HEADER HYDROLASE 23-AUG-00 1E73 TITLE 2-F-GLUCOSYLATED MYROSINASE FROM SINAPIS ALBA WITH BOUND L-ASCORBATE CAVEAT 1E73 MAN C 6 HAS WRONG CHIRALITY AT ATOM C5 NAG M 961 HAS WRONG CAVEAT 2 1E73 CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYROSINASE MA1; COMPND 3 CHAIN: M; COMPND 4 SYNONYM: THIOGLUCOSIDE GLUCOHYDROLASE; COMPND 5 EC: 3.2.1.147 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 CELLULAR_LOCATION: MYROSIN GRAINS KEYWDS HYDROLASE, FAMILY 1 GLYCOSYL HYDROLASE, GLUCOSINOLATE, MYROSINASE, KEYWDS 2 TIM BARREL, ASCORBATE, ACTIVATION, GLUCOSYL ENZYME EXPDTA X-RAY DIFFRACTION AUTHOR W.P.BURMEISTER REVDAT 9 20-NOV-24 1E73 1 REMARK REVDAT 8 13-DEC-23 1E73 1 HETSYN LINK REVDAT 7 29-JUL-20 1E73 1 CAVEAT COMPND REMARK HETNAM REVDAT 7 2 1 LINK SITE ATOM REVDAT 6 08-MAY-19 1E73 1 REMARK LINK REVDAT 5 14-SEP-11 1E73 1 REMARK HETSYN VERSN REVDAT 4 16-FEB-11 1E73 1 VERSN REVDAT 3 16-JUN-09 1E73 1 REMARK REVDAT 2 24-FEB-09 1E73 1 VERSN REVDAT 1 05-JAN-01 1E73 0 JRNL AUTH W.P.BURMEISTER,S.COTTAZ,P.ROLLIN,A.VASELLA,B.HENRISSAT JRNL TITL HIGH RESOLUTION X-RAY CRYSTALLOGRAPHY SHOWS THAT ASCORBATE JRNL TITL 2 IS A COFACTOR FOR MYROSINASE AND SUBSTITUTES FOR THE JRNL TITL 3 FUNCTION OF THE CATALYTIC BASE JRNL REF J.BIOL.CHEM. V. 275 39385 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10978344 JRNL DOI 10.1074/JBC.M006796200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.P.BURMEISTER,S.COTTAZ,H.DRIGUEZ,R.IORI,S.PALMIERI, REMARK 1 AUTH 2 B.HENRISSAT REMARK 1 TITL THE CRYSTAL STRUCTURES OF SINAPIS ALBA MYROSINASE AND A REMARK 1 TITL 2 COVALENT GLYCOSYL-ENZYME INTERMEDIATE PROVIDE INSIGHTS INTO REMARK 1 TITL 3 THE SUBSTRATE RECOGNITION AND ACTIVE-SITE MACHINERY OF AN REMARK 1 TITL 4 S-GLYCOSIDASE REMARK 1 REF STRUCTURE V. 5 663 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 9195886 REMARK 1 DOI 10.1016/S0969-2126(97)00221-9 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.8 REMARK 3 NUMBER OF REFLECTIONS : 95112 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4838 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 : 338 REMARK 3 SOLVENT ATOMS : 795 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.200 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.021 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.036 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.043 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.029 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.137 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.169 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.312 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.173 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 8.300 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 11.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 26.400; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.400 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.200 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.000 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC INDIVIDUAL B-FACTOR REMARK 3 REFINEMENT REMARK 4 REMARK 4 1E73 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1290005209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-97 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 : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.945 REMARK 200 MONOCHROMATOR : DIAMOND C(111) REMARK 200 OPTICS : BENT MULTILAYER, SAGITALLY REMARK 200 FOCUSING CRYSTAL 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 : 98776 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 34.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.7 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : 0.35200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1E4M REMARK 200 REMARK 200 REMARK: ONLY THE LIGANDS DIFFER 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -158.