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- PDB-1dwf: Study on radiation damage on a cryocooled crystal. Part 2: Struct... -

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Basic information

Entry
Database: PDB / ID: 1dwf
TitleStudy on radiation damage on a cryocooled crystal. Part 2: Structure after irradiation with 9.1*10e15 photons/mm2
ComponentsMYROSINASE MA1
KeywordsHYDROLASE / GLYCOSIDASE / RADIATION DAMAGE / RADIOLYSIS / CRYO-COOLED
Function / homology
Function and homology information


thioglucosidase / thioglucosidase activity / : / glucosinolate catabolic process / vacuole / beta-glucosidase activity / response to salt stress / 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 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: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Mar 29, 2017Group: Derived calculations / Structure summary
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _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_chiral / 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_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_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 13, 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

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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 area18030 Å2
ΔGint-224.9 kcal/mol
Surface area38650 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 / SINIGRINASE / THIOGLUCOSIDASE / THIOGLUCOSIDE GLUCOHYDROLASE


Mass: 56848.117 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-501 / Source method: isolated from a natural source
Details: AFTER IRRADIATION WITH 9.1*10E15 PHOTONS/MM2 OF PHOTONS
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


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


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / 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 ENTRY IS THE 2ND STRUCTURE OF A SERIES OF STRUCTURES IN A STUDY ON RADIATION DAMAGE IN CRYO- ...THIS ENTRY IS THE 2ND STRUCTURE OF A SERIES OF STRUCTURES IN A STUDY ON RADIATION DAMAGE IN CRYO-COOLED CRYSTALS. IT HAS BEEN COLLECTED AFTER IRRADIATION OF THE CRYSTAL WITH A DOSE OF 9.1*10E15 PHOTONS/MM2. THERE ARE OTHER RELATED ENTRIES CORRESPONDING TO THE STRUCTURE AFTER DIFFERENT RADIATION DOSES. THE STRUCTURE PRIOR TO IRRADIATION IS GIVEN IN ENTRY 1DWA
Nonpolymer detailsGLYCOSYLATION SITES: ASN 21 -- NAG 901 ASN 60 -- NAG 961 ASN 90 -- NAG 911 ASN 218 -- NAG 921 <-- (1,4)-NAG 923 ASN 244 -- NAG 931 ASN 265 -- NAG 941 <-- (1,3)-FUC 942 | (1,4)-NAG 943 <-- (1,4)-MAN 944 <-- (1,2)-XYS 945 ASN 292 -- NAG 951 <-- (1,3)-FUC 952 | (1,6)-MAN 957 | / (1,4)-NAG 953 <-- (1,4)-MAN 954 <-- (1,2)-XYS 955 \ (1,3)-MAN 956 ASN 346 -- NAG 971 ASN 361 -- NAG 981 <-- (1,4)-NAG 983 ASN 482 -- NAG 991
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: 51406 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 12
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4 / Rsym value: 0.147 / % 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-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MYR

1myr


Resolution: 2→17.4 Å / Rfactor Rfree error: 0.0034 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: AN OVERALL TEMPERATURE FACTOR REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE AIM OF THE STUDY IS TO LOOK AT THE EVOLUTION OF THE OCCUPANCY OF GROUPS SENSITIVE TO RADIATION DAMAGE. ...Details: AN OVERALL TEMPERATURE FACTOR REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE AIM OF THE STUDY IS TO LOOK AT THE EVOLUTION OF THE OCCUPANCY OF GROUPS SENSITIVE TO RADIATION DAMAGE. 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 HAS BEEN REFINED. DUE TO THIS REFINEMENT OCCUPANCIES DIFFERENT OR EVEN BIGGER THAT 1.0 ARE PRESENT IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2796 5 %RANDOM
Rwork0.169 ---
obs0.169 50381 99.8 %-
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 2→17.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 349 788 5154
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.029
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_deg3.002
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.6
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→2.07 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.245 251 5 %
Rwork0.236 4632 -
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_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.6

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