HEADER OXIDOREDUCTASE 01-APR-16 5J55 TITLE THE STRUCTURE AND MECHANISM OF NOV1, A RESVERATROL-CLEAVING TITLE 2 DIOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAROTENOID OXYGENASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOVOSPHINGOBIUM AROMATICIVORANS (STRAIN DSM SOURCE 3 12444 / F199); SOURCE 4 ORGANISM_TAXID: 279238; SOURCE 5 STRAIN: DSM 12444 / F199; SOURCE 6 GENE: SARO_0802; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIOXYGENASE, RESVERATROL, STILBENE, CAROTENOID, BETA-PROPELLER, KEYWDS 2 METALLOPROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.P.MCANDREW,J.H.PEREIRA,N.SATHITSUKSANOH,K.L.SALE,B.A.SIMMONS, AUTHOR 2 P.D.ADAMS REVDAT 4 27-SEP-23 5J55 1 REMARK REVDAT 3 16-MAR-22 5J55 1 HETSYN REVDAT 2 04-JAN-17 5J55 1 JRNL REVDAT 1 30-NOV-16 5J55 0 JRNL AUTH R.P.MCANDREW,N.SATHITSUKSANOH,M.M.MBUGHUNI,R.A.HEINS, JRNL AUTH 2 J.H.PEREIRA,A.GEORGE,K.L.SALE,B.G.FOX,B.A.SIMMONS,P.D.ADAMS JRNL TITL STRUCTURE AND MECHANISM OF NOV1, A RESVERATROL-CLEAVING JRNL TITL 2 DIOXYGENASE. JRNL REF PROC. NATL. ACAD. SCI. V. 113 14324 2016 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 27911781 JRNL DOI 10.1073/PNAS.1608917113 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2276 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 63823 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 49.6085 - 4.2130 1.00 4969 161 0.1400 0.1540 REMARK 3 2 4.2130 - 3.3442 1.00 4803 155 0.1200 0.1450 REMARK 3 3 3.3442 - 2.9215 1.00 4774 154 0.1300 0.1550 REMARK 3 4 2.9215 - 2.6544 1.00 4768 154 0.1400 0.1710 REMARK 3 5 2.6544 - 2.4642 1.00 4733 154 0.1400 0.1870 REMARK 3 6 2.4642 - 2.3189 1.00 4672 151 0.1300 0.1710 REMARK 3 7 2.3189 - 2.2028 1.00 4728 152 0.1400 0.1650 REMARK 3 8 2.2028 - 2.1069 1.00 4713 153 0.1300 0.1560 REMARK 3 9 2.1069 - 2.0258 1.00 4697 151 0.1500 0.1850 REMARK 3 10 2.0258 - 1.9559 0.99 4674 151 0.1500 0.1820 REMARK 3 11 1.9559 - 1.8947 0.95 4459 144 0.1900 0.2050 REMARK 3 12 1.8947 - 1.8406 0.86 3993 129 0.1800 0.1900 REMARK 3 13 1.8406 - 1.7921 0.71 3362 108 0.2000 0.2250 REMARK 3 14 1.7921 - 1.7484 0.53 2480 81 0.2200 0.2720 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.145 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.679 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.46 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 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 : 0.010 3970 REMARK 3 ANGLE : 0.975 5376 REMARK 3 CHIRALITY : 0.060 551 REMARK 3 PLANARITY : 0.007 713 REMARK 3 DIHEDRAL : 14.787 2320 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 148 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.8897 49.5908 58.3381 REMARK 3 T TENSOR REMARK 3 T11: 0.1006 T22: 0.1300 REMARK 3 T33: 0.1353 T12: -0.0031 REMARK 3 T13: 0.0084 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.7493 L22: 1.9701 REMARK 3 L33: 1.8412 L12: -0.0837 REMARK 3 L13: -0.0461 L23: -0.5437 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: -0.0404 S13: 0.0507 REMARK 3 S21: 0.0599 S22: 0.0011 S23: -0.0580 REMARK 3 S31: -0.1283 S32: 0.0043 S33: -0.0156 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 149 THROUGH 190 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.3681 41.2617 43.0086 REMARK 3 T TENSOR REMARK 3 T11: 0.1203 T22: 0.1776 REMARK 3 T33: 0.1831 