PDB Short entry for 1W9D HEADER HYDROLASE 08-OCT-04 1W9D TITLE S. ALBA MYROSINASE IN COMPLEX WITH S-ETHYL PHENYLACETOTHIOHYDROXIMATE- TITLE 2 O-SULFATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSIDASE; COMPND 3 CHAIN: M; COMPND 4 SYNONYM: MYROSINASE; COMPND 5 EC: 3.2.3.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINAPIS ALBA; SOURCE 3 ORGANISM_COMMON: WHITE MUSTARD; SOURCE 4 ORGANISM_TAXID: 3728; SOURCE 5 STRAIN: EMERGO; SOURCE 6 ORGAN: SEED; SOURCE 7 TISSUE: MYROSIN GRAINS KEYWDS THIOGLUCOSIDASE, THIOGLYCOSIDASE, MYROSINASE, HYDROLASE, THIO- KEYWDS 2 GLUCOSIDE, THIOHYDROXIMATE, GLUSOSINOLATE, GLUCOTROPAEOLIN EXPDTA X-RAY DIFFRACTION AUTHOR A.BOURDERIOUX,M.LEFOIX,D.GUEYRARD,A.TATIBOUET,S.COTTAZ,S.ARZT, AUTHOR 2 W.P.BURMEISTER,P.ROLLIN REVDAT 5 13-DEC-23 1W9D 1 HETSYN LINK REVDAT 4 29-JUL-20 1W9D 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 08-MAY-19 1W9D 1 REMARK LINK REVDAT 2 24-FEB-09 1W9D 1 VERSN REVDAT 1 19-MAY-05 1W9D 0 JRNL AUTH A.BOURDERIOUX,M.LEFOIX,D.GUEYRARD,A.TATIBOUET,S.COTTAZ, JRNL AUTH 2 S.ARZT,W.P.BURMEISTER,P.ROLLIN JRNL TITL THE GLUCOSINOLATE-MYROSINASE SYSTEM. NEW INSIGHTS INTO JRNL TITL 2 ENZYME-SUBSTRATE INTERACTIONS BY USE OF SIMPLIFIED JRNL TITL 3 INHIBITORS JRNL REF ORG.BIOMOL.CHEM. V. 3 1872 2005 JRNL REFN ISSN 1477-0520 JRNL PMID 15889170 JRNL DOI 10.1039/B502990B REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.P.BURMEISTER,S.COTTAZ,P.ROLLIN,A.VASELLA,B.HENRISSAT REMARK 1 TITL HIGH RESOLUTION X-RAY CRYSTALLOGRAPHY SHOWS THAT ASCORBATE REMARK 1 TITL 2 IS A COFACTOR FOR MYROSINASE AND SUBSTITUTES FOR THE REMARK 1 TITL 3 FUNCTION OF THE CATALYTIC BASE REMARK 1 REF J.BIOL.CHEM. V. 275 39385 2000 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10978344 REMARK 1 DOI 10.1074/JBC.M006796200 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 97986 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 7192 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.002 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.85 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9252 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 452 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4016 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 335 REMARK 3 SOLVENT ATOMS : 761 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99500 REMARK 3 B22 (A**2) : -0.43300 REMARK 3 B33 (A**2) : -0.56200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.09 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.09 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.799 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.82 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.480 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.420 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.160 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.510 ; 3.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 36.93 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CGT_PAR.TXT.PAR REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : CGT_TOP.TXT.