HEADER HYDROLASE 16-APR-20 6YPF TITLE NUDIX1 HYDROLASE FROM ROSA X HYBRIDA IN COMPLEX WITH GERANYL TITLE 2 PYROPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GERANYL DIPHOSPHATE PHOSPHOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUDIX HYDROLASE 1,RHNUDX1; COMPND 5 EC: 3.6.1.68; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROSA HYBRID CULTIVAR; SOURCE 3 ORGANISM_TAXID: 128735; SOURCE 4 ORGAN: PETALS; SOURCE 5 GENE: NUDIX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS NUDIX HYDROLASE, ROSE SCENT, SESQUITERPENES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DEGUT,S.RETY,C.TISNE,S.BAUDINO REVDAT 4 24-JAN-24 6YPF 1 REMARK REVDAT 3 16-DEC-20 6YPF 1 JRNL REVDAT 2 29-JUL-20 6YPF 1 JRNL REVDAT 1 22-JUL-20 6YPF 0 JRNL AUTH P.SUN,C.DEGUT,S.RETY,J.C.CAISSARD,L.HIBRAND-SAINT OYANT, JRNL AUTH 2 A.BONY,S.N.PARAMITA,C.CONART,J.L.MAGNARD,J.JEAUFFRE, JRNL AUTH 3 A.M.ABD-EL-HALIEM,J.MARIE-MAGDELAINE,T.THOUROUDE, JRNL AUTH 4 R.BALTENWECK,C.TISNE,F.FOUCHER,M.HARING,P.HUGUENEY, JRNL AUTH 5 R.C.SCHUURINK,S.BAUDINO JRNL TITL FUNCTIONAL DIVERSIFICATION IN THE NUDIX HYDROLASE GENE JRNL TITL 2 FAMILY DRIVES SESQUITERPENE BIOSYNTHESIS IN ROSA × JRNL TITL 3 WICHURANA. JRNL REF PLANT J. V. 104 185 2020 JRNL REFN ESSN 1365-313X JRNL PMID 32639596 JRNL DOI 10.1111/TPJ.14916 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 26594 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.550 REMARK 3 FREE R VALUE TEST SET COUNT : 2007 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 42.6800 - 3.5000 0.99 1900 147 0.1827 0.1933 REMARK 3 2 3.4900 - 2.7700 0.99 1810 149 0.1835 0.1914 REMARK 3 3 2.7700 - 2.4200 1.00 1787 145 0.1947 0.2117 REMARK 3 4 2.4200 - 2.2000 1.00 1780 144 0.1942 0.2172 REMARK 3 5 2.2000 - 2.0400 1.00 1736 145 0.2010 0.2012 REMARK 3 6 2.0400 - 1.9200 1.00 1764 140 0.2222 0.2206 REMARK 3 7 1.9200 - 1.8300 1.00 1747 146 0.2288 0.2590 REMARK 3 8 1.8300 - 1.7500 1.00 1730 146 0.2490 0.2533 REMARK 3 9 1.7500 - 1.6800 1.00 1751 145 0.2702 0.2844 REMARK 3 10 1.6800 - 1.6200 0.99 1723 140 0.2610 0.2763 REMARK 3 11 1.6200 - 1.5700 1.00 1744 140 0.2887 0.2879 REMARK 3 12 1.5700 - 1.5300 1.00 1720 140 0.3041 0.3339 REMARK 3 13 1.5300 - 1.4900 0.99 1723 143 0.3369 0.3839 REMARK 3 14 1.4900 - 1.4500 0.98 1672 137 0.3756 0.4003 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.198 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.67 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 : 0.012 1102 REMARK 3 ANGLE : 1.014 1501 REMARK 3 CHIRALITY : 0.087 158 REMARK 3 PLANARITY : 0.007 197 REMARK 3 DIHEDRAL : 16.781 157 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 13 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.0694 12.6598 3.8521 REMARK 3 T TENSOR REMARK 3 T11: 0.3571 T22: 0.2052 REMARK 3 T33: 0.2519 T12: -0.0197 REMARK 3 T13: -0.0825 T23: 0.0258 REMARK 3 L TENSOR REMARK 3 L11: 4.1567 L22: 4.8583 REMARK 3 L33: 7.2833 L12: 4.4111 REMARK 3 L13: 4.6493 L23: 4.4938 REMARK 3 S TENSOR REMARK 3 S11: 0.0745 S12: -0.0300 S13: -0.4053 REMARK 3 S21: -0.2915 S22: 0.0700 S23: 0.0639 REMARK 3 S31: 0.7436 S32: -0.2287 S33: -0.1330 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 24 THROUGH 46 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6403 11.5770 8.4849 REMARK 3 T TENSOR REMARK 3 T11: 0.3383 T22: 0.3739 REMARK 3 T33: 0.2268 T12: 0.1352 REMARK 3 T13: 