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- PDB-1dwj: study on radiation damage on a cryocooled crystal. Refined part 6... -

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Basic information

Entry
Database: PDB / ID: 1dwj
Titlestudy on radiation damage on a cryocooled crystal. Refined part 6: structure after a radiation dose of 54*10e15 photons/mm2
ComponentsMYROSINASE MA1
KeywordsHYDROLASE / GLYCOSIDASE / RADIATION DAMAGE / RADIOLYSIS / CRYO-COOLED
Function / homology
Function and homology information


thioglucosidase / thioglucosidase activity / glucosinolate glucohydrolase activity / vacuole / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesSINAPIS ALBA (white mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBurmeister, W.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structural Changes in a Cryo-Cooled Protein Crystal due to Radiation Damage
Authors: Burmeister, W.P.
#1: Journal: Structure / Year: 1997
Title: The Crystal Structures of Sinapis Alba Myrosinase and a Covalent Glycosyl-Enzyme Intermediate Provide Insights Into the Substrate Recognition and Active-Side Machinery of an S-Glycosidase
Authors: Burmeister, W.P. / Cottaz, S. / Driguez, H. / Iori, R. / Palmieri, S. / Henrissat, B.
History
DepositionDec 5, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: MYROSINASE MA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,37225
Polymers56,8481
Non-polymers5,52424
Water14,196788
1
M: MYROSINASE MA1
hetero molecules

M: MYROSINASE MA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,74550
Polymers113,6962
Non-polymers11,04948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area18010 Å2
ΔGint-223.2 kcal/mol
Surface area38950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.300, 136.400, 80.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules M

#1: Protein MYROSINASE MA1 / THIOGLUCOSIDE GLUCOHYDROLASE / SINIGRINASE / THIOGLUCOSIDASE


Mass: 56848.117 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-501 / Source method: isolated from a natural source / Details: AFTER IRRADIATION WITH 54*10E15 PHOTONS/MM2 / Source: (natural) SINAPIS ALBA (white mustard) / Cell: MYROSIN CELLS / Cellular location: MYROSIN GRAINS / Organ: SEED / Strain: EMERGO / References: UniProt: P29736, thioglucosidase

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Sugars , 4 types, 10 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 864.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5]/1-2-1-3-4/a3-b1_a4-c1_c4-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1189.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpa1-3][DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-5-5/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1_d6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 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

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Non-polymers , 4 types, 802 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 788 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIS STRUCTURE HAS BEEN REFINED AGAINS DATA COLLECTED ON A MYROSINASE CRYSTAL WHICH HAS BEEN ...THIS STRUCTURE HAS BEEN REFINED AGAINS DATA COLLECTED ON A MYROSINASE CRYSTAL WHICH HAS BEEN EXPOSED TO A DOSE OF 54*10E15 PHOTONS/MM2. THE DISULPHIDE BRIDGES ARE ASSUMED TO BE BROKEN DUE TO THE RADIATION DAMAGE. THE STRUCTURE IS RELATED TO ENTRY 1DWI, BUT THERE HAS BEEN AN ADDITIONAL POSITIONAL REFINEMENT.
Sequence detailsTHERE ARE SOME DISCREPANCIES IN THE SEQUENCE COMPARED TO ENTRY 1MYR AS THE X-RAY SEQUENCE HAS BEEN ...THERE ARE SOME DISCREPANCIES IN THE SEQUENCE COMPARED TO ENTRY 1MYR AS THE X-RAY SEQUENCE HAS BEEN CORRECTED WHEN HIGHER RESOLUTION DATA (1.2 A) BECAME AVAILABLE. THE SEQUENCE OF 1MYR (DETERMINED FROM THE X-RAY STRUCTURE) IS ESSENTIALLY IDENTICAL TO A PARTIAL SEQUENCE OF A MYROSINASE FROM SINAPIS ALBA (SWISS-PROT P29736). THE NUCLEOTIDE SEQUENCE OF THE GENE ENCODING THE CRYSTALLIZED ENZYME WAS NOT DETERMINED. SIGNIFICANT DIFFERENCES BEYOND THE UNCERTAINTY OF A SEQUENCE DETERMINED FROM A CRYSTAL STRUCTURE SHOW THAT THE ISOENZYME WHICH IS PRESENT IN THE DEPOSITORS' CRYSTALS IS DIFFERENT FROM THAT WHOSE PARTIAL SEQUENCE IS KNOWN. THE DEPOSITORS' SEQUENCE IS ABOUT 70% IDENTICAL TO THE ONLY KNOWN FULL-LENGTH SEQUENCE OF ANOTHER MYROSINASE ISOZYME FROM SINAPIS ALBA (SWISS-PROT P29092). ALL KNOWN MYROSINASE SEQUENCES (FROM SINAPSIS ALBA OR FROM OTHER CRUCIFERAE) ARE LONGER THAN 1MYR AT THEIR C-TERMINUS BY APPROXIMATELY 25 RESIDUES. IT IS THEREFORE POSSIBLE THAT THE SEQUENCE OF 1MYR IS ACTUALLY LONGER THAN THAT SEEN IN THE X-RAY STRUCTURE.

