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- PDB-7s8k: Crystal structure of a GH12-2 family cellulase from Thermococcus ... -

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Basic information

Entry
Database: PDB / ID: 7s8k
TitleCrystal structure of a GH12-2 family cellulase from Thermococcus sp. 2319x1
ComponentsCellulase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 12 / CELLULASE / GH12 / THERMOPHILIC
Function / homology
Function and homology information


cellulase / cellulase activity / xylan catabolic process / polysaccharide binding / metal ion binding
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / 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. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / 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. / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Concanavalin A-like lectin/glucanase domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-PE3 / cellulase
Similarity search - Component
Biological speciesThermococcus sp. 2319x1 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsStogios, P.J. / Skarina, T. / Khusnutdinova, A. / Yakunin, A.F. / Savchenko, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: GH12-2 family cellulase
Authors: Yakunin, A.F.
History
DepositionSep 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulase
B: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,01113
Polymers63,1302
Non-polymers1,88111
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-44 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.346, 55.975, 91.907
Angle α, β, γ (deg.)90.000, 126.564, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cellulase


Mass: 31565.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. 2319x1 (archaea) / Gene: ADU37_CDS22600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U3SGP7, cellulase

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Non-polymers , 5 types, 196 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulfate, 2% PEG400, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 18344 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.064 / Net I/σ(I): 8.66
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 836 / CC1/2: 0.651 / Rpim(I) all: 0.382 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VGI