0.0473 T23: 0.1206 REMARK 3 L TENSOR REMARK 3 L11: 5.2134 L22: 8.4706 REMARK 3 L33: 4.1072 L12: -0.2422 REMARK 3 L13: 0.3893 L23: -0.2323 REMARK 3 S TENSOR REMARK 3 S11: 0.1571 S12: 0.0679 S13: -0.3298 REMARK 3 S21: -0.9754 S22: -0.5042 S23: -0.5920 REMARK 3 S31: 0.5044 S32: 0.6861 S33: 0.2997 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 47 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.6477 14.0155 14.1016 REMARK 3 T TENSOR REMARK 3 T11: 0.1844 T22: 0.1201 REMARK 3 T33: 0.1473 T12: 0.0176 REMARK 3 T13: -0.0152 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 6.0817 L22: 1.8220 REMARK 3 L33: 4.3940 L12: -1.3972 REMARK 3 L13: 2.2317 L23: -2.0300 REMARK 3 S TENSOR REMARK 3 S11: 0.0906 S12: -0.1529 S13: -0.0828 REMARK 3 S21: 0.0200 S22: 0.0423 S23: 0.0415 REMARK 3 S31: 0.3034 S32: -0.1040 S33: -0.1484 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.4628 17.0814 8.1046 REMARK 3 T TENSOR REMARK 3 T11: 0.1730 T22: 0.1416 REMARK 3 T33: 0.1773 T12: 0.0212 REMARK 3 T13: -0.0241 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 2.5241 L22: 1.1902 REMARK 3 L33: 5.7731 L12: -0.7217 REMARK 3 L13: 2.3437 L23: -1.3461 REMARK 3 S TENSOR REMARK 3 S11: 0.1176 S12: 0.0415 S13: -0.0344 REMARK 3 S21: -0.0328 S22: -0.0732 S23: 0.0461 REMARK 3 S31: 0.2032 S32: 0.2740 S33: -0.0364 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 112 THROUGH 124 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.7890 6.3709 13.7125 REMARK 3 T TENSOR REMARK 3 T11: 0.2164 T22: 0.2752 REMARK 3 T33: 0.2818 T12: 0.1260 REMARK 3 T13: 0.0024 T23: 0.0680 REMARK 3 L TENSOR REMARK 3 L11: 1.7294 L22: 5.4263 REMARK 3 L33: 3.3514 L12: 2.9741 REMARK 3 L13: -0.9098 L23: -2.1111 REMARK 3 S TENSOR REMARK 3 S11: -0.0023 S12: 0.2710 S13: 0.0887 REMARK 3 S21: -0.4815 S22: -0.0517 S23: -0.1074 REMARK 3 S31: 0.6050 S32: 0.1859 S33: 0.0873 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 125 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.8407 15.4853 2.9221 REMARK 3 T TENSOR REMARK 3 T11: 0.3234 T22: 0.7626 REMARK 3 T33: 0.5989 T12: 0.1697 REMARK 3 T13: 0.1029 T23: 0.1481 REMARK 3 L TENSOR REMARK 3 L11: 4.6821 L22: 5.3971 REMARK 3 L33: 3.5366 L12: 1.2811 REMARK 3 L13: -0.2617 L23: 0.3982 REMARK 3 S TENSOR REMARK 3 S11: -0.0152 S12: 1.2653 S13: 0.6372 REMARK 3 S21: -0.5829 S22: 0.0412 S23: -0.9526 REMARK 3 S31: 0.2570 S32: 1.5922 S33: -0.1019 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 135 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.1227 19.1379 -1.0958 REMARK 3 T TENSOR REMARK 3 T11: 0.3443 T22: 0.5644 REMARK 3 T33: 0.3313 T12: 0.0091 REMARK 3 T13: -0.0269 T23: 0.0893 REMARK 3 L TENSOR REMARK 3 L11: 4.8462 L22: 6.0653 REMARK 3 L33: 5.9841 L12: -0.4722 REMARK 3 L13: -0.7334 L23: 0.8341 REMARK 3 S TENSOR REMARK 3 S11: 0.1482 S12: 0.1128 S13: -0.2922 REMARK 3 S21: -0.2113 S22: -0.3696 S23: 0.0363 REMARK 3 S31: -0.3430 S32: 0.7122 S33: 0.1950 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 6YPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 1.14.12 REMARK 200 DATA SCALING SOFTWARE : DIALS 1.14.12 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26639 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 104.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05642 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.05642 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 4KYX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM SULFATE, 100 MM SODIUM REMARK 280 ACETATE , 25% PEG400, 5MM GPP (SOAKING 1S), PH 4.