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- PDB-7z65: A GH18 from haloalkaliphilic bacterium unveils environment-depend... -

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Basic information

Entry
Database: PDB / ID: 7z65
TitleA GH18 from haloalkaliphilic bacterium unveils environment-dependent variations in the catalytic machinery of chitinases
ComponentsChitinase, GH18 family
KeywordsHYDROLASE / Chitinase / Chitin / Chitooligosaccharides / Substrate Assisted Catalysis.
Function / homology
Function and homology information


chitinase / chitin binding / carbohydrate metabolic process
Similarity search - Function
Bacterial repeat domain / Divergent InlB B-repeat domain / Secretion system C-terminal sorting domain / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesChitinivibrio alkaliphilus ACht1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.108 Å
AuthorsMadhuprakash, J. / Dalhus, B. / Rohr, A.K. / Bissaro, B. / Vaaje-Kolstad, G. / Sorlie, M. / Eijsink, V.G.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/006426 India
Department of Science & Technology (DST, India)IFA16-LSPA-40 India
CitationJournal: To Be Published
Title: A GH18 from haloalkaliphilic bacterium unveils environment-dependent variations in the catalytic machinery of chitinases
Authors: Madhuprakash, J. / Dalhus, B. / Rohr, A.K. / Bissaro, B. / Vaaje-Kolstad, G. / Sorlie, M. / Eijsink, V.G.H.
History
DepositionMar 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase, GH18 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6413
Polymers31,5171
Non-polymers1242
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint7 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.060, 62.340, 75.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase, GH18 family


Mass: 31516.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinivibrio alkaliphilus ACht1 (bacteria)
Gene: CALK_0774 / Plasmid: pNIC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: U7D706
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.05 Å3/Da / Density % sol: 39.9 % / Description: Rod shaped
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG 8000, 100 mM Imidazole pH 8.0, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.108→47.985 Å / Num. obs: 102783 / % possible obs: 99.6 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.093 / Net I/σ(I): 12
Reflection shellResolution: 1.108→1.112 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1013 / CC1/2: 0.362 / Rrim(I) all: 0.607 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Inhouse model

Resolution: 1.108→47.985 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 5016 4.88 %
Rwork0.1765 97766 -
obs0.1772 102782 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.38 Å2 / Biso mean: 12.2354 Å2 / Biso min: 3.36 Å2
Refinement stepCycle: final / Resolution: 1.108→47.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 16 341 2575
Biso mean--18.54 23.94 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072375
X-RAY DIFFRACTIONf_angle_d0.9413258
X-RAY DIFFRACTIONf_chiral_restr0.073349
X-RAY DIFFRACTIONf_plane_restr0.007426
X-RAY DIFFRACTIONf_dihedral_angle_d15.005873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.108-1.12060.32881640.3326319799
1.1206-1.13380.32821430.3264321299
1.1338-1.14760.29981560.3186321199
1.1476-1.16210.34451670.30623215100
1.1621-1.17740.3271600.3053258100
1.1774-1.19350.32561660.29293226100
1.1935-1.21060.3071730.2923188100
1.2106-1.22870.27621680.28413249100
1.2287-1.24790.29391770.27433219100
1.2479-1.26830.2841720.2683239100
1.2683-1.29020.29761680.2623238100
1.2902-1.31370.26151780.25283246100
1.3137-1.33890.28251640.24873236100
1.3389-1.36630.25221580.23693252100
1.3663-1.3960.25661520.22253242100
1.396-1.42840.22461540.21063279100
1.4284-1.46420.21991760.2013214100
1.4642-1.50380.19381640.1833261100
1.5038-1.5480.18941890.16983236100
1.548-1.5980.1781700.15733270100
1.598-1.65510.19211670.14483256100
1.6551-1.72140.15721830.13723264100
1.7214-1.79970.15731650.13753271100
1.7997-1.89460.15871730.13193280100
1.8946-2.01330.14431600.1313327499
2.0133-2.16870.16181570.1244329399
2.1687-2.3870.13581590.1225332699
2.387-2.73240.14631930.1246325899
2.7324-3.44230.15591490.12963386100
3.4423-47.9850.12561910.1305347099
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)
12.75980.32691.45841.63910.53874.39430.048-0.03120.1368-0.01220.0013-0.1345-0.24260.1696-0.04350.04930.00360.02580.058-0.01640.0513-6.5595-2.815315.2257
20.48030.13410.04631.0687-0.08530.70140.0517-0.06830.00990.0765-0.03330.0177-0.0055-0.0171-0.01630.043-0.00470.00080.0528-0.00880.0386-17.7494-8.721721.6318
31.47190.6305-0.46161.5440.12751.564-0.007-0.041-0.22040.0501-0.0446-0.01890.23530.00920.03040.071-0.0039-0.00350.0521-0.00510.0439-15.8756-22.401814.9106
41.2934-0.1147-0.09971.18760.25011.03580.02550.03770.0106-0.0905-0.0004-0.0501-0.00620.0701-0.0160.05580.01160.00890.0695-0.00550.034-6.9293-14.18274.019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 39 )A0 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 175 )A40 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 215 )A176 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 303 )A216 - 303

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