3vgi


Resolution: 2.55→28.74 Å / SU ML: 0.252 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.3182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 918 5.01 %RANDOM
Rwork0.1807 17423 --
obs0.1828 18341 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.58 Å2
Refinement stepCycle: LAST / Resolution: 2.55→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4397 0 72 185 4654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00464613
X-RAY DIFFRACTIONf_angle_d0.8256306
X-RAY DIFFRACTIONf_chiral_restr0.054655
X-RAY DIFFRACTIONf_plane_restr0.0036811
X-RAY DIFFRACTIONf_dihedral_angle_d17.49551650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.690.32151230.29162348X-RAY DIFFRACTION94.86
2.69-2.850.31361320.25662484X-RAY DIFFRACTION99.96
2.85-3.070.28741310.23482503X-RAY DIFFRACTION100
3.07-3.380.24661310.20972474X-RAY DIFFRACTION100
3.38-3.870.21211320.16852516X-RAY DIFFRACTION100
3.87-4.870.16791320.12712516X-RAY DIFFRACTION100
4.87-28.740.18861370.15592582X-RAY DIFFRACTION99.93
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)
17.70538379734-4.99088780992-1.689233340856.260646037141.07470362858.95128895271-0.116382826260.418587086504-0.755598416424-0.0715948118375-0.0259343663849-0.4353909814480.994086508159-0.01360502351530.1118720805440.3796947292820.0224671540770.03039710673340.270299333422-0.03301409483510.483049504235-15.39817735236.993105097757.92569730071
21.419197205710.8839124249860.2988487990821.409105255371.884854036812.220683839870.0369759887395-0.0497987814581-0.241428302620.1244410539510.0309283734415-0.2279712165570.1475217009240.115392734078-0.07413157566080.2992636639440.0142931472232-0.01706996279670.2582535565580.06944106399220.320183791295-17.26799419118.84833242049.80322487125
32.4206620485-0.4627599848880.2140038955880.3990366959050.838610733273.498135818860.0845116260763-0.156044071597-0.02728806063370.0736895933398-0.05893988671020.02508393617310.222163321104-0.417034647685-0.002952848103310.285317526504-0.04737825208780.01590450363840.2208224619970.01549168998590.311820343186-25.398741884227.068096483314.4829129049
44.501852754750.904936806496-0.3004878906241.02050164607-0.0383012081492.330536101060.138983504589-0.1387137570320.3813938644790.07599607958080.002719530943040.00540812776593-0.2249355009660.0444120370611-0.1546214964450.280797307358-0.002117551231560.04720323493760.1607746309490.01666806206670.289030443761-19.229139333236.84817646018.56586328666
51.512041574580.2280245597630.1027160574852.367014208551.715901307442.056198380750.0128789773503-0.245466671218-0.09469804789470.0402842775992-0.05443847694790.079824793541-0.0219476515018-0.1103026416240.03232684864530.291260387325-0.001349191675190.004091985850790.2813519119340.0525771188680.277284282781-24.651369367827.385859666514.3708654415
63.527572052551.207948412032.662200335291.749579989992.975389236856.18953619609-0.2095758275360.008159059975750.0573874637971-0.2274775761650.209606672806-0.119434738036-0.4591444258130.3722568273340.02829358878120.2414909415280.0182007081516-0.02390766638110.243118130650.0687388380220.268020077731-10.721015535727.526294775910.7988716407
71.32187849367-2.022711539831.290006391455.403040926150.09251936012323.06869026738-0.0303197320189-0.577155460560.07623052172010.385984395853-0.3327725704820.1714112832760.0512697632621-0.1127168820430.2926310563560.374648177209-0.07931050642960.03576786022750.408914725872-0.03932401266310.226322238817-49.641404892624.519200329939.8920737337
81.066776366740.2544319070630.2086357318052.038431252271.171790787052.56804998990.0680780412473-0.2191997275240.05660217626350.198881046448-0.06296676732360.03528342350120.162174914217-0.08813791623380.006490067650090.1850985694810.00706795616450.01891007674090.3318841389630.01046550871080.26451985998-49.137717735121.60230461129.3170423176
92.4011160592-0.676348724257-0.9042972476053.548023052381.375970109621.65641052950.0317217652265-0.1673026375330.137459281039-0.0584555635521-0.0618849991367-0.011857392436-0.0276483128026-0.1215572887140.02087152614060.2276996521530.0146498221089-0.01808589496920.3175361850970.002035574689670.20603365352-50.458007727823.482659852719.064500657
103.891678453533.91622881888-2.705180976534.71272391526-1.748336208832.83421241687-0.2963603746610.5083241676470.438681001973-0.3209319952690.2699899092020.4001880229080.0458204407441-0.4222790022110.02284834251510.2548533695750.0934151298466-0.04680713498920.343621396204-0.04047082431730.242942530009-58.889608670824.62709405748.07343260413
112.58188448297-3.70443306208-2.721413969526.492159365032.265181873665.523128869130.1181394362140.1053860213450.120470571397-0.181376091343-0.2781508941770.143589180265-0.304011065761-0.356224327230.1278929066530.192561223949-0.00381491320466-0.0534127253760.216403276764-0.0005854245306160.296968746166-51.800024543426.713693659912.4377670815
122.550137401340.2089616731290.1363923791471.915901019981.612178334072.234541070840.02706080389490.148056518815-0.127666269921-0.0591262676731-0.1235389003680.03798261476130.036051049498-0.230246713840.07851299168810.2457584999890.01060157916660.01283673102450.2446717999920.01566599193980.177270665468-50.74274110819.903052832715.2711665663
132.070714842260.5858367059550.330179439095.312658220732.17994403282.600830640960.149289333321-0.0918500422132-0.03496437775230.169623377446-0.2295009052710.02594153279790.198614892127-0.5414089184720.105901192430.181132011338-0.0100217770421-0.03248245664230.3670213422850.0259622909670.248439100516-59.323144845818.68877811519.599541939
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 17 )AA-1 - 171 - 19
22chain 'A' and (resid 18 through 131 )AA18 - 13120 - 133
33chain 'A' and (resid 132 through 161 )AA132 - 161134 - 163
44chain 'A' and (resid 162 through 220 )AA162 - 220164 - 222
55chain 'A' and (resid 221 through 247 )AA221 - 247223 - 249
66chain 'A' and (resid 248 through 271 )AA248 - 271250 - 273
77chain 'B' and (resid -2 through 17 )BF-2 - 171 - 20
88chain 'B' and (resid 18 through 106 )BF18 - 10621 - 109
99chain 'B' and (resid 107 through 161 )BF107 - 161110 - 164
1010chain 'B' and (resid 162 through 188 )BF162 - 188165 - 191
1111chain 'B' and (resid 189 through 203 )BF189 - 203192 - 206
1212chain 'B' and (resid 204 through 247 )BF204 - 247207 - 250
1313chain 'B' and (resid 248 through 275 )BF248 - 275251 - 278

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