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- PDB-7v0i: Crystal structure of a CelR catalytic domain active site mutant w... -

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Basic information

Entry
Database: PDB / ID: 7v0i
TitleCrystal structure of a CelR catalytic domain active site mutant with bound cellohexaose substrate
ComponentsGlucanase
KeywordsHYDROLASE/SUBSTRATE / biomass deconstruction / glycoside hydrolase family 9 / GH9 / cellulose binding domain 3c / CBM3c / HYDROLASE / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 ...Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBingman, C.A. / Kuch, N. / Kutsche, M.E. / Parker, A. / Smith, R.W. / Fox, B.G.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018409 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008349 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Contribution of calcium ligands in substrate binding and product release in the Acetovibrio thermocellus glycoside hydrolase family 9 cellulase CelR.
Authors: Kuch, N.J. / Kutschke, M.E. / Parker, A. / Bingman, C.A. / Fox, B.G.
History
DepositionMay 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: Glucanase
B: Glucanase
C: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2289
Polymers160,1353
Non-polymers3,0936
Water11,854658
1
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4093
Polymers53,3781
Non-polymers1,0312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4093
Polymers53,3781
Non-polymers1,0312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4093
Polymers53,3781
Non-polymers1,0312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.302, 162.419, 210.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

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Components

#1: Protein Glucanase /


Mass: 53378.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Gene: Cthe_0578 / Production host: Escherichia coli (E. coli)
References: UniProt: A3DCY5, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: JCSGD2B, 0.2M magnesium chloride, 0.1M HEPES buffer, pH 7.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→39.87 Å / Num. obs: 125496 / % possible obs: 100 % / Redundancy: 7.471 % / Biso Wilson estimate: 34.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.082 / Χ2: 0.889 / Net I/σ(I): 16.86 / Num. measured all: 937581 / Scaling rejects: 40
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.957.5071.3481.469143921692110.5951.44699.9
1.95-27.5311.0371.8767384894889470.7241.113100
2-2.067.5450.7762.5765772871887170.8210.833100
2.06-2.127.5390.613.3564096850385020.8760.654100
2.12-2.197.5630.484.3562194822382230.9150.515100
2.19-2.277.5490.3935.4560187797379730.940.421100
2.27-2.367.5310.3126.8957761767076700.9630.335100
2.36-2.457.5640.2428.8456243743674360.9750.26100
2.45-2.567.5290.19311.2553253707370730.9830.207100
2.56-2.697.5410.15214.4251465682568250.9890.163100
2.69-2.837.5140.12417.548676647964780.9920.133100
2.83-37.4810.09322.6845981614661460.9950.1100
3-3.217.4370.07228.243022578557850.9970.077100
3.21-3.477.3470.05435.7239658539853980.9980.058100
3.47-3.87.330.04243.1836347496049590.9990.045100
3.8-4.257.3070.03549.533152453745370.9990.037100
4.25-4.917.3130.0352.4429338401240120.9990.032100
4.91-6.017.3010.02851.7824822340034000.9990.03100
6.01-8.57.1880.02353.9119337269126900.9990.025100
8.5-39.876.440.02252.989750155015140.9990.02497.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å39.87 Å
Translation1.9 Å39.87 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSFeb 5, 2021 BUILT=20210322data reduction
XSCALEFeb 5, 2021 BUILT=20210322data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UNP

