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- PDB-3w6e: Crystal structure of catalytic domain of chitinase from Ralstonia... -

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Basic information

Entry
Database: PDB / ID: 3w6e
TitleCrystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 (E162Q)
ComponentsLysozyme-like chitinolytic enzyme
KeywordsHYDROLASE / GH family 23 / enzyme / Glycoside hydrolase / chitinase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Carbohydrate-binding module family 5/12 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Lysozyme-like chitinolytic enzyme
Similarity search - Component
Biological speciesRalstonia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsArimori, T. / Kawamoto, N. / Okazaki, N. / Nakazawa, M. / Miyatake, K. / Fukamizo, T. / Ueda, M. / Tamada, T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structures of the Catalytic Domain of a Novel Glycohydrolase Family 23 Chitinase from Ralstonia sp. A-471 Reveals a Unique Arrangement of the Catalytic Residues for Inverting Chitin Hydrolysis
Authors: Arimori, T. / Kawamoto, N. / Shinya, S. / Okazaki, N. / Nakazawa, M. / Miyatake, K. / Fukamizo, T. / Ueda, M. / Tamada, T.
History
DepositionFeb 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme-like chitinolytic enzyme
B: Lysozyme-like chitinolytic enzyme
C: Lysozyme-like chitinolytic enzyme
D: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1798
Polymers81,3424
Non-polymers8374
Water4,414245
1
A: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5742
Polymers20,3351
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4582
Polymers20,3351
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5742
Polymers20,3351
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5742
Polymers20,3351
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.913, 99.913, 241.135
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Lysozyme-like chitinolytic enzyme


Mass: 20335.465 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 89-252 / Mutation: E162Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia (bacteria) / Strain: A-471 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: B7XCV4, chitinase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.41 % / Mosaicity: 0.292 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11.1% (w/v) PEG 3350, 1.8% (v/v) isopropanol, 44.4mM CaCl2, 44.4mM HEPES (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 39762 / Num. obs: 39695 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.4 % / Rmerge(I) obs: 0.102 / Χ2: 1.505 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.1913.60.37119490.93199.8
2.19-2.2313.80.35519390.944199.9
2.23-2.2713.90.33519500.9661100
2.27-2.3214.60.30819151.0151100
2.32-2.3714.80.28919431.0431100
2.37-2.42150.26919451.037199.9
2.42-2.4815.30.25219471.08199.9
2.48-2.5515.90.21919601.136199.9
2.55-2.6216.10.20319651.218199.9
2.62-2.7116.50.17519631.247199.8
2.71-2.8116.70.16319381.309199.9
2.81-2.9217.20.13919631.395199.9
2.92-3.0517.40.12419771.479199.8
3.05-3.2117.70.10919841.611199.9
3.21-3.4118.20.09319871.776199.8
3.41-3.6818.40.0820091.9241100
3.68-4.0518.70.06720012.172199.9
4.05-4.6318.70.0620382.253199.8
4.63-5.8318.40.0620792.169199.7
5.83-5016.80.05422432.267199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W6B

3w6b


Resolution: 2.15→48.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.312 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1980 5 %RANDOM
Rwork0.187 ---
obs0.1886 39426 99.35 %-
all-39762 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.32 Å2 / Biso mean: 23.6967 Å2 / Biso min: 7.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 53 245 5076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224966
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.9546739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.825609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97323.761234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57415723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8631521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213897
X-RAY DIFFRACTIONr_mcbond_it0.341.53022
X-RAY DIFFRACTIONr_mcangle_it0.65924792
X-RAY DIFFRACTIONr_scbond_it0.94131944
X-RAY DIFFRACTIONr_scangle_it1.5394.51947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.149-2.2050.2771400.232673285998.391
2.205-2.2650.2891310.2232657280999.252
2.265-2.330.2321420.2032567272599.413
2.33-2.4020.2221380.22488263999.507
2.402-2.4810.2521350.2082398255399.217
2.481-2.5670.2081180.1872379251499.324
2.567-2.6640.2181130.1962263239099.414
2.664-2.7730.2181340.1922185233799.23
2.773-2.8950.2811380.22066221499.548
2.895-3.0360.225920.1922059215999.629
3.036-3.20.243890.1951925203598.968
3.2-3.3930.205870.1871843193699.69
3.393-3.6260.204980.181728183799.401
3.626-3.9150.177830.1651628172099.477
3.915-4.2860.17840.1571501159099.686
4.286-4.7870.203810.1581375145999.794
4.787-5.5190.183580.1691236130299.386
5.519-6.7370.225490.1951072112699.556
6.737-9.4390.222450.17185590199.889
9.439-48.9180.21250.20454857998.964
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)
10.50690.1023-0.24490.75450.45090.65740.0242-0.03840.07280.1041-0.08320.08840.06980.04310.0590.1224-0.02170.04070.0358-0.06650.1134-9.9059.411.347
20.7095-0.01970.13562.55511.4570.93330.01530.06790.0236-0.086-0.19260.25570.0545-0.02070.17730.1021-0.0047-0.05570.0409-0.05530.10311.75929.129-0.515
31.46550.6561-0.76812.0543-0.51210.36490.04090.18980.06610.01870.06760.12280.0168-0.0622-0.10850.1135-0.01340.03650.02490.02030.0883-34.06224.901-0.864
40.98290.39340.67350.26240.61272.35840.04570.05-0.00880.02750.07010.0530.13640.1865-0.11590.0720.0339-0.03320.0636-0.01660.070728.01837.95923.235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 252
2X-RAY DIFFRACTION2B103 - 253
3X-RAY DIFFRACTION3C103 - 253
4X-RAY DIFFRACTION4D102 - 254

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