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, A, B, C 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 135.30000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 120.90000 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 M1515 LIES ON A SPECIAL POSITION. REMARK 375 HOH M2025 LIES ON A SPECIAL POSITION. REMARK 375 HOH M2274 LIES ON A SPECIAL POSITION. REMARK 375 HOH M2299 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ACTIVE SITE NUCLEOPHILE: GLU409 AT THE POSITION OF THE REMARK 400 GENERAL ACID/BASE: GLN187 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 O2 SO4 M 1504 O2 SO4 M 1509 2.14 REMARK 500 O4 NAG C 2 C2 BMA C 3 2.15 REMARK 500 O4 NAG A 1 O5 NAG A 2 2.17 REMARK 500 O6 BMA C 3 C5 MAN C 6 2.19 REMARK 500 O2 BMA C 3 O5 XYP C 4 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU M 409 CD GLU M 409 OE1 0.077 REMARK 500 PRO M 501 CD PRO M 501 N 0.090 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS M 14 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG M 57 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP M 70 CB - CG - OD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 THR M 71 OG1 - CB - CG2 ANGL. DEV. = -15.4 DEGREES REMARK 500 ASP M 74 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP M 87 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG M 95 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG M 109 NH1 - CZ - NH2 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG M 109 NE - CZ - NH2 ANGL. DEV. = -8.9 DEGREES REMARK 500 GLU M 115 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 ASP M 162 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP M 162 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP M 177 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG M 242 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG M 259 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASN M 265 CB - CG - OD1 ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG M 269 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG M 269 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLU M 372 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 TYR M 383 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG M 420 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ASP M 479 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASN M 482 CA - CB - CG ANGL. DEV. = -13.9 DEGREES REMARK 500 ASN M 482 CB - CG - OD1 ANGL. DEV. = 15.4 DEGREES 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 -137.11 43.20 REMARK 500 HIS M 141 57.84 -107.63 REMARK 500 TRP M 142 -11.30 78.97 REMARK 500 TYR M 152 17.25 -144.22 REMARK 500 THR M 184 -76.46 -83.60 REMARK 500 GLN M 187 83.76 36.97 REMARK 500 ASN M 218 102.74 -161.71 REMARK 500 TYR M 385 88.88 -158.39 REMARK 500 ASN M 466 -16.05 72.77 REMARK 500 ASN M 482 86.96 -163.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TRP M 457 -14.60 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 M2002 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH M2016 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH M2033 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH M2045 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH M2079 DISTANCE = 6.27 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 M1515 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS M 56 NE2 REMARK 620 2 HIS M 56 NE2 113.9 REMARK 620 3 ASP M 70 OD2 106.9 116.5 REMARK 620 4 ASP M 70 OD2 117.1 103.8 98.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E4M RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA REMARK 900 RELATED ID: 1E6Q RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA WITH THE BOUND TRANSITION STATE REMARK 900 ANALOGUE GLUCO-TETRAZOLE REMARK 900 RELATED ID: 1E6S RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA WITH BOUND GLUCO-HYDROXIMOLACTAM AND REMARK 900 SULFATE REMARK 900 RELATED ID: 1E6X RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA WITH A BOUND TRANSITION STATE ANALOGUE, REMARK 900 D-GLUCONO-1,5-LACTONE REMARK 900 RELATED ID: 1E70 RELATED DB: PDB REMARK 900 2-F-GLUCOSYLATED MYROSINASE FROM SINAPIS ALBA REMARK 900 RELATED ID: 1E71 RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA WITH BOUND ASCORBATE REMARK 900 RELATED ID: 1E72 RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA WITH BOUND GLUCO-HYDROXIMOLACTAM AND REMARK 900 SULFATE OR ASCORBATE REMARK 900 RELATED ID: 1MYR RELATED DB: PDB REMARK 900 MYROSINASE FROM SINAPIS ALBA REMARK 900 RELATED ID: 2MYR RELATED DB: PDB REMARK 900 MYROSINASE, 2-DEOXY-2-FLUORO-GLUCOSYL ENZYME DBREF 1E73 M 1 501 UNP P29736 MYRA_SINAL 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 