3FW9 - Header Asymmetric Unit

HEADER FLAVOPROTEIN 17-JAN-09 3FW9

TITLE STRUCTURE OF BERBERINE BRIDGE ENZYME IN COMPLEX WITH (S)-SCOULERINE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETICULINE OXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BERBERINE BRIDGE-FORMING ENZYME, BBE, COMPND 5 TETRAHYDROPROTOBERBERINE SYNTHASE; COMPND 6 EC: 1.21.3.3; COMPND 7 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHSCHOLZIA CALIFORNICA; SOURCE 3 ORGANISM_COMMON: CALIFORNIA POPPY; SOURCE 4 ORGANISM_TAXID: 3467; SOURCE 5 GENE: BBE1; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: KM71H; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZA

KEYWDS BI-COVALENT FLAVINYLATION, N-GLYCOSYLATION, ALAKLOID BIOSYNTHESIS, KEYWDS 2 OXIDOREDUCTASE, ALKALOID METABOLISM, CYTOPLASMIC VESICLE, FAD, KEYWDS 3 FLAVOPROTEIN, GLYCOPROTEIN

EXPDTA X-RAY DIFFRACTION

AUTHOR A.WINKLER,P.MACHEROUX,K.GRUBER

REVDAT 2 13-JUL-11 3FW9 1 VERSN REVDAT 1 19-MAY-09 3FW9 0

JRNL AUTH A.WINKLER,K.MOTZ,S.RIEDL,M.PUHL,P.MACHEROUX,K.GRUBER JRNL TITL STRUCTURAL ROLES OF BIOCOVALENT FLANINYLATION IN BERBERINE JRNL TITL 2 BRIDGE ENZYME JRNL REF TO BE PUBLISHED JRNL REFN

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.WINKLER,A.LYSKOWSKI,S.RIEDL,M.PUHL,T.M.KUTCHAN, REMARK 1 AUTH 2 P.MACHEROUX,K.GRUBER REMARK 1 TITL A CONCERTED MECHANISM FOR BERBERINE BRIDGE ENZYME. REMARK 1 REF NAT. CHEM. BIOL. V. 4 739 2008 REMARK 1 REFN ISSN 1552-4450

REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 95974 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.9700 - 4.6260 0.99 3418 174 0.1680 0.1680 REMARK 3 2 4.6260 - 3.6720 1.00 3246 185 0.1370 0.1510 REMARK 3 3 3.6720 - 3.2080 1.00 3210 150 0.1580 0.1640 REMARK 3 4 3.2080 - 2.9150 1.00 3168 166 0.1720 0.2030 REMARK 3 5 2.9150 - 2.7060 1.00 3162 157 0.1760 0.1950 REMARK 3 6 2.7060 - 2.5460 1.00 3092 180 0.1720 0.1990 REMARK 3 7 2.5460 - 2.4190 1.00 3143 160 0.1630 0.1880 REMARK 3 8 2.4190 - 2.3140 1.00 3091 172 0.1590 0.2030 REMARK 3 9 2.3140 - 2.2250 1.00 3093 180 0.1570 0.1790 REMARK 3 10 2.2250 - 2.1480 1.00 3067 200 0.1600 0.2040 REMARK 3 11 2.1480 - 2.0810 1.00 3056 197 0.1600 0.1860 REMARK 3 12 2.0810 - 2.0210 1.00 3068 155 0.1650 0.1720 REMARK 3 13 2.0210 - 1.9680 1.00 3119 150 0.1650 0.2010 REMARK 3 14 1.9680 - 1.9200 1.00 3099 166 0.1670 0.2010 REMARK 3 15 1.9200 - 1.8760 1.00 3093 148 0.1690 0.1970 REMARK 3 16 1.8760 - 1.8360 1.00 3085 168 0.1690 0.2010 REMARK 3 17 1.8360 - 1.8000 1.00 3055 158 0.1700 0.1890 REMARK 3 18 1.8000 - 1.7660 1.00 3055 157 0.1730 0.2020 REMARK 3 19 1.7660 - 1.7340 1.00 3078 168 0.1700 0.2060 REMARK 3 20 1.7340 - 1.7050 1.00 3078 138 0.1710 0.2160 REMARK 3 21 1.7050 - 1.6770 1.00 3064 152 0.1730 0.2120 REMARK 3 22 1.6770 - 1.6510 1.00 3080 163 0.1780 0.1950 REMARK 3 23 1.6510 - 1.6270 1.00 3070 146 0.1820 0.2310 REMARK 3 24 1.6270 - 1.6040 1.00 3040 174 0.1900 0.2470 REMARK 3 25 1.6040 - 1.5830 1.00 3061 149 0.1970 0.2190 REMARK 3 26 1.5830 - 1.5620 1.00 3033 153 0.2040 0.2200 REMARK 3 27 1.5620 - 1.5430 1.00 3079 158 0.2090 0.2560 REMARK 3 28 1.5430 - 1.5240 1.00 3018 162 0.2160 0.2410 REMARK 3 29 1.5240 - 1.5060 1.00 3094 152 0.2200 0.2540 REMARK 3 30 1.5060 - 1.4890 0.38 1161 60 0.3090 0.3050 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 64.05 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.55500 REMARK 3 B22 (A**2) : -6.55500 REMARK 3 B33 (A**2) : -10.95600 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.024 4294 REMARK 3 ANGLE : 1.029 5855 REMARK 3 CHIRALITY : 0.067 640 REMARK 3 PLANARITY : 0.005 735 REMARK 3 DIHEDRAL : 18.257 1564 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 26:114) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8983 -2.7810 -33.2379 REMARK 3 T TENSOR REMARK 3 T11: 0.1592 T22: 0.2875 REMARK 3 T33: 0.2561 T12: 0.0291 REMARK 3 T13: 0.0017 T23: -0.0407 REMARK 3 L TENSOR REMARK 3 L11: 0.4936 L22: 0.9610 REMARK 3 L33: 0.8735 L12: -0.1582 REMARK 3 L13: 0.2163 L23: 0.1966 REMARK 3 S TENSOR REMARK 3 S11: 0.0933 S12: 0.2964 S13: -0.1685 REMARK 3 S21: -0.1776 S22: -0.0407 S23: -0.1025 REMARK 3 S31: 0.0670 S32: 0.2360 S33: -0.0521 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 115:244) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3638 7.5324 -13.9017 REMARK 3 T TENSOR REMARK 3 T11: 0.1087 T22: 0.1199 REMARK 3 T33: 0.1992 T12: -0.0081 REMARK 3 T13: 0.0015 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.7983 L22: 0.5054 REMARK 3 L33: 0.7349 L12: 0.0874 REMARK 3 L13: 0.4015 L23: 0.2297 REMARK 3 S TENSOR REMARK 3 S11: 0.0582 S12: 0.0576 S13: -0.0002 REMARK 3 S21: 0.0142 S22: 0.0253 S23: -0.0395 REMARK 3 S31: -0.0037 S32: 0.1047 S33: -0.0719 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 245:349) REMARK 3 ORIGIN FOR THE GROUP (A): -28.0751 -7.3168 4.4395 REMARK 3 T TENSOR REMARK 3 T11: 0.1499 T22: 0.1331 REMARK 3 T33: 0.2389 T12: -0.0134 REMARK 3 T13: -0.0127 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.4822 L22: 0.2218 REMARK 3 L33: 0.5986 L12: 0.4276 REMARK 3 L13: -0.0772 L23: -0.1857 REMARK 3 S TENSOR REMARK 3 S11: 0.0562 S12: -0.2220 S13: -0.0945 REMARK 3 S21: 0.0327 S22: -0.0451 S23: 0.0170 REMARK 3 S31: 0.0803 S32: -0.0003 S33: -0.0118 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 350:460) REMARK 3 ORIGIN FOR THE GROUP (A): -39.1067 -4.0280 -10.2457 REMARK 3 T TENSOR REMARK 3 T11: 0.1263 T22: 0.1512 REMARK 3 T33: 0.2338 T12: -0.0090 REMARK 3 T13: -0.0004 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 1.0264 L22: 0.6537 REMARK 3 L33: 0.4510 L12: 0.4837 REMARK 3 L13: -0.0278 L23: -0.0559 REMARK 3 S TENSOR REMARK 3 S11: 0.0297 S12: 0.0876 S13: -0.0464 REMARK 3 S21: 0.0345 S22: 0.0376 S23: 0.0304 REMARK 3 S31: 0.0228 S32: -0.0630 S33: -0.0600 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 461:520) REMARK 3 ORIGIN FOR THE GROUP (A): -36.7031 12.2810 -27.1826 REMARK 3 T TENSOR REMARK 3 T11: 0.1586 T22: 0.1605 REMARK 3 T33: 0.2496 T12: 0.0430 REMARK 3 T13: 0.0068 T23: 0.0458 REMARK 3 L TENSOR REMARK 3 L11: 0.8689 L22: 0.0938 REMARK 3 L33: 1.2074 L12: -0.3237 REMARK 3 L13: 0.2756 L23: -0.2079 REMARK 3 S TENSOR REMARK 3 S11: 0.0746 S12: 0.1107 S13: 0.1425 REMARK 3 S21: -0.0256 S22: -0.0132 S23: 0.0969 REMARK 3 S31: -0.1972 S32: -0.2270 S33: -0.0772 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 3FW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB051120.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95974 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.489 REMARK 200 RESOLUTION RANGE LOW (A) : 45.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.60000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3D2J REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUMCHLORIDE, 30% PEG-4000, REMARK 280 0.1 M TRIS/HCL, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 298K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 123.58500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.36000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.79250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.36000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 185.37750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.36000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.79250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.36000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 185.37750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 123.58500 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT.

