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- PDB-7vt4: Crystal structure of mutant E393Q of MtGlu5 -

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Basic information

Entry
Database: PDB / ID: 7vt4
TitleCrystal structure of mutant E393Q of MtGlu5
ComponentsEndoglucanase H
KeywordsHYDROLASE / cellulase / GH5 / Meiothermus taiwanensis WR-220 / endo-beta-1 / 4-glucanase
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
Galactose-binding lectin / : / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMeiothermus taiwanensis WR-220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsYe, T.J. / Ko, P.T. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase.
Authors: Ye, T.J. / Huang, K.F. / Ko, T.P. / Wu, S.H.
History
DepositionOct 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase H
B: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,75421
Polymers105,9522
Non-polymers1,80119
Water27,7431540
1
A: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,92511
Polymers52,9761
Non-polymers94910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18270 Å2
MethodPISA
2
B: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,82910
Polymers52,9761
Non-polymers8539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.249, 114.350, 80.149
Angle α, β, γ (deg.)90.000, 103.235, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 16 - 452 / Label seq-ID: 16 - 452

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 16 through 452)AA
22chain 'B'BB

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Components

#1: Protein Endoglucanase H


Mass: 52976.133 Da / Num. of mol.: 2 / Mutation: E393Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis WR-220 (bacteria)
Production host: Escherichia coli B (bacteria) / References: UniProt: A0A399DY85, cellulase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1540 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M citric acid, 0.7M ammonium sulfate, 20% PEG 400, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 97424 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.61 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Χ2: 0.913 / Net I/σ(I): 22.06
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 0.059 / Num. unique obs: 9740 / Rpim(I) all: 0.035 / Rrim(I) all: 0.872

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mmu

3mmu


Resolution: 1.93→26.97 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 4288 4.91 %
Rwork0.1581 83083 -
obs0.16 87371 89.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.54 Å2
Refinement stepCycle: LAST / Resolution: 1.93→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7033 0 101 1550 8684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00837323
X-RAY DIFFRACTIONf_angle_d0.9499984
X-RAY DIFFRACTIONf_chiral_restr0.06171016
X-RAY DIFFRACTIONf_plane_restr0.00641309
X-RAY DIFFRACTIONf_dihedral_angle_d17.32762604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.2278680.20441147X-RAY DIFFRACTION36.72
1.95-1.980.2235890.2181257X-RAY DIFFRACTION41.96
1.98-20.2406700.20021512X-RAY DIFFRACTION48.66
2-2.020.27981050.19971682X-RAY DIFFRACTION55.51
2.02-2.050.28851200.21252023X-RAY DIFFRACTION65.42
2.05-2.080.2341030.20672301X-RAY DIFFRACTION74.57
2.08-2.110.21681340.20032562X-RAY DIFFRACTION82.88
2.11-2.140.21851520.20052710X-RAY DIFFRACTION88.83
2.14-2.170.25381470.19182873X-RAY DIFFRACTION93.7
2.17-2.210.25141510.18563025X-RAY DIFFRACTION97.78
2.21-2.250.22731530.19013088X-RAY DIFFRACTION99.51
2.25-2.290.23011470.18223135X-RAY DIFFRACTION100
2.29-2.330.23681490.17823088X-RAY DIFFRACTION100
2.33-2.380.20411570.17143063X-RAY DIFFRACTION100
2.38-2.430.24091610.16643103X-RAY DIFFRACTION100
2.43-2.490.20231840.16353074X-RAY DIFFRACTION100
2.49-2.550.20831440.16183068X-RAY DIFFRACTION100
2.55-2.620.20181670.16293069X-RAY DIFFRACTION100
2.62-2.70.21541630.16053107X-RAY DIFFRACTION100
2.7-2.780.20831690.16023084X-RAY DIFFRACTION100
2.78-2.880.20391570.15823113X-RAY DIFFRACTION100
2.88-30.18951650.15793062X-RAY DIFFRACTION99.97
3-3.130.1891540.15993101X-RAY DIFFRACTION99.94
3.13-3.30.18871330.15073124X-RAY DIFFRACTION99.97
3.3-3.510.18841450.143134X-RAY DIFFRACTION99.97
3.51-3.780.16811610.1273098X-RAY DIFFRACTION99.97
3.78-4.150.14451650.12013112X-RAY DIFFRACTION100
4.15-4.750.15751670.1183097X-RAY DIFFRACTION99.97
4.75-5.980.17491490.14593136X-RAY DIFFRACTION99.88
5.98-26.970.18961590.18283135X-RAY DIFFRACTION98.71
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)
10.026048239883-0.00857583036414-0.0088090810770.0339714247818-0.02628456245950.0781451592423-0.001874224795560.0365944981950.0208730877583-0.00579247836244-0.0655692080203-0.05183789141370.001101850067180.113486296517-0.1406567483830.0612248581822-0.00425148491620.01102090326360.165130759675-0.009391207795480.084224278795417.4171377106-2.4577284833434.1111355115
20.004556467354250.002403687030540.0002596922227410.00446273010220.001120157778040.003786992756430.0292232185465-0.0880333710748-0.0395564628988-0.002621144216030.0257624664769-0.01183158770790.020748041058-0.03771199492470.007521653228950.113400585942-0.0160125428038-0.04507636657030.22348616395-0.0373996015720.160190557929-19.2264003735-4.6859878194427.813122305
30.01759770693930.0007413809177940.00237336606020.008484625723610.01510306788450.0281279433987-0.013158074309-0.03663407556080.06212395542940.00139616625958-0.0391064575828-0.00241791411568-0.0349246068772-0.0293323997367-0.04872159440110.0940002795377-0.01211814647150.001091591783680.100111113218-0.03821078139180.08109321770946.331580539199.8374606412435.8358845337
40.0217157360190.0110250451146-0.006190042653470.02791474599850.01866418850750.0424299691252-0.0314955624221-0.0425874386768-0.0219252576410.0243088527569-0.02276119627480.05703388545910.0984121418786-0.0570043943513-0.07819670585650.0353446745841-0.1045671131160.0317244082582-0.0899275768316-0.007746386161320.08158798736219.965154516-0.771295281264-2.30368230071
50.00394341482454-7.17784670776E-5-0.004668382389160.02518358100190.007850594137810.01069483373150.02449885840420.0194898855825-0.00351767362697-0.03071677843270.02648674521250.006184330322370.0179509356092-0.004016453080860.02880232403960.225774399952-0.0220729983126-0.06669439393430.01978427536430.003280909866410.20408276669154.4627299115-20.4993446609-2.21734339346
60.0110960270277-0.007186538388450.007699768077010.00921895633763-0.008492129741930.0108125326107-0.000907485982420.009386215885860.0545345539242-0.0264645970327-0.0233128061817-0.04508733740630.02109455533660.0380096137229-0.002006985423230.0726110904102-0.0002216392143730.01161382600930.0423014431299-0.006850089276380.06924992797835.79021760184.49492953721-3.02767706617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 242 )
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 363 )
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 452 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 242 )
5X-RAY DIFFRACTION5chain 'B' and (resid 243 through 363 )
6X-RAY DIFFRACTION6chain 'B' and (resid 364 through 452 )

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