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INHIBITOR TOPOLOGY AND PARAMETERS SAME REMARK 3 AS IN ENTRY 1W9B, ONLY MOST OF THE ATOMS OF THE GLUCOSE GROUP REMARK 3 HAVE BEEN DELETED. THE INHIBITOR HAS BEEN RENAMED FROM CGT TO REMARK 3 SEH AFTER REFINEMENT REMARK 4 REMARK 4 1W9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1290021271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : DIAMOND 111 AND SI220 REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 146755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1E4M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP METHOD, 12 MG/ML PROTEIN REMARK 280 IN 30 MM HEPES, PH 6.5, 0.05 % NAN3, PRECIPITANT 66% SAT. REMARK 280 AMMONIUM SULFATE, 100MM TRIS-HCL PH 7.0, PH 7.00, VAPOR REMARK 280 DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 67.65000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 67.65000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.60000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.30000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 67.65000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.60000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.30000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 67.65000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.60000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 ZN ZN M1502 LIES ON A SPECIAL POSITION. REMARK 375 HOH M2026 LIES ON A SPECIAL POSITION. REMARK 375 HOH M2267 LIES ON A SPECIAL POSITION. REMARK 375 HOH M2294 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP M 1 REMARK 465 GLU M 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C2 SEH M 999 C1 GOL M 1514 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR M 72 -135.24 40.05 REMARK 500 HIS M 141 53.87 -105.50 REMARK 500 TRP M 142 -11.93 75.55 REMARK 500 TYR M 152 20.84 -144.88 REMARK 500 THR M 184 -75.83 -81.02 REMARK 500 GLN M 187 80.98 32.81 REMARK 500 ASN M 218 101.87 -160.61 REMARK 500 ASN M 410 119.60 -170.04 REMARK 500 ALA M 458 100.74 70.57 REMARK 500 ASN M 466 -18.79 76.78 REMARK 500 ASN M 482 87.26 -157.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH M2048 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH M2155 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH M2211 DISTANCE = 6.62 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN M1502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS M 56 NE2 REMARK 620 2 HIS M 56 NE2 115.4 REMARK 620 3 ASP M 70 OD2 116.6 105.3 REMARK 620 4 ASP M 70 OD2 108.7 117.0 91.8 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MYR RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA REMARK 900 RELATED ID: 1W9B RELATED DB: PDB REMARK 900 S. ALBA MYROSINASE IN COMPLEX WITH CARBA- GLUCOTROPAEOLIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 OUR SEQUENCE IS AN X-RAY SEQUENCE BASED ON THE ASSIGNMENT REMARK 999 OF THE RESIDUES BY THEIR ELECTRON DENSITY. SOME REMARK 999 AMBIGUITIES MAY EXIST. FURTHERMORE A DIFFERENT ISOFORM REMARK 999 OF THE ENZYME MAY BE PRESENT IN THE CRYSTAL. THE SEQUENCE REMARK 999 WAS ORIGINALLY IDENTIFIED DURING THE DETERMINATION OF THE REMARK 999 STRUCTURE IN PDB ENTRY 1E4M. DBREF 1W9D M 1 501 PDB 1W9D 1W9D 1 501 SEQRES 1 M 501 ASP GLU GLU ILE THR CYS GLN GLU ASN LEU PRO PHE THR SEQRES 2 M 501 CYS GLY ASN THR ASP ALA LEU ASN SER SER SER PHE SER SEQRES 3 M 501 SER ASP PHE ILE PHE GLY VAL ALA SER SER ALA TYR GLN SEQRES 4 M 501 ILE GLU GLY THR ILE GLY ARG GLY LEU ASN ILE TRP ASP SEQRES 5 M 501 GLY PHE THR HIS ARG TYR PRO ASN LYS SER GLY PRO ASP SEQRES 6 M 501 HIS GLY ASN GLY ASP THR THR CYS ASP SER PHE SER TYR SEQRES 7 M 501 TRP GLN LYS ASP ILE ASP VAL LEU ASP GLU LEU ASN ALA SEQRES 8 M 501 THR GLY TYR ARG PHE SER ILE ALA TRP SER ARG ILE ILE SEQRES 9 M 501 PRO ARG GLY LYS ARG SER ARG GLY VAL ASN GLU LYS GLY SEQRES 10 M 501 ILE ASP TYR TYR HIS GLY LEU ILE SER GLY LEU ILE LYS SEQRES 11 M 501 LYS GLY ILE THR PRO PHE VAL THR LEU PHE HIS TRP ASP SEQRES 12 M 501 LEU PRO GLN