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- PDB-6xsu: GH5-4 broad specificity endoglucanase from Ruminococcus flavefaciens -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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

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Experimental details

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Experiment

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

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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.

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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

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EDG

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

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)
10.540014349028-0.1865656241210.07687166860850.394674356706-0.04293745603150.4936242300190.008933528086260.03987382945340.0164780040669-0.0666201459204-0.009925331137250.030966536186-0.0410067683235-0.0368920994877-0.005983984824030.0412972637961-0.007496251741460.007560246161680.0491730993420.006949577714310.03700316658225.20494787386.1504461325722.5676268373
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

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