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- PDB-7vt5: Crystal structure of CBM deleted MtGlu5 from Meiothermus taiwanen... -

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Basic information

Entry
Database: PDB / ID: 7vt5
TitleCrystal structure of CBM deleted MtGlu5 from Meiothermus taiwanensis WR-220
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
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
METHIONINE / TRYPTOPHAN / Endoglucanase H
Similarity search - Component
Biological speciesMeiothermus taiwanensis WR-220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5223
Polymers39,1691
Non-polymers3532
Water8,899494
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.549, 75.348, 82.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endoglucanase H


Mass: 39168.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CBM deleted MtGlu5
Source: (gene. exp.) Meiothermus taiwanensis WR-220 (bacteria)
Production host: Escherichia coli B (bacteria) / References: UniProt: A0A399DY85, cellulase
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.09 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 20mM Tris, 100mM NaCl, pH 8.0

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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: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 51808 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.34 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Χ2: 1.435 / Net I/σ(I): 26.14
Reflection shellResolution: 1.46→1.51 Å / Rmerge(I) obs: 0.503 / Num. unique obs: 4780 / CC1/2: 0.856 / Rpim(I) all: 0.32 / Rrim(I) all: 0.6 / Χ2: 1.156

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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: 1.46→24.22 Å / SU ML: 0.1268 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1743 2615 5.05 %
Rwork0.148 49118 -
obs0.1494 51733 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.15 Å2
Refinement stepCycle: LAST / Resolution: 1.46→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 24 494 3078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132709
X-RAY DIFFRACTIONf_angle_d1.14543694
X-RAY DIFFRACTIONf_chiral_restr0.0978369
X-RAY DIFFRACTIONf_plane_restr0.0086488
X-RAY DIFFRACTIONf_dihedral_angle_d18.747986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.28611080.25342103X-RAY DIFFRACTION78.68
1.49-1.510.27651330.23972464X-RAY DIFFRACTION92.32
1.51-1.550.22941360.22432544X-RAY DIFFRACTION94.5
1.55-1.580.26251100.20832566X-RAY DIFFRACTION95.91
1.58-1.620.26041390.20062586X-RAY DIFFRACTION96.26
1.62-1.660.26391360.18952562X-RAY DIFFRACTION95.5
1.66-1.70.19441270.18322518X-RAY DIFFRACTION93.99
1.7-1.750.19851300.17052504X-RAY DIFFRACTION93.07
1.75-1.810.16911360.16342488X-RAY DIFFRACTION93.12
1.81-1.870.20671260.1532498X-RAY DIFFRACTION92.66
1.87-1.950.16681300.14742524X-RAY DIFFRACTION94.11
1.95-2.040.16571240.14072620X-RAY DIFFRACTION95.91
2.04-2.140.16521610.14062633X-RAY DIFFRACTION98.1
2.14-2.280.15431530.13682685X-RAY DIFFRACTION99.72
2.28-2.450.15951390.14312726X-RAY DIFFRACTION99.83
2.45-2.70.17261500.13952708X-RAY DIFFRACTION99.62
2.7-3.090.16091500.13452755X-RAY DIFFRACTION99.93
3.09-3.890.15071700.11942747X-RAY DIFFRACTION100
3.89-24.220.16031570.13642887X-RAY DIFFRACTION99.22
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)
10.4325145068470.4580494685160.02447545082660.765330556724-0.1907681165660.32416762869-0.00642217076831-0.0121077360655-0.08665042173430.0123498379875-0.000710190180695-0.116397287311-0.0361726447743-0.00639115530146-0.0002528579994830.1114984916880.00318526102629-0.006969813889540.117907711847-0.003242662038910.12931252608615.554191196618.503149317316.413178027
20.4233663659670.0992312381461-0.1109268083430.424024301067-0.08966446617750.335328450187-0.0242274379574-0.00488576837632-0.13927248678-0.0044423419049-0.020275195622-0.1658088122060.029640748846-0.017422510832-0.07038396323680.126878206964-0.00135687183191-0.009692874793340.1132115482550.008257571824370.1633312161869.898853962450.82686086697618.2097935874
30.04131290516510.0497163695967-0.02841220980560.0121432623968-0.0007537984395490.03740033000970.0886271179274-0.0124250810817-0.05435250587510.01342400559760.04823782893640.142413950414-0.007795882714790.0174743337353-0.0001199213047420.136117965095-0.00365418920257-0.007606418771330.1502954768840.01825227457420.117098698996-5.925112514714.281611105215.0483340058
40.492429796701-0.01629182558780.03936950869450.0392698282056-0.005221818112350.006240004060390.0145732034949-0.01306383587390.01107420319250.001373858860260.01040902947820.01012350589930.002138666910770.00198547978268-4.11802833328E-50.383014295049-0.108735863595-0.105770519140.276428164994-0.04005846710940.2440267608161.628656075547.906380432481.52272181106
54.797244456741.64789914825.261520498891.720965204142.213484883245.916225060670.0268827174006-0.0314023418187-0.00362952673287-0.0785774635171-0.07957863331720.01641197507590.147932946964-0.07416025655640.04552595709260.459235656464-0.0189400573470.01975275424520.321997184231-0.07238782525210.61735554790114.20749074547.743723743819.84195562061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 218 )
2X-RAY DIFFRACTION2chain 'A' and (resid 219 through 305 )
3X-RAY DIFFRACTION3chain 'A' and (resid 306 through 327 )
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 401 )
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 402 )

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