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: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HOH A1017 LIES ON A SPECIAL POSITION.

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 SER A 101 -82.21 -105.77 REMARK 500 TYR A 111 18.93 -146.71 REMARK 500 GLU A 287 -122.27 51.23 REMARK 500 PHE A 313 56.69 -149.17 REMARK 500 PHE A 392 -136.74 -94.79 REMARK 500 ARG A 409 -120.27 -117.09 REMARK 500 HIS A 459 48.63 -107.51 REMARK 500 LEU A 491 -127.29 44.85 REMARK 500 ASP A 505 59.00 -144.59 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 A 562 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH A 566 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 587 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH A 593 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 900 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH A 987 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A 988 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH A1062 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A1075 DISTANCE = 5.22 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 MG A 524 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 45 OD1 REMARK 620 2 ASP A 47 OD1 81.3 REMARK 620 3 HOH A 4 O 85.4 93.0 REMARK 620 4 HOH A 5 O 100.1 175.6 91.3 REMARK 620 5 HOH A 578 O 170.2 89.1 93.0 89.7 REMARK 620 6 HOH A 576 O 92.9 85.0 177.6 90.7 88.4 REMARK 620 N 1 2 3 4 5

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SLX A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 521 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 522 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 524

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D2D RELATED DB: PDB REMARK 900 RELATED ID: 3D2H RELATED DB: PDB REMARK 900 RELATED ID: 3D2J RELATED DB: PDB REMARK 900 RELATED ID: 3FW7 RELATED DB: PDB REMARK 900 RELATED ID: 3FW8 RELATED DB: PDB