1E73 ASN M 21 ASN GLYCOSYLATION SITE MODRES 1E73 ASN M 60 ASN GLYCOSYLATION SITE MODRES 1E73 ASN M 90 ASN GLYCOSYLATION SITE MODRES 1E73 ASN M 218 ASN GLYCOSYLATION SITE MODRES 1E73 ASN M 244 ASN GLYCOSYLATION SITE MODRES 1E73 ASN M 265 ASN GLYCOSYLATION SITE MODRES 1E73 ASN M 292 ASN GLYCOSYLATION SITE MODRES 1E73 ASN M 346 ASN GLYCOSYLATION SITE MODRES 1E73 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 M 901 14 HET NAG M 911 14 HET NAG M 931 14 HET NAG M 961 14 HET NAG M 971 14 HET NAG M 991 14 HET ASC M 995 12 HET G2F M 999 11 HET SO4 M1502 5 HET SO4 M1503 5 HET SO4 M1504 5 HET SO4 M1505 5 HET SO4 M1506 5 HET SO4 M1507 5 HET SO4 M1508 5 HET SO4 M1509 5 HET GOL M1510 6 HET GOL M1511 7 HET GOL M1512 6 HET GOL M1513 6 HET ZN M1515 1 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 ASC ASCORBIC ACID HETNAM G2F 2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM ZN ZINC ION 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 ASC VITAMIN C HETSYN G2F 2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE; 2-DEOXY-2-FLUORO-D- HETSYN 2 G2F GLUCOSE; 2-DEOXY-2-FLUORO-GLUCOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 12(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 11 ASC C6 H8 O6 FORMUL 12 G2F C6 H11 F O5 FORMUL 13 SO4 8(O4 S 2-) FORMUL 21 GOL 4(C3 H8 O3) FORMUL 25 ZN ZN 2+ FORMUL 26 HOH *795(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 TRP M 79 1 6 HELIX 6 6 TYR M 78 ASN M 90 1 13 HELIX 7 7 ALA M 99 ILE M 104 1 6 HELIX 8 8 LYS M 108 GLY M 112 5 5 HELIX 9 9 ASN M 114 LYS M 131 1 18 HELIX 10 10 PRO M 145 GLU M 153 1 9 HELIX 11 11 GLY M 154 PRO M 158 5 5 HELIX 12 12 GLN M 159 GLY M 176 1 18 HELIX 13 13 TYR M 189 GLY M 197 1 9 HELIX 14 14 THR M 221 TYR M 245 1 25 HELIX 15 15 THR M 246 GLY M 249 5 4 HELIX 16 16 ASP M 268 LEU M 283 1 16 HELIX 17 17 LEU M 283 GLY M 293 1 11 HELIX 18 18 PRO M 296 GLY M 304 1 9 HELIX 19 19 GLU M 305 LEU M 307 5 3 HELIX 20 20 SER M 311 LYS M 319 1 9 HELIX 21 21 THR M 348 ALA M 353 5 6 HELIX 22 22 ASP M 377 ASN M 381 5 5 HELIX 23 23 PRO M 386 TYR M 400 1 15 HELIX 24 24 ASN M 419 LEU M 425 1 7 HELIX 25 25 ASP M 426 ASP M 448 1 23 HELIX 26 26 LYS M 489 SER M 500 1 12 SHEET 1 A 7 THR M 134 THR M 138 0 SHEET 2 A 7 GLY M 93 SER M 97 1 N TYR M 94 O THR M 134 SHEET 3 A 7 ILE M 30 ALA M 34 1 N VAL M 33 O GLY M 93 SHEET 4 A 7 VAL M 451 ALA M 456 1 N TYR M 454 O ILE M 30 SHEET 5 A 7 ILE M 405 GLU M 409 1 N ILE M 405 O LYS M 452 SHEET 6 A 7 LEU M 325 TYR M 329 1 N LEU M 325 O TYR M 406 SHEET 7 A 7 THR M 255 THR M 258 1 N MET M 256 O GLY M 326 SHEET 1 B 2 TYR M 181 LEU M 183 0 SHEET 2 B 2 LYS M 251 GLY M 253 1 N LYS M 251 O TRP M 182 SHEET 1 C 3 TRP M 260 PRO M 263 0 SHEET 2 C 3 THR M 332 PRO M 337 1 N GLN M 333 O TRP M 260 SHEET 3 C 3 ALA M 355 THR M 358 -1 N THR M 358 O TYR M 334 SSBOND 1 CYS M 6 CYS M 438 1555 1555 2.19 SSBOND 2 CYS M 14 CYS M 434 1555 1555 2.12 SSBOND 3 CYS M 206 CYS M 214 1555 1555 2.07 LINK ND2 ASN M 21 C1 NAG M 901 1555 1555 1.80 LINK ND2 ASN M 60 C1 NAG M 961 1555 1555 1.49 LINK ND2 ASN M 90 C1 NAG M 911 1555 1555 1.80 LINK ND2 ASN M 218 C1 NAG A 1 1555 1555 1.78 LINK ND2 ASN M 244 C1 NAG M 931 1555 1555 1.79 LINK ND2 ASN M 265 C1 NAG B 1 1555 1555 1.78 LINK ND2 ASN M 292 C1 NAG C 1 1555 1555 1.76 LINK ND2 ASN M 346 C1 NAG M 971 1555 1555 1.51 LINK OE1 GLU M 409 C1 G2F M 999 1555 1555 1.55 LINK ND2 ASN M 482 C1 NAG M 991 1555 1555 1.46 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.35 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.37 LINK O3 NAG B 1 C1 FUC B 5 1555 1555 1.41 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.37 LINK O2 BMA B 3 C1 XYP B 4 1555 1555 1.40 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.38 LINK O3 NAG C 1 C1 FUC C 7 1555 1555 1.42 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.38 LINK O2 BMA C 3 C1 XYP C 4 1555 1555 1.43 LINK O3 BMA C 3 C1 MAN C 5 1555 1555 1.45 LINK O6 BMA C 3 C1 MAN C 6 1555 1555 1.44 LINK NE2 HIS M 56 ZN ZN M1515 3656 1555 2.04 LINK NE2 HIS M 56 ZN ZN M1515 1555 1555 2.09 LINK OD2 ASP M 70 ZN ZN M1515 1555 1555 2.04 LINK OD2 ASP M 70 ZN ZN M1515 3656 1555 2.08 CISPEP 1 LEU M 10 PRO M 11 0 -2.38 CISPEP 2 ALA M 202 PRO M 203 0 6.28 CISPEP 3 TRP M 457 ALA M 458 0 -27.26 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