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- PDB-5df0: Crystal structure of AcMNPV Chitinase A in complex WITH CHITOTRIO... -

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Basic information

Entry
Database: PDB / ID: 5df0
TitleCrystal structure of AcMNPV Chitinase A in complex WITH CHITOTRIO-THIAZOLINE DITHIOAMIDE
ComponentsAc-ChiA
KeywordsHYDROLASE / Chitinase / AcMNPV / chitin / Glycosidase
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II ...Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Roll / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-58Y / Chem-SN5 / Ac-ChiA
Similarity search - Component
Biological speciesAutographa californica nuclear polyhedrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.251 Å
AuthorsMou, T.-C. / Sprang, S.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: To Be Published
Title: Crystal structure of AcMNPV Chitinase A
Authors: Mou, T.-C. / Sprang, S.R.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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

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Assembly

Deposited unit
A: Ac-ChiA
B: Ac-ChiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,51018
Polymers121,7502
Non-polymers2,76016
Water28816
1
A: Ac-ChiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,32110
Polymers60,8751
Non-polymers1,4469
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ac-ChiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1898
Polymers60,8751
Non-polymers1,3147
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.712, 112.766, 129.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ac-ChiA / Chitinase


Mass: 60875.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nuclear polyhedrosis virus
Gene: ChiA, Ac-ChiA / Production host: Alphabaculovirus / References: UniProt: Q70SQ1, chitinase

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Sugars , 2 types, 8 molecules

#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#3: Sugar ChemComp-SN5 / 2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose / N-ethanethioyl-beta-D-glucosamine / 2-deoxy-2-(ethanethioylamino)-beta-D-glucose / 2-deoxy-2-(ethanethioylamino)-D-glucose / 2-deoxy-2-(ethanethioylamino)-glucose


Type: D-saccharide, beta linking / Mass: 237.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO5S

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Non-polymers , 4 types, 24 molecules

#4: Chemical ChemComp-58Y / (2R,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methylhexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol


Mass: 221.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO4S
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, MES / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.251→28.09 Å / Num. obs: 20513 / % possible obs: 89.64 % / Redundancy: 5.4 % / Rsym value: 0.125 / Net I/σ(I): 3.58
Reflection shellResolution: 3.251→3.367 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.13 / Rsym value: 0.127 / % possible all: 81.95

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EDQ

1edq


Resolution: 3.251→14.978 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2856 1978 9.75 %
Rwork0.2259 --
obs0.2318 20291 89.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.251→14.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 171 16 8521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028724
X-RAY DIFFRACTIONf_angle_d0.48511878
X-RAY DIFFRACTIONf_dihedral_angle_d10.2385008
X-RAY DIFFRACTIONf_chiral_restr0.0431285
X-RAY DIFFRACTIONf_plane_restr0.0031520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2506-3.3310.38551260.30031174X-RAY DIFFRACTION81
3.331-3.420.33611310.28181203X-RAY DIFFRACTION85
3.42-3.51940.3411340.27831247X-RAY DIFFRACTION85
3.5194-3.63140.36631280.28091175X-RAY DIFFRACTION83
3.6314-3.75930.33831280.25911196X-RAY DIFFRACTION82
3.7593-3.90720.28291460.22831345X-RAY DIFFRACTION92
3.9072-4.08160.261460.21691347X-RAY DIFFRACTION94
4.0816-4.2920.28721490.20141377X-RAY DIFFRACTION95
4.292-4.55380.26311470.20031370X-RAY DIFFRACTION94
4.5538-4.8940.23791470.18881363X-RAY DIFFRACTION92
4.894-5.36580.26881440.19771328X-RAY DIFFRACTION91
5.3658-6.0960.27821440.22121337X-RAY DIFFRACTION91
6.096-7.51520.27141550.21671428X-RAY DIFFRACTION95
7.5152-14.97810.22411530.19591423X-RAY DIFFRACTION92

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