DBREF 3FW9 A 26 520 UNP P30986 RETO_ESCCA 26 520

SEQRES 1 A 495 ASP LEU LEU SER CYS LEU THR PHE ASN GLY VAL ARG ASN SEQRES 2 A 495 HIS THR VAL PHE SER ALA ASP SER ASP SER ASP PHE ASN SEQRES 3 A 495 ARG PHE LEU HIS LEU SER ILE GLN ASN PRO LEU PHE GLN SEQRES 4 A 495 ASN SER LEU ILE SER LYS PRO SER ALA ILE ILE LEU PRO SEQRES 5 A 495 GLY SER LYS GLU GLU LEU SER ASN THR ILE ARG CYS ILE SEQRES 6 A 495 ARG LYS GLY SER TRP THR ILE ARG LEU ARG SER GLY GLY SEQRES 7 A 495 HIS SER TYR GLU GLY LEU SER TYR THR SER ASP THR PRO SEQRES 8 A 495 PHE ILE LEU ILE ASP LEU MET ASN LEU ASN ARG VAL SER SEQRES 9 A 495 ILE ASP LEU GLU SER GLU THR ALA TRP VAL GLU SER GLY SEQRES 10 A 495 SER THR LEU GLY GLU LEU TYR TYR ALA ILE THR GLU SER SEQRES 11 A 495 SER SER LYS LEU GLY PHE THR ALA GLY TRP CYS PRO THR SEQRES 12 A 495 VAL GLY THR GLY GLY HIS ILE SER GLY GLY GLY PHE GLY SEQRES 13 A 495 MET MET SER ARG LYS TYR GLY LEU ALA ALA ASP ASN VAL SEQRES 14 A 495 VAL ASP ALA ILE LEU ILE ASP ALA ASN GLY ALA ILE LEU SEQRES 15 A 495 ASP ARG GLN ALA MET GLY GLU ASP VAL PHE TRP ALA ILE SEQRES 16 A 495 ARG GLY GLY GLY GLY GLY VAL TRP GLY ALA ILE TYR ALA SEQRES 17 A 495 TRP LYS ILE LYS LEU LEU PRO VAL PRO GLU LYS VAL THR SEQRES 18 A 495 VAL PHE ARG VAL THR LYS ASN VAL ALA ILE ASP GLU ALA SEQRES 19 A 495 THR SER LEU LEU HIS LYS TRP GLN PHE VAL ALA GLU GLU SEQRES 20 A 495 LEU GLU GLU ASP PHE THR LEU SER VAL LEU GLY GLY ALA SEQRES 21 A 495 ASP GLU LYS GLN VAL TRP LEU THR MET LEU GLY PHE HIS SEQRES 22 A 495 PHE GLY LEU LYS THR VAL ALA LYS SER THR PHE ASP LEU SEQRES 23 A 495 LEU PHE PRO GLU LEU GLY LEU VAL GLU GLU ASP TYR LEU SEQRES 24 A 495 GLU MET SER TRP GLY GLU SER PHE ALA TYR LEU ALA GLY SEQRES 25 A 495 LEU GLU THR VAL SER GLN LEU ASN ASN ARG PHE LEU LYS SEQRES 26 A 495 PHE ASP GLU ARG ALA PHE LYS THR LYS VAL ASP LEU THR SEQRES 27 A 495 LYS GLU PRO LEU PRO SER LYS ALA PHE TYR GLY LEU LEU SEQRES 28 A 495 GLU ARG LEU SER LYS GLU PRO ASN GLY PHE ILE ALA LEU SEQRES 29 A 495 ASN GLY PHE GLY GLY GLN MET SER LYS ILE SER SER ASP SEQRES 30 A 495 PHE THR PRO PHE PRO HIS ARG SER GLY THR ARG LEU MET SEQRES 31 A 495 VAL GLU TYR ILE VAL ALA TRP ASN GLN SER GLU GLN LYS SEQRES 32 A 495 LYS LYS THR GLU PHE LEU ASP TRP LEU GLU LYS VAL TYR SEQRES 33 A 495 GLU PHE MET LYS PRO PHE VAL SER LYS ASN PRO ARG LEU SEQRES 34 A 495 GLY TYR VAL ASN HIS ILE ASP LEU ASP LEU GLY GLY ILE SEQRES 35 A 495 ASP TRP GLY ASN LYS THR VAL VAL ASN ASN ALA ILE GLU SEQRES 36 A 495 ILE SER ARG SER TRP GLY GLU SER TYR PHE LEU SER ASN SEQRES 37 A 495 TYR GLU ARG LEU ILE ARG ALA LYS THR LEU ILE ASP PRO SEQRES 38 A 495 ASN ASN VAL PHE ASN HIS PRO GLN SER ILE PRO PRO MET SEQRES 39 A 495 ALA

