: 10.83 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1235 / Rpim(I) all: 0.06651 / Rrim(I) all: 0.1409 / Net I/σ(I): 5.38
Reflection shellResolution: 1.41→1.46 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.4048 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 9774 / CC1/2: 0.729 / CC star: 0.918 / Rpim(I) all: 0.2843 / Rrim(I) all: 0.4987 / % possible all: 79.24

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EDG
Resolution: 1.41→56.75 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1705 1918 1.62 %
Rwork0.1491 116236 -
obs0.1495 118154 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.41 Å2
Refinement stepCycle: LAST / Resolution: 1.41→56.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 12 901 6399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685833
X-RAY DIFFRACTIONf_angle_d0.90387964
X-RAY DIFFRACTIONf_chiral_restr0.0769866
X-RAY DIFFRACTIONf_plane_restr0.00491038
X-RAY DIFFRACTIONf_dihedral_angle_d13.112134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.440.3192960.30246204X-RAY DIFFRACTION71.81
1.44-1.480.29211170.27127467X-RAY DIFFRACTION86.11
1.48-1.530.26361430.25367820X-RAY DIFFRACTION90.79
1.53-1.570.21731320.22848240X-RAY DIFFRACTION95.46
1.57-1.630.24361460.20248479X-RAY DIFFRACTION98.19
1.63-1.70.21411390.18988580X-RAY DIFFRACTION99.45
1.7-1.770.20531450.1748607X-RAY DIFFRACTION99.87
1.77-1.870.18291430.16058683X-RAY DIFFRACTION99.94
1.87-1.980.15961180.1388642X-RAY DIFFRACTION99.98
1.98-2.140.14561640.12398617X-RAY DIFFRACTION100
2.14-2.350.16911510.11778674X-RAY DIFFRACTION100
2.35-2.690.16251130.12288724X-RAY DIFFRACTION100
2.69-3.390.13981790.12458694X-RAY DIFFRACTION100
3.39-56.750.12981320.12618805X-RAY DIFFRACTION99.64
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.540014349028-0.1865656241210.07687166860850.394674356706-0.04293745603150.4936242300190.008933528086260.03987382945340.0164780040669-0.0666201459204-0.009925331137250.030966536186-0.0410067683235-0.0368920994877-0.005983984824030.0412972637961-0.007496251741460.007560246161680.0491730993420.006949577714310.03700316658225.20494787386.1504461325722.5676268373
20.07339794128-0.05929511455650.01879794518120.056064014827-0.004864378014060.0977652813823-0.0113962730575-0.00731995759537-0.00906683670285-0.0007270860337960.0125710208295-0.0814335216542-0.0155236772840.073165392521-2.06893670154E-70.0840254115655-0.004865942213920.006340439978040.0876196293852-0.001375239791730.10745400556738.44907373968.0508360918228.0831675695
30.399267885301-0.00180346301232-0.1673472496730.07978684209910.1350218124130.2960626862180.04578031470640.02288849523660.0449912244744-0.114910660897-0.0259733619992-0.0733521870648-0.06803110416570.0140118964969-1.48730570299E-90.0859395362370.001437135567380.008661224894430.07555640400870.00116401151440.075659814204529.054269447916.271224936221.641915039
40.06138863360590.015184134066-0.005372166961730.03026544011790.00779785860051-0.008317556828860.06653559335870.01115292829040.136202967361-0.133585142277-0.0601459493642-0.0970204279007-0.1070331535470.007415716538743.21281443777E-70.1333839626030.0205886452270.01634926960730.106363802640.006799237234110.10767008325721.725179538724.740114563415.1728789642
50.1980649293080.05877851551080.1112449517910.30823840742-0.08478301020960.18166303832-0.0124485857434-0.03872322939950.007726354318960.01326452995530.01021346778210.0163504782525-0.006904141698180.0102551316507-6.41659446938E-80.09901099435130.000758950109929-0.0007191081235370.07989863965490.001372238599190.083913788585119.054233886116.941735637625.6910012967