T12: 0.0218 REMARK 3 T13: 0.0669 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 1.3075 L22: 1.3880 REMARK 3 L33: 2.7537 L12: -0.2141 REMARK 3 L13: 0.8218 L23: -0.4664 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: 0.1476 S13: -0.0521 REMARK 3 S21: -0.2627 S22: -0.0076 S23: -0.2832 REMARK 3 S31: 0.0070 S32: 0.2868 S33: -0.0221 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 191 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5786 38.1115 35.0640 REMARK 3 T TENSOR REMARK 3 T11: 0.1758 T22: 0.1660 REMARK 3 T33: 0.1327 T12: 0.0287 REMARK 3 T13: 0.0382 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 0.9728 L22: 2.0661 REMARK 3 L33: 1.6990 L12: 0.5527 REMARK 3 L13: 0.0930 L23: 0.5311 REMARK 3 S TENSOR REMARK 3 S11: 0.0066 S12: 0.1741 S13: -0.0591 REMARK 3 S21: -0.2823 S22: -0.0129 S23: -0.0911 REMARK 3 S31: -0.1039 S32: 0.1073 S33: 0.0054 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 294 THROUGH 325 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0567 41.2293 40.5524 REMARK 3 T TENSOR REMARK 3 T11: 0.1640 T22: 0.2062 REMARK 3 T33: 0.1830 T12: 0.0559 REMARK 3 T13: -0.0236 T23: -0.0474 REMARK 3 L TENSOR REMARK 3 L11: 1.9044 L22: 7.0086 REMARK 3 L33: 0.5157 L12: -1.7873 REMARK 3 L13: -0.1455 L23: 0.1545 REMARK 3 S TENSOR REMARK 3 S11: 0.1027 S12: 0.0950 S13: 0.0571 REMARK 3 S21: -0.1916 S22: -0.1428 S23: 0.5193 REMARK 3 S31: -0.0962 S32: -0.2330 S33: 0.0435 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 326 THROUGH 373 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7672 26.8434 43.0693 REMARK 3 T TENSOR REMARK 3 T11: 0.1383 T22: 0.0949 REMARK 3 T33: 0.1604 T12: -0.0157 REMARK 3 T13: 0.0057 T23: -0.0208 REMARK 3 L TENSOR REMARK 3 L11: 1.4947 L22: 1.8356 REMARK 3 L33: 4.0958 L12: 0.0841 REMARK 3 L13: -0.0813 L23: 1.3190 REMARK 3 S TENSOR REMARK 3 S11: 0.0449 S12: 0.0061 S13: -0.0865 REMARK 3 S21: -0.0243 S22: -0.1324 S23: 0.1075 REMARK 3 S31: 0.2133 S32: -0.1974 S33: 0.0797 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 374 THROUGH 404 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5865 31.4899 55.7172 REMARK 3 T TENSOR REMARK 3 T11: 0.1375 T22: 0.3095 REMARK 3 T33: 0.1848 T12: -0.0920 REMARK 3 T13: 0.0164 T23: -0.0439 REMARK 3 L TENSOR REMARK 3 L11: 6.2156 L22: 8.3463 REMARK 3 L33: 4.3675 L12: -3.0000 REMARK 3 L13: -1.1894 L23: 2.1891 REMARK 3 S TENSOR REMARK 3 S11: 0.0167 S12: 0.0212 S13: 0.0758 REMARK 3 S21: -0.1256 S22: -0.2549 S23: 0.3440 REMARK 3 S31: 0.0683 S32: -0.7320 S33: 0.1642 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 405 THROUGH 441 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3652 29.6170 61.5405 REMARK 3 T TENSOR REMARK 3 T11: 0.1917 T22: 0.1546 REMARK 3 T33: 0.1430 T12: -0.0609 REMARK 3 T13: 0.0182 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 1.6792 L22: 3.9117 REMARK 3 L33: 2.9652 L12: 0.1638 REMARK 3 L13: -0.1562 L23: 0.8755 REMARK 3 S TENSOR REMARK 3 S11: 0.0756 S12: -0.1433 S13: -0.1827 REMARK 3 S21: 0.3385 S22: -0.1467 S23: -0.0170 REMARK 3 S31: 0.4549 S32: -0.2335 S33: 0.0467 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 442 THROUGH 488 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.3716 35.9654 65.5549 REMARK 3 T TENSOR REMARK 3 T11: 0.1725 T22: 0.1531 REMARK 3 T33: 0.1061 T12: -0.0332 REMARK 3 