MODRES 3FW9 ASN A 38 ASN GLYCOSYLATION SITE MODRES 3FW9 ASN A 471 ASN GLYCOSYLATION SITE

HET FAD A 1 53 HET SLX A 2 24 HET NAG A 521 14 HET NAG A 522 14 HET MAN A 3 11 HET NAG A 523 14 HET MG A 524 1

HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM SLX (13AS)-3,10-DIMETHOXY-5,8,13,13A-TETRAHYDRO-6H- HETNAM 2 SLX ISOQUINO[3,2-A]ISOQUINOLINE-2,9-DIOL HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM MAN ALPHA-D-MANNOSE HETNAM MG MAGNESIUM ION

HETSYN SLX (S)-SCOULERINE

FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 SLX C19 H21 N O4 FORMUL 4 NAG 3(C8 H15 N O6) FORMUL 4 MAN C6 H12 O6 FORMUL 6 MG MG 2+ FORMUL 7 HOH *603(H2 O)

HELIX 1 1 ASP A 26 ASN A 34 1 9 HELIX 2 2 SER A 48 SER A 57 1 10 HELIX 3 3 ASN A 60 GLN A 64 5 5 HELIX 4 4 SER A 79 LYS A 92 1 14 HELIX 5 5 THR A 144 SER A 156 1 13 HELIX 6 6 GLY A 170 GLY A 177 1 8 HELIX 7 7 MET A 183 GLY A 188 1 6 HELIX 8 8 LEU A 189 ASP A 192 5 4 HELIX 9 9 ASP A 208 GLY A 213 1 6 HELIX 10 10 GLY A 213 ARG A 221 1 9 HELIX 11 11 ALA A 255 LEU A 273 1 19 HELIX 12 12 LEU A 301 PHE A 313 1 13 HELIX 13 13 PRO A 314 GLY A 317 5 4 HELIX 14 14 VAL A 319 TYR A 323 5 5 HELIX 15 15 SER A 327 ALA A 336 1 10 HELIX 16 16 THR A 340 ASN A 346 5 7 HELIX 17 17 PRO A 368 GLU A 382 1 15 HELIX 18 18 GLY A 393 LYS A 398 5 6 HELIX 19 19 ASN A 423 LYS A 428 5 6 HELIX 20 20 LYS A 429 LYS A 445 1 17 HELIX 21 21 PRO A 446 VAL A 448 5 3 HELIX 22 22 TYR A 456 ILE A 460 5 5 HELIX 23 23 ASP A 461 GLY A 465 5 5 HELIX 24 24 ASN A 471 ASN A 477 1 7 HELIX 25 25 ASN A 477 LEU A 491 1 15 HELIX 26 26 ASN A 493 ASP A 505 1 13

SHEET 1 A 4 HIS A 39 VAL A 41 0 SHEET 2 A 4 ALA A 73 ILE A 75 -1 O ILE A 74 N THR A 40 SHEET 3 A 4 PHE A 117 ASP A 121 1 O LEU A 119 N ILE A 75 SHEET 4 A 4 THR A 96 ARG A 100 1 N ARG A 98 O ILE A 120 SHEET 1 B 5 VAL A 128 ASP A 131 0 SHEET 2 B 5 THR A 136 GLU A 140 -1 O TRP A 138 N SER A 129 SHEET 3 B 5 ALA A 230 LYS A 237 -1 O TRP A 234 N VAL A 139 SHEET 4 B 5 VAL A 194 ILE A 200 -1 N ILE A 198 O TYR A 232 SHEET 5 B 5 ILE A 206 LEU A 207 -1 O LEU A 207 N LEU A 199 SHEET 1 C 2 LEU A 159 GLY A 160 0 SHEET 2 C 2 LEU A 239 PRO A 240 -1 O LEU A 239 N GLY A 160 SHEET 1 D 7 LEU A 324 MET A 326 0 SHEET 2 D 7 VAL A 245 VAL A 254 -1 N VAL A 245 O MET A 326 SHEET 3 D 7 GLN A 289 HIS A 298 -1 O MET A 294 N VAL A 250 SHEET 4 D 7 PHE A 277 ASP A 286 -1 N LEU A 282 O THR A 293 SHEET 5 D 7 GLY A 385 GLY A 391 -1 O LEU A 389 N VAL A 281 SHEET 6 D 7 LEU A 414 TRP A 422 -1 O MET A 415 N ASN A 390 SHEET 7 D 7 ALA A 355 LEU A 362 -1 N ASP A 361 O VAL A 416