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.76200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 69.52400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 69.52400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.76200 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 TOTAL BURIED SURFACE AREA: 650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL 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 A 375 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 GLY A 2 REMARK 465 ASN A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 VAL A 6 REMARK 465 VAL A 7 REMARK 465 VAL A 8 REMARK 465 ALA A 9 REMARK 465 GLU A 10 REMARK 465 THR A 11 REMARK 465 ALA A 12 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 LEU A 86 REMARK 465 ASP A 87 REMARK 465 GLU A 88 REMARK 465 ALA A 89 REMARK 465 LYS A 90 REMARK 465 PRO A 91 REMARK 465 THR A 150 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 HZ1 LYS A 65 OD1 ASP A 143 2565 1.33 REMARK 500 O HOH A 373 O HOH A 401 6445 1.99 REMARK 500 O HOH A 366 O HOH A 378 6555 2.03 REMARK 500 O HOH A 315 O HOH A 387 6455 2.09 REMARK 500 NZ LYS A 65 OD1 ASP A 143 2565 2.14 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 ASN A 128 57.28 -155.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GPP A 201 DBREF 6YPF A 1 150 UNP M4I1C6 NUDT1_ROSHC 1 150 SEQRES 1 A 150 MET GLY ASN GLU THR VAL VAL VAL ALA GLU THR ALA GLY SEQRES 2 A 150 SER ILE LYS VAL ALA VAL VAL VAL CYS LEU LEU ARG GLY SEQRES 3 A 150 GLN ASN VAL LEU LEU GLY ARG ARG ARG SER SER LEU GLY SEQRES 4 A 150 ASP SER THR PHE SER LEU PRO SER GLY HIS LEU GLU PHE SEQRES 5 A 150 GLY GLU SER PHE GLU GLU CYS ALA ALA ARG GLU LEU LYS SEQRES 6 A 150 GLU GLU THR ASP LEU ASP ILE GLY LYS ILE GLU LEU LEU SEQRES 7 A 150 THR VAL THR ASN ASN LEU PHE LEU ASP GLU ALA LYS PRO SEQRES 8 A 150 SER GLN TYR VAL ALA VAL PHE MET ARG ALA VAL LEU ALA SEQRES 9 A 150 ASP PRO ARG GLN GLU PRO GLN ASN ILE GLU PRO GLU PHE SEQRES 10 A 150 CYS ASP GLY TRP GLY TRP TYR GLU TRP ASP ASN LEU PRO SEQRES 11 A 150 LYS PRO LEU PHE TRP PRO LEU ASP ASN VAL VAL GLN ASP SEQRES 12 A 150 GLY PHE ASN PRO PHE PRO THR HET GPP A 201 36 HETNAM GPP GERANYL DIPHOSPHATE FORMUL 2 GPP C10 H20 O7 P2 FORMUL 3 HOH *109(H2 O) HELIX 1 AA1 SER A 55 ASP A 69 1 15 HELIX 2 AA2 ASP A 127 LEU A 129 5 3 HELIX 3 AA3 PHE A 134 ASP A 143 1 10 SHEET 1 AA1 5 PHE A 43 SER A 44 0 SHEET 2 AA1 5 ASN A 28 ARG A 34 -1 N GLY A 32 O SER A 44 SHEET 3 AA1 5 ILE A 15 ARG A 25 -1 N ARG A 25 O ASN A 28 SHEET 4 AA1 5 GLN A 93 LEU A 103 1 O MET A 99 N CYS A 22 SHEET 5 AA1 5 ILE A 72 ASN A 83 -1 N GLY A 73 O VAL A 102 SHEET 1 AA2 4 SER A 47 HIS A 49 0 SHEET 2 AA2 4 ILE A 15 ARG A 25 -1 N VAL A 19 O GLY A 48 SHEET 3 AA2 4 ASN A 28 ARG A 34 -1 O ASN A 28 N ARG A 25 SHEET 4 AA2 4 CYS A 118 GLU A 125 -1 O TYR A 124 N VAL A 29 CISPEP 1 LYS A 131 PRO A 132 0 0.37 SITE 1 AC1 9 VAL A 20 ARG A 34 SER A 47 HIS A 49 SITE 2 AC1 9 TYR A 94 PHE A 98 PHE A 134 PRO A 136 SITE 3 AC1 9 HOH A 301 CRYST1 49.287 49.287 104.286 90.00 90.00 120.00 P 31 2 1 6 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 0.020289 0.011714 0.000000 0.00000 SCALE2 0.000000 0.023428 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009589 0.00000