7unp


Resolution: 1.9→39.87 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 3037 2.41 %
Rwork0.1854 122807 -
obs0.1865 125496 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.4 Å2 / Biso mean: 49.4363 Å2 / Biso min: 21.02 Å2
Refinement stepCycle: final / Resolution: 1.9→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10782 0 375 660 11817
Biso mean--65.18 43.89 -
Num. residues----1353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.930.35161540.3235359551397
1.93-1.960.30511530.303155175670100
1.96-1.990.33161530.295155575710100
1.99-2.030.33321500.291155355685100
2.03-2.070.3116820.275355615643100
2.07-2.110.335790.265455965675100
2.11-2.160.30221520.254255395691100
2.16-2.210.31181550.246455085663100
2.21-2.260.30381500.239155825732100
2.26-2.320.28381540.225955285682100
2.32-2.390.27111520.21655625714100
2.39-2.470.27421500.2255685718100
2.47-2.560.25121530.211755285681100
2.56-2.660.28281400.200255985738100
2.66-2.780.3327140.201957025716100
2.78-2.920.26041500.201856095759100
2.93-3.110.23321480.197855715719100
3.11-3.350.22081510.186956165767100
3.35-3.680.22471510.163355955746100
3.68-4.220.17831490.141556535802100
4.22-5.310.17441510.127456845835100
5.31-39.870.19011460.15185839598599
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)
10.4148-0.15520.27120.3758-0.34021.0879-0.1921-0.4139-0.59910.1104-0.2291-0.55590.31660.27230.32040.46310.11570.13060.43860.26540.652310.791-64.502-20.287
22.3384-0.7106-0.17371.6113-0.44812.3105-0.1128-0.6603-0.35370.2657-0.0799-0.11930.28260.11640.15520.48670.02190.12520.49930.13990.3801-5.745-61.099-9.703
32.01940.20670.46092.43-0.88964.578-0.2274-0.2242-0.19760.06570.17240.32880.5656-0.998-0.02990.2951-0.03340.13050.3256-0.02870.3347-20.632-56.569-23.394
41.97571.2261-0.91173.0044-1.82482.4707-0.15320.1053-0.0986-0.28720.00420.1280.0707-0.24250.1620.32460.02120.04970.2902-0.02770.235-9.982-49.182-37.222
50.50650.0538-0.08230.8986-0.10231.1662-0.1131-0.0146-0.2475-0.0765-0.01640.13360.2563-0.29240.10880.3931-0.03480.09890.3162-0.01020.3768-11.358-61.79-28.041
65.20014.08834.16155.54995.58375.6016-0.4316-0.56210.85710.68860.1354-0.847-0.25940.40790.38260.86380.087-0.17670.3744-0.09320.801-5.829-25.678-25.264
75.3928-0.97695.45089.3498-0.02778.6399-0.7672-1.71980.2755-0.1182-0.2551-0.40760.7463-0.85220.90020.59760.1860.12020.72310.03360.43816.787-32.308-28.473
80.70911.4076-2.09632.763-4.11066.0974-0.6495-0.16830.08760.2182-0.9181-0.4010.185-0.0161.4140.4368-0.04430.05530.63890.02560.59040.022-48.334-25.883
91.4784-0.5892-0.41812.70690.45021.26240.08370.04840.0871-0.1324-0.19460.2819-0.1196-0.22790.10280.29860.0815-0.05250.3708-0.12380.3206-20.926-19.771-32.236
102.4559-1.34280.51833.745-1.19833.1148-0.0265-0.1515-0.08260.4058-0.14590.41510.0144-0.33980.16190.35540.0210.05850.4032-0.15830.3343-25.503-22.084-18.189
111.290.4926-0.51492.06510.18541.7278-0.0655-0.63110.26830.42640.01750.01290.08920.11910.01170.48760.0906-0.03120.5619-0.23680.3934-11.725-11.258-10.603
121.2952-0.3841-0.44853.13692.12643.2070.0844-0.08970.4313-0.25750.1374-0.2166-0.38950.2457-0.22320.30330.01440.00620.2261-0.0670.3224-2.764-11.401-34.511
132.5315-1.5193-0.73735.69280.63741.57970.1932-0.07180.5927-0.3671-0.07760.0927-0.4089-0.0981-0.11880.42870.0484-0.01360.2785-0.11910.4087-10.816-6.535-31.836
142.31550.137-0.0041.28150.11271.3229-0.14580.11570.149-0.1720.0037-0.1863-0.29980.43150.1410.3303-0.0942-0.00150.39090.05340.244128.832-22.8-38.04
154.7741-0.5662-0.20671.3961.65122.9213-0.1857-0.4390.7523-0.03010.06660.0784-0.37490.22910.10930.3457-0.0841-0.06140.363-0.01250.282726.741-15.228-24.657
161.6490.24480.26431.57430.53591.8209-0.0569-0.4222-0.14640.2223-0.0773-0.29-0.02230.49520.09840.24910.0185-0.02150.5680.1260.305634.346-35.036-19.932
174.0142-0.69581.39592.6598-1.36471.5433-0.11780.3158-0.3556-0.44480.0755-0.14930.34250.11480.06530.2878-0.00450.07230.254-0.03850.203518.581-40.84-43.721
182.9688-0.2260.44121.93530.22520.9381-0.09830.0907-0.3358-0.4567-0.0377-0.51380.09640.55530.07580.27490.03790.10140.48890.07780.36734.655-38.457-37.123
191.55281.0881-0.12921.7791-0.4281.0133-0.3514-0.0231-0.5859-0.38510.0352-0.35310.54870.01650.21590.50680.060.24390.22880.02920.45830.751-64.082-33.556
207.62787.65343.02618.60194.5284.45730.33620.0517-0.86380.617-0.324-1.13980.82190.1247-0.01510.58260.17830.20030.3610.18830.62692.763-73.638-22.392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 190:229 )C190 - 229
2X-RAY DIFFRACTION2( CHAIN C AND RESID 230:353 )C230 - 353
3X-RAY DIFFRACTION3( CHAIN C AND RESID 354:392 )C354 - 392
4X-RAY DIFFRACTION4( CHAIN C AND RESID 393:445 )C393 - 445
5X-RAY DIFFRACTION5( CHAIN C AND RESID 446:469 )C446 - 469
6X-RAY DIFFRACTION6( CHAIN D AND RESID 1:6 )D1 - 6
7X-RAY DIFFRACTION7( CHAIN E AND RESID 1:6 )E1 - 6
8X-RAY DIFFRACTION8( CHAIN F AND RESID 1:6 )F1 - 6
9X-RAY DIFFRACTION9( CHAIN A AND RESID 19:167 )A19 - 167
10X-RAY DIFFRACTION10( CHAIN A AND RESID 168:229 )A168 - 229
11X-RAY DIFFRACTION11( CHAIN A AND RESID 230:353 )A230 - 353
12X-RAY DIFFRACTION12( CHAIN A AND RESID 354:432 )A354 - 432
13X-RAY DIFFRACTION13( CHAIN A AND RESID 433:469 )A433 - 469
14X-RAY DIFFRACTION14( CHAIN B AND RESID 19:189 )B19 - 189
15X-RAY DIFFRACTION15( CHAIN B AND RESID 190:229 )B190 - 229
16X-RAY DIFFRACTION16( CHAIN B AND RESID 230:392 )B230 - 392
17X-RAY DIFFRACTION17( CHAIN B AND RESID 393:432 )B393 - 432
18X-RAY DIFFRACTION18( CHAIN B AND RESID 433:469 )B433 - 469
19X-RAY DIFFRACTION19( CHAIN C AND RESID 19:167 )C19 - 167
20X-RAY DIFFRACTION20( CHAIN C AND RESID 168:189 )C168 - 189

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