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- PDB-4tx8: Crystal Structure of a Family GH18 Chitinase from Chromobacterium... -

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Basic information

Entry
Database: PDB / ID: 4tx8
TitleCrystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum
ComponentsProbable chitinase A
KeywordsHYDROLASE / Chitinase Family 18 Glycoside Hydrolase
Function / homology
Function and homology information


chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate-binding module superfamily 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycoside hydrolase family 18, catalytic domain ...Carbohydrate-binding module superfamily 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Probable chitinase A
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsPereira, H.M. / Lobo, M.D.P. / Brandao-Neto, J. / Grangeiro, T.B.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: To Be Published
Title: Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum
Authors: Pereira, H.M. / Lobo, M.D.P. / Brandao-Neto, J. / Grangeiro, T.B.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_audit_support ...diffrn_source / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7958
Polymers45,7531
Non-polymers1,0427
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-14 kcal/mol
Surface area14560 Å2
2
A: Probable chitinase A
hetero molecules

A: Probable chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,59116
Polymers91,5072
Non-polymers2,08414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7830 Å2
ΔGint-54 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.480, 120.480, 106.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Probable chitinase A


Mass: 45753.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: CV_2935 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q7NTW8
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 298 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 4.22 Å3/Da / Density % sol: 70.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.7 M Sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 25/09/2011
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.17→53.88 Å / Num. obs: 40464 / % possible obs: 96.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 32.86 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-IDRejects% possible all
2.17-2.2350.5792.31098.4
9.7-53.884.60.0221091.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
PDB_EXTRACT3.14data extraction
xia2data scaling
PHASERphasing
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ED7

1ed7


Resolution: 2.17→48.67 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 2026 5.01 %Random selection
Rwork0.168 ---
obs0.1692 40433 96.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 69 292 3122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032911
X-RAY DIFFRACTIONf_angle_d0.8723980
X-RAY DIFFRACTIONf_dihedral_angle_d15.1811037
X-RAY DIFFRACTIONf_chiral_restr0.032430
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1701-2.22430.28761270.25242768X-RAY DIFFRACTION98
2.2243-2.28450.2371480.22392733X-RAY DIFFRACTION98
2.2845-2.35170.24261420.22182750X-RAY DIFFRACTION98
2.3517-2.42760.23321450.21232734X-RAY DIFFRACTION98
2.4276-2.51430.22681410.20742741X-RAY DIFFRACTION97
2.5143-2.6150.24381250.19662746X-RAY DIFFRACTION97
2.615-2.7340.21151600.1942712X-RAY DIFFRACTION97
2.734-2.87810.2121330.18812753X-RAY DIFFRACTION97
2.8781-3.05840.17611630.18082703X-RAY DIFFRACTION96
3.0584-3.29450.20981460.18062734X-RAY DIFFRACTION96
3.2945-3.6260.18011520.15092724X-RAY DIFFRACTION96
3.626-4.15040.17561480.13512724X-RAY DIFFRACTION95
4.1504-5.22810.12721440.12692753X-RAY DIFFRACTION94
5.2281-48.68270.18771520.15482832X-RAY DIFFRACTION92
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)
10.5126-0.7091-0.69121.72850.76720.9399-0.10490.20660.362-0.0407-0.03710.0088-0.4968-0.13870.02930.3340.0191-0.03230.19690.0270.3068-43.0853-15.1103-11.7455
21.1427-0.019-0.06851.38880.16571.15930.05220.1454-0.2028-0.2673-0.0279-0.0185-0.0264-0.00570.01680.24680.0040.01910.2280.04230.2507-33.0565-24.7115-13.8896
32.252-0.44070.18793.00030.68381.4448-0.10720.25280.1252-0.11490.0175-0.3528-0.16420.46910.07910.2686-0.07140.03280.27550.07350.3449-25.8604-15.9622-11.7376
41.4990.1816-0.21792.39490.18210.6747-0.0777-0.16650.05160.2858-0.0021-0.1489-0.1562-0.06260.25340.2566-0.0097-0.00930.17350.00710.3601-31.1276-14.7959-0.6621
52.38060.39420.61323.04890.15823.8328-0.2660.13890.48990.40660.0707-0.3094-0.31420.25970.20530.445-0.0783-0.10310.23050.040.4606-25.72-5.4128-1.3618
61.21960.5572-0.46590.7291-0.89592.06170.0032-0.11960.13550.0779-0.01980.0927-0.3982-0.02480.07080.27950.001-0.00150.1957-0.0030.2611-39.445-12.17024.3984
72.04160.3907-0.48730.8936-0.57352.2893-0.0438-0.1506-0.08410.17020.03050.1385-0.2512-0.3291-0.01790.23880.0471-0.00410.2783-0.00750.2763-49.7904-19.20633.767
81.90840.1023-0.3411.4648-0.88612.92620.0796-0.2280.16860.28360.1060.1295-0.4242-0.5104-0.09780.25190.09090.00450.3064-0.00020.2915-53.7792-15.81273.1058
94.5167-2.11411.01673.1537-0.35662.73660.24550.088-0.3984-0.2473-0.13280.38010.2561-0.4196-0.14170.2362-0.0569-0.0220.31970.02690.3091-51.2392-29.9378-6.8118
102.5906-0.47870.31962.8806-1.36292.9713-0.0790.12850.10250.08390.13490.356-0.2218-0.6964-0.12840.21280.0298-0.04730.3557-0.02690.2773-56.1975-20.5717-6.4968
117.051-0.9166-0.15571.96370.10341.85650.22260.3144-0.1932-0.3365-0.14780.10320.1344-0.1748-0.07960.2692-0.0184-0.03780.2364-0.00880.2383-43.2331-29.2975-15.7718
122.97110.2447-0.32942.5296-0.23462.57870.24710.3994-0.0876-0.7891-0.2080.44130.0925-0.2606-0.02370.42220.0383-0.07380.3241-0.07980.2976-34.6909-45.8393-23.5382
133.8158-0.16810.02053.1325-0.52311.99930.12690.0543-0.1543-0.3061-0.18850.03650.0768-0.05560.06390.31230.0297-0.02390.1782-0.05340.2676-30.5036-45.5252-17.0707
143.3107-1.17560.00053.7255-1.85753.41360.01610.60450.2704-0.8130.1559-0.3567-0.1044-0.16290.04760.49940.02890.00410.31220.00540.3266-32.2645-38.2673-24.2038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 168 )
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 186 )
6X-RAY DIFFRACTION6chain 'A' and (resid 187 through 251 )
7X-RAY DIFFRACTION7chain 'A' and (resid 252 through 289 )
8X-RAY DIFFRACTION8chain 'A' and (resid 290 through 327 )
9X-RAY DIFFRACTION9chain 'A' and (resid 328 through 352 )
10X-RAY DIFFRACTION10chain 'A' and (resid 353 through 375 )
11X-RAY DIFFRACTION11chain 'A' and (resid 376 through 396 )
12X-RAY DIFFRACTION12chain 'A' and (resid 2 through 22 )
13X-RAY DIFFRACTION13chain 'A' and (resid 23 through 47 )
14X-RAY DIFFRACTION14chain 'A' and (resid 48 through 54 )

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