T13: 0.0182 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.5279 L22: 3.0750 REMARK 3 L33: 2.3228 L12: 0.6167 REMARK 3 L13: -0.0204 L23: -0.0194 REMARK 3 S TENSOR REMARK 3 S11: 0.0398 S12: -0.1421 S13: -0.1120 REMARK 3 S21: 0.3021 S22: -0.0604 S23: 0.1217 REMARK 3 S31: 0.1981 S32: -0.1743 S33: 0.0137 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 5J55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-14 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 : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68233 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.440 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: 5J53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16 M MGCL2, 0.08 M TRIS PH 8.5, 18% REMARK 280 (W/V) PEG 4000, AND 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 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 0.00000 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 46.12300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.56100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.29050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.12300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.56100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.29050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.12300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.56100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.29050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.12300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.56100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.29050 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: 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 A1044 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1091 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1139 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 MET A 1 REMARK 465 ARG A 383 REMARK 465 GLY A 384 REMARK 465 GLY A 385 REMARK 465 SER A 386 REMARK 465 ALA A 387 REMARK 465 GLY A 388 REMARK 465 GLY A 389 REMARK 465 GLU A 489 REMARK 465 LYS A 490 REMARK 465 VAL A 491 REMARK 465 LEU A 492 REMARK 465 ALA A 493 REMARK 465 ALA A 494 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 OH TYR A 101 HAC V55 A 503 1.46 REMARK 500 O HOH A 989 O HOH A 1088 1.80 REMARK 500 O HOH A 1012 O HOH A 1088 2.01 REMARK 500 O HOH A 626 O HOH A 669 2.02 REMARK 500 O HOH A 668 O HOH A 1036 2.03 REMARK 500 O HOH A 975 O HOH A 1048 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 841 O HOH A 841 4566 2.08 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 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -5.8 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 SER A 17 -71.36 -114.44 REMARK 500 ASP A 25 66.09 60.42 REMARK 500 ASP A 46 96.53 -160.11 REMARK 500 PHE A 310 78.78 -119.31 REMARK 500 LEU A 475 -112.40 -107.14 REMARK 500 REMARK 500 REMARK: NULL 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 FE A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 167 NE2 REMARK 620 2 HIS A 218 NE2 93.7 REMARK 620 3 HIS A 284 NE2 105.6 102.0 REMARK 620 4 HIS A 476 NE2 92.0 155.1 99.8 REMARK 620 5 OXY A 502 O1 172.0 87.5 81.8 83.7 REMARK 620 6 OXY A 502 O2 141.3 78.3 113.1 82.2 31.5 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 