THR LEU GLN ASP GLU TYR GLU GLY PHE LEU SEQRES 13 M 501 ASP PRO GLN ILE ILE ASP ASP PHE LYS ASP TYR ALA ASP SEQRES 14 M 501 LEU CYS PHE GLU GLU PHE GLY ASP SER VAL LYS TYR TRP SEQRES 15 M 501 LEU THR ILE ASN GLN LEU TYR SER VAL PRO THR ARG GLY SEQRES 16 M 501 TYR GLY SER ALA LEU ASP ALA PRO GLY ARG CYS SER PRO SEQRES 17 M 501 THR VAL ASP PRO SER CYS TYR ALA GLY ASN SER SER THR SEQRES 18 M 501 GLU PRO TYR ILE VAL ALA HIS HIS GLN LEU LEU ALA HIS SEQRES 19 M 501 ALA LYS VAL VAL ASP LEU TYR ARG LYS ASN TYR THR HIS SEQRES 20 M 501 GLN GLY GLY LYS ILE GLY PRO THR MET ILE THR ARG TRP SEQRES 21 M 501 PHE LEU PRO TYR ASN ASP THR ASP ARG HIS SER ILE ALA SEQRES 22 M 501 ALA THR GLU ARG MET LYS GLU PHE PHE LEU GLY TRP PHE SEQRES 23 M 501 MET GLY PRO LEU THR ASN GLY THR TYR PRO GLN ILE MET SEQRES 24 M 501 ILE ASP THR VAL GLY GLU ARG LEU PRO SER PHE SER PRO SEQRES 25 M 501 GLU GLU SER ASN LEU VAL LYS GLY SER TYR ASP PHE LEU SEQRES 26 M 501 GLY LEU ASN TYR TYR PHE THR GLN TYR ALA GLN PRO SER SEQRES 27 M 501 PRO ASN PRO VAL ASN SER THR ASN HIS THR ALA MET MET SEQRES 28 M 501 ASP ALA GLY ALA LYS LEU THR TYR ILE ASN ALA SER GLY SEQRES 29 M 501 HIS TYR ILE GLY PRO LEU PHE GLU LYS ASP LYS ALA ASP SEQRES 30 M 501 SER THR ASP ASN ILE TYR TYR TYR PRO LYS GLY ILE TYR SEQRES 31 M 501 SER VAL MET ASP TYR PHE LYS ASN LYS TYR TYR ASN PRO SEQRES 32 M 501 LEU ILE TYR VAL THR GLU ASN GLY ILE SER THR PRO GLY SEQRES 33 M 501 ASP GLU ASN ARG ASN GLN SER MET LEU ASP TYR THR ARG SEQRES 34 M 501 ILE ASP TYR LEU CYS SER HIS LEU CYS PHE LEU ASN LYS SEQRES 35 M 501 VAL ILE LYS GLU LYS ASP VAL ASN VAL LYS GLY TYR LEU SEQRES 36 M 501 ALA TRP ALA LEU GLY ASP ASN TYR GLU PHE ASN LYS GLY SEQRES 37 M 501 PHE THR VAL ARG PHE GLY LEU SER TYR ILE ASP TRP ASN SEQRES 38 M 501 ASN VAL THR ASP ARG ASP LEU LYS LYS SER GLY GLN TRP SEQRES 39 M 501 TYR GLN SER PHE ILE SER PRO MODRES 1W9D ASN M 21 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 90 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 218 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 244 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 265 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 292 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 346 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 361 ASN GLYCOSYLATION SITE MODRES 1W9D ASN M 482 ASN GLYCOSYLATION SITE HET NAG A 1 14 HET NAG A 2 14 HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET XYP B 4 9 HET FUC B 5 10 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET XYP C 4 9 HET MAN C 5 11 HET MAN C 6 11 HET FUC C 7 10 HET NAG D 1 14 HET NAG D 2 14 HET NAG M 901 14 HET NAG M 911 14 HET NAG M 931 14 HET NAG M 961 15 HET NAG M 971 14 HET NAG M 991 14 HET SEH M 999 17 HET ZN M1502 1 HET SO4 M1503 5 HET SO4 M1504 5 HET SO4 M1505 5 HET SO4 M1506 5 HET GOL M1512 6 HET GOL M1513 6 HET GOL M1514 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM SEH S-BENZYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN SEH ETHYL (1E)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 14(C8 H15 N O6) FORMUL 3 BMA 2(C6 H12 O6) FORMUL 3 XYP 2(C5 H10 O5) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 4 MAN 2(C6 H12 O6) FORMUL 12 SEH C10 H13 N O4 S2 FORMUL 13 ZN ZN 2+ FORMUL 14 SO4 4(O4 S 2-) FORMUL 18 GOL 3(C3 H8 O3) FORMUL 21 HOH *761(H2 O) HELIX 1 1 ASN M 21 PHE M 25 5 5 HELIX 2 2 SER M 36 GLU M 41 1 6 HELIX 3 3 ASN M 49 TYR M 58 1 10 HELIX 4 4 TYR M 58 GLY M 63 1 6 HELIX 5 5 ASP M 74 ASN M 90 1 17 HELIX 6 6 ALA M 99 ILE M 104 1 6 HELIX 7 7 LYS M 108 GLY M 112 