60.2251655092240.06083379622740.07427125778160.185419178603-0.07318715269950.1068142002640.02529921588130.0883774502312-0.0104683530922-0.107238300457-0.04975735330740.0537375900384-0.0697670213714-0.0138111261084-8.98810002588E-80.1185793956230.0130341639802-0.00472621392920.102161143653-0.003696226380020.086870802565614.506499094716.925157360315.8084508354
70.0839429809076-0.138522485265-0.07451705581810.2581290350740.07793722354380.143009817944-0.0124910030824-0.0363798624690.006314432777740.03884190188630.01045133692980.0466172408344-0.0458943687515-0.0505053969436-0.00362270156410.0659972929427-0.001362544207450.01010988677840.0850097769333-0.003770353888160.06985356187113.810788205510.922989210135.8213607991
80.1434025529530.0109101269807-0.1542820623050.289294631945-0.08537804731020.183195826788-0.0189034427344-0.009446550886-0.00598924675326-0.00219627697243-0.0007421798690250.092817495275-0.00784676969262-0.115235899669-9.38940350699E-80.0898588549319-0.001802519910760.0006897883017270.110622805838-0.003661651146320.097896129008512.12931009584.0641178660737.0536471482
90.102386607542-0.00887310284225-0.001852933875620.04745211374140.04400988441710.06037928835480.0251891915251-0.022070407866-0.0968925950490.00450362093633-0.03435284445190.03279715207690.11062448147-0.04471053225990.0008542956624770.100012771272-0.006358112267790.003232017827610.106376029179-0.0003500954407590.10259969357617.3872778045-3.532475024739.7979978746
100.406779141004-0.151177819945-0.106692442670.34465707378-0.2550473221760.3282437615670.00979199552311-0.0610776551484-0.03310964210570.0634566099179-0.0440473686843-0.07069957057810.02598533002190.0772838659951.35645297933E-70.08902419128780.0051468939197-0.00556137688160.1037234995380.01041883282750.098827937162131.16329028052.2751385597237.8742448507
110.8922795441030.4100379916980.3478985905931.578452965380.5433002388890.709838983428-0.04126980668020.0594791729057-0.0140717843176-0.1881689082850.031348750173-0.0222242019012-0.06070494273220.0037606179531-0.04008872801930.051468836506-0.002317376430930.01090910129760.04859648275430.00324812443850.03402942333944.040011465965.47236836253-16.4823885082
120.388322230778-0.08891720026470.05336444152480.5316253913630.05120560654020.394013517598-0.005771754456530.009487256598480.0325821846522-0.0705524783743-0.01379982559060.0327473839816-0.0373161820972-0.02765799778335.06411184419E-100.0875597349542-0.00107412435518-0.004708283774550.07288448974320.0002475064676930.08423345968281.0462754070914.7841781575-19.1492935627
130.4552340370210.006896788974750.09983068423850.341783408614-0.08828569486410.5895225324650.0160806539749-0.01964576002270.00382125306150.0133650736876-0.01577064338740.03785967308620.0307606103685-0.05210424142450.0007121867188770.0721026369534-0.0027753884110.004509770879910.0825239767861-0.002486626312970.0803297855988-2.395273257472.38491651455-1.77342714185
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 34 through 65 )AA34 - 651 - 36
22chain 'A' and (resid 66 through 89 )AA66 - 8937 - 60
33chain 'A' and (resid 90 through 150 )AA90 - 15061 - 125
44chain 'A' and (resid 151 through 168 )AA151 - 168126 - 145
55chain 'A' and (resid 169 through 197 )AA169 - 197146 - 176
66chain 'A' and (resid 198 through 231 )AA198 - 231177 - 212
77chain 'A' and (resid 232 through 278 )AA232 - 278213 - 260
88chain 'A' and (resid 279 through 315 )AA279 - 315261 - 301
99chain 'A' and (resid 316 through 333 )AA316 - 333302 - 321
1010chain 'A' and (resid 334 through 381 )AA334 - 381322 - 376
1111chain 'B' and (resid 35 through 65 )BB35 - 651 - 32
1212chain 'B' and (resid 66 through 252 )BB66 - 25233 - 230
1313chain 'B' and (resid 253 through 382 )BB253 - 382231 - 373

+
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