FE A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OXY A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V55 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5J53 RELATED DB: PDB REMARK 900 5J53 CONTAINS THE APO PROTEIN REMARK 900 RELATED ID: 5J54 RELATED DB: PDB REMARK 900 5J54 CONTAINS THE RESVERATROL-BOUND PROTEIN DBREF 5J55 A 1 494 UNP Q2GA76 Q2GA76_NOVAD 1 494 SEQRES 1 A 494 MET ALA GLN PHE PRO ASN THR PRO SER PHE THR GLY PHE SEQRES 2 A 494 ASN THR PRO SER ARG ILE GLU ALA ASP ILE ALA ASP LEU SEQRES 3 A 494 ALA HIS GLU GLY THR ILE PRO GLN GLY LEU ASN GLY ALA SEQRES 4 A 494 PHE TYR ARG VAL GLN PRO ASP PRO GLN PHE PRO PRO ARG SEQRES 5 A 494 LEU ASP ASP ASP ILE ALA PHE ASN GLY ASP GLY MET ILE SEQRES 6 A 494 THR ARG PHE HIS ILE HIS ASP GLY GLN VAL ASP PHE ARG SEQRES 7 A 494 GLN ARG TRP ALA LYS THR ASP LYS TRP LYS LEU GLU ASN SEQRES 8 A 494 ALA ALA GLY LYS ALA LEU PHE GLY ALA TYR ARG ASN PRO SEQRES 9 A 494 LEU THR ASP ASP GLU ALA VAL LYS GLY GLU ILE ARG SER SEQRES 10 A 494 THR ALA ASN THR ASN ALA PHE VAL PHE GLY GLY LYS LEU SEQRES 11 A 494 TRP ALA MET LYS GLU ASP SER PRO ALA LEU VAL MET ASP SEQRES 12 A 494 PRO ALA THR MET GLU THR PHE GLY PHE GLU LYS PHE GLY SEQRES 13 A 494 GLY LYS MET THR GLY GLN THR PHE THR ALA HIS PRO LYS SEQRES 14 A 494 VAL ASP PRO LYS THR GLY ASN MET VAL ALA ILE GLY TYR SEQRES 15 A 494 ALA ALA SER GLY LEU CYS THR ASP ASP VAL THR TYR MET SEQRES 16 A 494 GLU VAL SER PRO GLU GLY GLU LEU VAL ARG GLU VAL TRP SEQRES 17 A 494 PHE LYS VAL PRO TYR TYR CYS MET MET HIS ASP PHE GLY SEQRES 18 A 494 ILE THR GLU ASP TYR LEU VAL LEU HIS ILE VAL PRO SER SEQRES 19 A 494 ILE GLY SER TRP GLU ARG LEU GLU GLN GLY LYS PRO HIS SEQRES 20 A 494 PHE GLY PHE ASP THR THR MET PRO VAL HIS LEU GLY ILE SEQRES 21 A 494 ILE PRO ARG ARG ASP GLY VAL ARG GLN GLU ASP ILE ARG SEQRES 22 A 494 TRP PHE THR ARG ASP ASN CYS PHE ALA SER HIS VAL LEU SEQRES 23 A 494 ASN ALA TRP GLN GLU GLY THR LYS ILE HIS PHE VAL THR SEQRES 24 A 494 CYS GLU ALA LYS ASN ASN MET PHE PRO PHE PHE PRO ASP SEQRES 25 A 494 VAL HIS GLY ALA PRO PHE ASN GLY MET GLU ALA MET SER SEQRES 26 A 494 HIS PRO THR ASP TRP VAL VAL ASP MET ALA SER ASN GLY SEQRES 27 A 494 GLU ASP PHE ALA GLY ILE VAL LYS LEU SER ASP THR ALA SEQRES 28 A 494 ALA GLU PHE PRO ARG ILE ASP ASP ARG PHE THR GLY GLN SEQRES 29 A 494 LYS THR ARG HIS GLY TRP PHE LEU GLU MET ASP MET LYS SEQRES 30 A 494 ARG PRO VAL GLU LEU ARG GLY GLY SER ALA GLY GLY LEU SEQRES 31 A 494 LEU MET ASN CYS LEU PHE HIS LYS ASP PHE GLU THR GLY SEQRES 32 A 494 ARG GLU GLN HIS TRP TRP CYS GLY PRO VAL SER SER LEU SEQRES 33 A 494 GLN GLU PRO CYS PHE VAL PRO ARG ALA LYS ASP ALA PRO SEQRES 34 A 494 GLU GLY ASP GLY TRP ILE VAL GLN VAL CYS ASN ARG LEU SEQRES 35 A 494 GLU GLU GLN ARG SER ASP LEU LEU ILE PHE ASP ALA LEU SEQRES 36 A 494 ASP ILE GLU LYS GLY PRO VAL ALA THR VAL ASN ILE PRO SEQRES 37 A 494 ILE ARG LEU ARG PHE GLY LEU HIS GLY ASN TRP ALA ASN SEQRES 38 A 494 ALA ASP GLU ILE GLY LEU ALA GLU LYS VAL LEU ALA ALA HET FE A 501 1 HET OXY A 502 2 HET V55 A 503 19 HET PGE A 504 10 HETNAM FE FE (III) ION HETNAM OXY OXYGEN MOLECULE HETNAM V55 4-HYDROXY-3-METHOXYBENZALDEHYDE HETNAM PGE TRIETHYLENE GLYCOL HETSYN V55 P-VANILLIN FORMUL 2 FE FE 3+ FORMUL 3 OXY O2 FORMUL 4 V55 C8 H8 O3 FORMUL 5 PGE C6 H14 O4 FORMUL 6 HOH *542(H2 O) HELIX 