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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: 3.2 Å3/Da / Density % sol: 50 %
Description: DOSE 0.1*10E15 PHOTONS/MM2 USED FOR DATA COLLECTION, I/ SIGMA VALUES ARE STRONGLY AFFECTED BY A FEW ZINGERS ON THE DETECTOR
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP METHOD, 12 MG/ML PROTEIN IN 30 MM HEPES, PH 6.5, 0.05 % NAN3 PRECIPITANT 66% SATURATED AMMONIUM SULFATE, 100MM TRIS-HCL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
230 mMHEPES1drop
366 %satammonium sulfate1reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9475
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 1998 / Details: BENT MULTILAYER MIRROR, SAGITALLY FOCUSING CRYSTAL
RadiationMonochromator: C(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9475 Å / Relative weight: 1
ReflectionResolution: 2→34.9 Å / Num. obs: 51380 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 2.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 0.7 / Rsym value: 0.958 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DWI

1dwi


Resolution: 2.4→15 Å / Rfactor Rfree error: 0.0063 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: AN OVERALL TEMPERATURE FACTOR REFINEMENT, A POSITIONAL REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE MODEL IS NOT SUPPOSED TO BE USED AS A MODEL OF MYROSINASE. A MODEL REPLACING ...Details: AN OVERALL TEMPERATURE FACTOR REFINEMENT, A POSITIONAL REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE MODEL IS NOT SUPPOSED TO BE USED AS A MODEL OF MYROSINASE. A MODEL REPLACING ENTRY 1MYR WILL BE DEPOSITED LATER. NO COORDINATES ARE GIVEN FOR RESIDUES 1 - 2. PRO 501 IS THE LAST RESIDUE SEEN IN ELECTRON DENSITY. THE PROTEIN COULD EXTEND BEYOND PRO 501. THE OCCUPANCY OF CERTAIN GROUPS WHICH ARE SENSITIVE TO RADIATION DAMAGE HAVE BEEN REFINED. DUE TO THIS REFINEMENT OCCUPANCIES DIFFERENT TO OR EVEN GREATER THAN 1.0 ARE PRESENT IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1482 5 %RANDOM
Rwork0.186 ---
obs0.186 29237 99.8 %-
Displacement parametersBiso mean: 42.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 349 788 5154
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.024
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.613
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.81.5
X-RAY DIFFRACTIONx_mcangle_it4.92
X-RAY DIFFRACTIONx_scbond_it3.82
X-RAY DIFFRACTIONx_scangle_it4.92.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.32 164 5 %
Rwork0.306 2750 -
obs--99.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.3

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