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- PDB-7z64: A GH18 from haloalkaliphilic bacterium unveils environment-depend... -

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Basic information

Entry
Database: PDB / ID: 7z64
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


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 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chitinase, GH18 family
Similarity search - Component
Biological speciesChitinivibrio alkaliphilus ACht1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 10, 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

Downloads & links

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Assembly

Deposited unit
A: Chitinase, GH18 family
B: Chitinase, GH18 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,87812
Polymers61,9852
Non-polymers2,89310
Water15,277848
1
A: Chitinase, GH18 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4396
Polymers30,9921
Non-polymers1,4465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase, GH18 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4396
Polymers30,9921
Non-polymers1,4465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.970, 62.420, 102.650
Angle α, β, γ (deg.)90.000, 102.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitinase, GH18 family


Mass: 30992.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinivibrio alkaliphilus ACht1 (bacteria)
Gene: CALK_0774 / Production host: Escherichia coli (E. coli) / References: UniProt: U7D706
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.15M KBr, 30% w/v PEG-MME 2K

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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 PILATUS3 2M / Detector: PIXEL / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.31→100.118 Å / Num. obs: 192384 / % possible obs: 98.6 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 1.31→1.332 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9230 / CC1/2: 0.376 / Rrim(I) all: 0.653

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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: Native structure (PDB deposit 1292121539)

Resolution: 1.31→100.118 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1657 9653 5.02 %
Rwork0.148 182729 -
obs0.1489 192382 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.44 Å2 / Biso mean: 18.4254 Å2 / Biso min: 7.37 Å2
Refinement stepCycle: final / Resolution: 1.31→100.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 352 848 5560
Biso mean--19.73 33.92 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084739
X-RAY DIFFRACTIONf_angle_d1.0946480
X-RAY DIFFRACTIONf_chiral_restr0.075716
X-RAY DIFFRACTIONf_plane_restr0.007824
X-RAY DIFFRACTIONf_dihedral_angle_d14.7191650
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.31-1.32460.37643030.3463579394
1.3246-1.34020.31122890.3373589796
1.3402-1.35660.33293150.3271595496
1.3566-1.37370.3313420.3132600298
1.3737-1.39180.30773440.3019601198
1.3918-1.41090.31423410.2863609899
1.4109-1.4310.27643020.27611099
1.431-1.45240.28023130.2619607999
1.4524-1.47510.25873190.2432611499
1.4751-1.49930.22433160.2276610399
1.4993-1.52510.23843070.2165606198
1.5251-1.55290.20433530.1951606699
1.5529-1.58280.22143140.1858602798
1.5828-1.61510.18683070.1757614599
1.6151-1.65020.17813420.16236154100
1.6502-1.68860.16613440.15646084100
1.6886-1.73080.16513000.14686183100
1.7308-1.77760.17283340.14036139100
1.7776-1.82990.16093410.1346136100
1.8299-1.8890.15333210.12646172100
1.889-1.95650.14573020.12366132100
1.9565-2.03480.13913190.1216613899
2.0348-2.12750.12553100.1185613399
2.1275-2.23960.12893180.1101607398
2.2396-2.380.11972980.10516209100
2.38-2.56370.11793390.1061612799
2.5637-2.82180.12873200.1114614899
2.8218-3.23010.14193100.1205616798
3.2301-4.06960.13663480.1183607098
4.0696-100.1180.15133420.1302620497
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)
11.7779-0.3908-0.63861.24320.19421.2587-0.05970.0018-0.10180.0879-0.00050.12720.179-0.13880.06450.1508-0.03910.01760.09930.00440.108113.822.806435.5953
21.3387-1.6314-0.19163.62270.29511.5093-0.0626-0.1006-0.03320.28690.0030.14780.1068-0.1220.05890.1683-0.03650.03650.1224-0.00940.114712.930413.126848.4957
39.4874-7.3526-0.78755.72490.7490.8489-0.0444-0.22360.0840.39310.0573-0.0409-0.054-0.0424-0.02250.2385-0.01930.01510.1059-0.01890.101919.168719.398951.3657
40.57880.0465-0.30960.5740.06881.46150.0399-0.01920.0460.064-0.00460.0073-0.1143-0.0205-0.03320.1087-0.00490.0060.07950.00310.099822.524617.279828.922
50.976-0.121-1.71710.6958-0.22584.47830.0543-0.02360.12780.01770.00160.014-0.07420.0514-0.04730.04930.0096-0.02080.0716-0.01250.122117.938744.51821.6549
60.70960.0241-0.18852.4567-1.79232.8990.0109-0.07960.12530.1585-0.016-0.0357-0.17890.03710.00450.04030.0058-0.01070.0936-0.02770.126414.016746.26946.9046
70.6701-0.27260.00663.2858-1.32971.0049-0.0283-0.06150.04730.12520.05890.1681-0.0225-0.1166-0.03080.0739-0.0075-0.01140.1161-0.02150.11453.281935.45548.121
80.4703-0.60380.43897.1871-5.61055.4763-0.02090.0303-0.0077-0.00430.07460.33590.0558-0.1818-0.05810.0837-0.0335-0.00920.1116-0.01260.1484-1.247729.89592.4411
90.71990.1941-0.38170.5319-0.10930.9407-0.04250.0153-0.0373-0.0623-0.0061-0.01390.09160.00810.05090.06440.0035-0.01010.079-0.00370.08920.353930.4297-5.5896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 111 )A0 - 111
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 154 )A112 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 174 )A155 - 174
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 298 )A175 - 298
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 69 )B0 - 69
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 111 )B70 - 111
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 154 )B112 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 175 )B155 - 175
9X-RAY DIFFRACTION9chain 'B' and (resid 176 through 298 )B176 - 298

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