1 AA1 THR A 7 THR A 15 5 9 HELIX 2 AA2 ILE A 57 GLY A 61 5 5 HELIX 3 AA3 THR A 84 GLY A 94 1 11 HELIX 4 AA4 ASN A 103 ASP A 107 5 5 HELIX 5 AA5 ASP A 108 LYS A 112 5 5 HELIX 6 AA6 LYS A 154 LYS A 158 5 5 HELIX 7 AA7 SER A 237 GLN A 243 1 7 HELIX 8 AA8 ARG A 268 ILE A 272 5 5 HELIX 9 AA9 GLY A 320 ALA A 323 5 4 HELIX 10 AB1 ASP A 358 THR A 362 5 5 HELIX 11 AB2 ASP A 456 GLY A 460 5 5 HELIX 12 AB3 ASP A 483 ILE A 485 5 3 SHEET 1 AA1 5 ALA A 21 ILE A 23 0 SHEET 2 AA1 5 GLN A 74 TRP A 81 -1 O PHE A 77 N ILE A 23 SHEET 3 AA1 5 GLY A 63 HIS A 71 -1 N ILE A 65 O ARG A 80 SHEET 4 AA1 5 GLY A 38 PRO A 45 -1 N ARG A 42 O THR A 66 SHEET 5 AA1 5 GLY A 477 ASN A 481 -1 O ASN A 478 N TYR A 41 SHEET 1 AA2 5 HIS A 28 GLY A 30 0 SHEET 2 AA2 5 ALA A 463 ILE A 467 -1 O THR A 464 N GLU A 29 SHEET 3 AA2 5 ARG A 446 ASP A 453 -1 N LEU A 449 O VAL A 465 SHEET 4 AA2 5 GLY A 433 ARG A 441 -1 N GLN A 437 O LEU A 450 SHEET 5 AA2 5 SER A 414 LEU A 416 -1 N SER A 415 O ASN A 440 SHEET 1 AA3 5 HIS A 28 GLY A 30 0 SHEET 2 AA3 5 ALA A 463 ILE A 467 -1 O THR A 464 N GLU A 29 SHEET 3 AA3 5 ARG A 446 ASP A 453 -1 N LEU A 449 O VAL A 465 SHEET 4 AA3 5 GLY A 433 ARG A 441 -1 N GLN A 437 O LEU A 450 SHEET 5 AA3 5 CYS A 420 PRO A 423 -1 N VAL A 422 O TRP A 434 SHEET 1 AA4 4 ASN A 122 PHE A 126 0 SHEET 2 AA4 4 LYS A 129 MET A 133 -1 O TRP A 131 N PHE A 124 SHEET 3 AA4 4 LEU A 140 MET A 142 -1 O LEU A 140 N ALA A 132 SHEET 4 AA4 4 THR A 149 PHE A 152 -1 O GLY A 151 N VAL A 141 SHEET 1 AA5 4 LYS A 169 VAL A 170 0 SHEET 2 AA5 4 MET A 177 TYR A 182 -1 O VAL A 178 N LYS A 169 SHEET 3 AA5 4 ASP A 191 VAL A 197 -1 O MET A 195 N ALA A 179 SHEET 4 AA5 4 LEU A 203 LYS A 210 -1 O VAL A 207 N TYR A 194 SHEET 1 AA6 4 GLY A 221 ILE A 222 0 SHEET 2 AA6 4 TYR A 226 ILE A 231 -1 O VAL A 228 N GLY A 221 SHEET 3 AA6 4 VAL A 256 PRO A 262 -1 O GLY A 259 N LEU A 229 SHEET 4 AA6 4 ARG A 273 ARG A 277 -1 O ARG A 273 N ILE A 260 SHEET 1 AA7 2 SER A 234 GLY A 236 0 SHEET 2 AA7 2 PHE A 248 PHE A 250 -1 O GLY A 249 N ILE A 235 SHEET 1 AA8 4 PHE A 281 GLU A 291 0 SHEET 2 AA8 4 LYS A 294 ALA A 302 -1 O ALA A 302 N PHE A 281 SHEET 3 AA8 4 SER A 325 ASP A 333 -1 O TRP A 330 N PHE A 297 SHEET 4 AA8 4 GLY A 343 LYS A 346 -1 O VAL A 345 N ASP A 329 SHEET 1 AA9 4 ALA A 352 ARG A 356 0 SHEET 2 AA9 4 HIS A 368 GLU A 373 -1 O TRP A 370 N ARG A 356 SHEET 3 AA9 4 CYS A 394 ASP A 399 -1 O CYS A 394 N GLU A 373 SHEET 4 AA9 4 GLU A 405 TRP A 409 -1 O GLN A 406 N HIS A 397 LINK NE2 HIS A 167 FE FE A 501 1555 1555 2.12 LINK NE2 HIS A 218 FE FE A 501 1555 1555 2.04 LINK NE2 HIS A 284 FE FE A 501 1555 1555 2.11 LINK NE2 HIS A 476 FE FE A 501 1555 1555 1.98 LINK FE FE A 501 O1 OXY A 502 1555 1555 1.92 LINK FE FE A 501 O2 OXY A 502 1555 1555 2.33 SITE 1 AC1 5 HIS A 167 HIS A 218 HIS A 284 HIS A 476 SITE 2 AC1 5 OXY A 502 SITE 1 AC2 7 THR A 121 HIS A 218 HIS A 284 LEU A 475 SITE 2 AC2 7 HIS A 476 FE A 501 V55 A 503 SITE 1 AC3 8 PHE A 59 TYR A 101 ASN A 120 THR A 121 SITE 2 AC3 8 LYS A 134 HIS A 218 LEU A 475 OXY A 502 SITE 1 AC4 4 VAL A 211 TRP A 274 HOH A 639 HOH A1057 CRYST1 92.246 101.122 144.581 90.00 90.00 90.00 I 2 2 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 0.010841 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009889 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006917 0.00000