SSBOND 1 CYS A 30 CYS A 89 1555 1555 2.04

LINK ND2 ASN A 38 C1 NAG A 521 1555 1555 1.44 LINK OD1 ASP A 45 MG MG A 524 1555 1555 2.39 LINK OD1 ASP A 47 MG MG A 524 1555 1555 2.12 LINK ND2 ASN A 471 C1 NAG A 523 1555 1555 1.44 LINK O4 NAG A 521 C1 NAG A 522 1555 1555 1.44 LINK O4 NAG A 522 C1 MAN A 3 1555 1555 1.44 LINK MG MG A 524 O HOH A 4 1555 1555 2.22 LINK MG MG A 524 O HOH A 5 1555 1555 2.03 LINK MG MG A 524 O HOH A 578 1555 1555 2.17 LINK MG MG A 524 O HOH A 576 1555 1555 2.00 LINK ND1 HIS A 104 C8M FAD A 1 1555 1555 1.64 LINK SG CYS A 166 C6 FAD A 1 1555 1555 1.79

CISPEP 1 ASN A 451 PRO A 452 0 0.08

SITE 1 AC1 33 HOH A 10 HOH A 17 LEU A 99 ARG A 100 SITE 2 AC1 33 SER A 101 GLY A 102 GLY A 103 HIS A 104 SITE 3 AC1 33 SER A 105 TYR A 106 SER A 110 LEU A 122 SITE 4 AC1 33 SER A 141 GLY A 164 TRP A 165 CYS A 166 SITE 5 AC1 33 VAL A 169 GLY A 170 GLY A 172 GLY A 173 SITE 6 AC1 33 HIS A 174 PHE A 180 GLY A 225 GLY A 226 SITE 7 AC1 33 GLY A 229 ILE A 231 TYR A 456 ASN A 458 SITE 8 AC1 33 HOH A 619 HOH A 624 HOH A 646 HOH A 831 SITE 9 AC1 33 HOH A1083 SITE 1 AC2 9 TYR A 106 TRP A 165 MET A 182 LEU A 282 SITE 2 AC2 9 ASP A 352 PHE A 356 ASN A 390 GLU A 417 SITE 3 AC2 9 HOH A 831 SITE 1 AC3 6 ASN A 38 LEU A 76 ASN A 124 LYS A 428 SITE 2 AC3 6 NAG A 522 HOH A1086 SITE 1 AC4 5 MAN A 3 ARG A 52 LEU A 56 NAG A 521 SITE 2 AC4 5 HOH A1068 SITE 1 AC5 1 NAG A 522 SITE 1 AC6 7 PRO A 314 ASN A 471 VAL A 474 HOH A 612 SITE 2 AC6 7 HOH A 714 HOH A 830 HOH A1053 SITE 1 AC7 6 HOH A 4 HOH A 5 ASP A 45 ASP A 47 SITE 2 AC7 6 HOH A 576 HOH A 578

CRYST1 68.720 68.720 247.170 90.00 90.00 90.00 P 41 21 2 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 0.014552 0.000000 0.000000 0.00000

SCALE2 0.000000 0.014552 0.000000 0.00000

SCALE3 0.000000 0.000000 0.004046 0.00000