5 5 HELIX 8 8 ASN M 114 LYS M 131 1 18 HELIX 9 9 PRO M 145 GLU M 153 1 9 HELIX 10 10 GLY M 154 PRO M 158 5 5 HELIX 11 11 GLN M 159 GLY M 176 1 18 HELIX 12 12 TYR M 189 GLY M 197 1 9 HELIX 13 13 THR M 221 TYR M 245 1 25 HELIX 14 14 THR M 246 GLY M 249 5 4 HELIX 15 15 ASP M 268 LEU M 283 1 16 HELIX 16 16 LEU M 283 GLY M 293 1 11 HELIX 17 17 PRO M 296 GLY M 304 1 9 HELIX 18 18 GLU M 305 LEU M 307 5 3 HELIX 19 19 SER M 311 LYS M 319 1 9 HELIX 20 20 THR M 348 ALA M 353 5 6 HELIX 21 21 ASP M 377 ASN M 381 5 5 HELIX 22 22 PRO M 386 TYR M 400 1 15 HELIX 23 23 ASN M 419 LEU M 425 1 7 HELIX 24 24 ASP M 426 ASP M 448 1 23 HELIX 25 25 LYS M 489 SER M 500 1 12 SHEET 1 MA 9 LYS M 251 GLY M 253 0 SHEET 2 MA 9 TYR M 181 ILE M 185 1 O TRP M 182 N GLY M 253 SHEET 3 MA 9 THR M 134 PHE M 140 1 O VAL M 137 N LEU M 183 SHEET 4 MA 9 GLY M 93 SER M 97 1 O TYR M 94 N PHE M 136 SHEET 5 MA 9 ILE M 30 ALA M 34 1 O VAL M 33 N ARG M 95 SHEET 6 MA 9 VAL M 451 TRP M 457 1 O LYS M 452 N ILE M 30 SHEET 7 MA 9 ILE M 405 GLU M 409 1 O ILE M 405 N LYS M 452 SHEET 8 MA 9 LEU M 325 PRO M 337 1 O LEU M 325 N TYR M 406 SHEET 9 MA 9 THR M 255 PRO M 263 1 O MET M 256 N ASN M 328 SHEET 1 MB 9 LYS M 251 GLY M 253 0 SHEET 2 MB 9 TYR M 181 ILE M 185 1 O TRP M 182 N GLY M 253 SHEET 3 MB 9 THR M 134 PHE M 140 1 O VAL M 137 N LEU M 183 SHEET 4 MB 9 GLY M 93 SER M 97 1 O TYR M 94 N PHE M 136 SHEET 5 MB 9 ILE M 30 ALA M 34 1 O VAL M 33 N ARG M 95 SHEET 6 MB 9 VAL M 451 TRP M 457 1 O LYS M 452 N ILE M 30 SHEET 7 MB 9 ILE M 405 GLU M 409 1 O ILE M 405 N LYS M 452 SHEET 8 MB 9 LEU M 325 PRO M 337 1 O LEU M 325 N TYR M 406 SHEET 9 MB 9 ALA M 355 THR M 358 -1 O LYS M 356 N GLN M 336 SHEET 1 MC 2 LEU M 370 GLU M 372 0 SHEET 2 MC 2 ILE M 382 TYR M 383 -1 O ILE M 382 N PHE M 371 SHEET 1 MD 2 THR M 414 PRO M 415 0 SHEET 2 MD 2 VAL M 471 ARG M 472 -1 O ARG M 472 N THR M 414 SHEET 1 ME 2 SER M 476 ASP M 479 0 SHEET 2 ME 2 ASN M 482 LEU M 488 -1 O ASN M 482 N ASP M 479 SSBOND 1 CYS M 6 CYS M 438 1555 1555 2.04 SSBOND 2 CYS M 14 CYS M 434 1555 1555 2.04 SSBOND 3 CYS M 206 CYS M 214 1555 1555 2.03 LINK ND2 ASN M 21 C1 NAG M 901 1555 1555 1.45 LINK ND2 ASN M 90 C1 NAG M 911 1555 1555 1.45 LINK ND2 ASN M 218 C1 NAG A 1 1555 1555 1.45 LINK ND2 ASN M 244 C1 NAG M 931 1555 1555 1.45 LINK ND2 ASN M 265 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN M 292 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN M 346 C1 NAG M 971 1555 1555 1.45 LINK ND2 ASN M 361 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN M 482 C1 NAG M 991 1555 1555 1.45 LINK C2 SEH M 999 C3 GOL M1514 1555 1555 2.02 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.39 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.38 LINK O3 NAG B 1 C1 FUC B 5 1555 1555 1.40 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.39 LINK O2 BMA B 3 C1 XYP B 4 1555 1555 1.38 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.38 LINK O3 NAG C 1 C1 FUC C 7 1555 1555 1.40 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.38 LINK O2 BMA C 3 C1 XYP C 4 1555 1555 1.39 LINK O3 BMA C 3 C1 MAN C 5 1555 1555 1.40 LINK O6 BMA C 3 C1 MAN C 6 1555 1555 1.40 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.39 LINK NE2 HIS M 56 ZN ZN M1502 3656 1555 2.00 LINK NE2 HIS M 56 ZN ZN M1502 1555 1555 2.04 LINK OD2 ASP M 70 ZN ZN M1502 3656 1555 2.11 LINK OD2 ASP M 70 ZN ZN M1502 1555 1555 2.06 CISPEP 1 LEU M 10 PRO M 11 0 -0.64 CISPEP 2 ALA M 202 PRO M 203 0 0.92 CRYST1 135.300 137.200 80.600 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012407 0.00000