HEADER TRANSFERASE 09-OCT-21 7VMY TITLE CRYSTAL STRUCTURE OF LIMF PRENYLTRANSFERASE BOUND WITH GSPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYNF/TRUF/PATF FAMILY PEPTIDE O-PRENYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LIMNOTHRIX SP. CACIAM 69D; SOURCE 3 ORGANISM_TAXID: 1890733; SOURCE 4 GENE: BJG00_018450; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIPP, PRENYLATION, PRENYLTRANSFERASE, ABBA FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.HAMADA,S.KOBAYASHI,C.OKADA,Y.ZHANG,S.INOUE,Y.GOTO,H.SUGA,K.OGATA, AUTHOR 2 T.SENGOKU REVDAT 4 29-NOV-23 7VMY 1 REMARK REVDAT 3 24-AUG-22 7VMY 1 JRNL REVDAT 2 10-AUG-22 7VMY 1 AUTHOR REVDAT 1 03-AUG-22 7VMY 0 JRNL AUTH Y.ZHANG,K.HAMADA,D.T.NGUYEN,S.INOUE,M.SATAKE,S.KOBAYASHI, JRNL AUTH 2 C.OKADA,K.OGATA,M.OKADA,T.SENGOKU,Y.GOTO,H.SUGA JRNL TITL LIMF IS A VERSATILE PRENYLTRANSFERASE FOR JRNL TITL 2 HISTIDINE-C-GERANYLATION ON DIVERSE NON-NATURAL SUBSTRATES JRNL REF NAT CATAL 2022 JRNL REFN ESSN 2520-1158 JRNL DOI 10.1038/S41929-022-00822-2 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 47469 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.220 REMARK 3 FREE R VALUE TEST SET COUNT : 2005 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 31.5200 - 4.2600 0.99 3305 143 0.1553 0.1720 REMARK 3 2 4.2600 - 3.3800 0.99 3274 147 0.1399 0.1639 REMARK 3 3 3.3800 - 2.9600 0.98 3283 141 0.1629 0.1968 REMARK 3 4 2.9600 - 2.6900 0.98 3290 149 0.1845 0.2376 REMARK 3 5 2.6900 - 2.4900 0.98 3246 149 0.1822 0.2387 REMARK 3 6 2.4900 - 2.3500 0.98 3244 144 0.1815 0.2112 REMARK 3 7 2.3500 - 2.2300 0.98 3267 147 0.1733 0.2650 REMARK 3 8 2.2300 - 2.1300 0.97 3238 140 0.1898 0.2458 REMARK 3 9 2.1300 - 2.0500 0.97 3229 136 0.1869 0.2537 REMARK 3 10 2.0500 - 1.9800 0.97 3209 151 0.1819 0.2407 REMARK 3 11 1.9800 - 1.9200 0.97 3246 138 0.1846 0.2279 REMARK 3 12 1.9200 - 1.8600 0.96 3203 143 0.1984 0.2382 REMARK 3 13 1.8600 - 1.8100 0.96 3186 139 0.2302 0.2788 REMARK 3 14 1.8100 - 1.7700 0.96 3244 138 0.2621 0.3562 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.982 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.11 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 : 0.013 4985 REMARK 3 ANGLE : 1.419 6757 REMARK 3 CHIRALITY : 0.082 727 REMARK 3 PLANARITY : 0.011 875 REMARK 3 DIHEDRAL : 18.979 682 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 9 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0150 68.8657 40.4943 REMARK 3 T TENSOR REMARK 3 T11: 0.1756 T22: 0.1550 REMARK 3 T33: 0.1958 T12: -0.0075 REMARK 3 T13: -0.0265 T23: 0.0279 REMARK 3 L TENSOR REMARK 3 L11: 2.9222 L22: 2.0290 REMARK 3 L33: 3.1428 L12: -0.4355 REMARK 3 L13: -0.7511 L23: 0.5287 REMARK 3 S TENSOR REMARK 3 S11: 0.1284 S12: 0.2529 S13: 0.1292 REMARK 3 S21: -0.2622 S22: 0.0494 S23: 0.1598 REMARK 3 S31: 0.0123 S32: -0.2635 S33: 0.0277 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8980 65.0555 51.5337 REMARK 3 T TENSOR REMARK 3 T11: 0.1198 T22: 0.1694 REMARK 3 T33: 0.1246 T12: -0.0034 REMARK 3 T13: 0.0073 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 3.0422 L22: 2.5157 REMARK 3 L33:2.0743688 L12: -0.3295 REMARK 3 L13: 0.0384 L23: 0.0763 REMARK 3 S TENSOR REMARK 3 S11: 0.0266 S12: -0.2257 S13: 0.1042 REMARK 3 S21: 0.1547 S22: -0.0790 S23: -0.0381 REMARK 3 S31: -0.0671 S32: -0.1408 S33: -0.0067 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.3087 49.6940 55.6809 REMARK 3 T TENSOR REMARK 3 T11: 0.1106 T22: 0.1896 REMARK 3 T33: 0.2020 T12: 0.0162 REMARK 3 T13: 0.0237 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 2.6028 L22: 3.3670 REMARK 3 L33: 2.9151 L12: 0.4330 REMARK 3 L13: 0.0130 L23: 0.5056 REMARK 3 S TENSOR REMARK 3 S11: -0.0458 S12: -0.0506 S13: -0.3306 REMARK 3 S21: 0.0249 S22: -0.0178 S23: 0.1592 REMARK 3 S31: 0.2145 S32: -0.1003 S33: 0.0257 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 242 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8098 51.5161 58.3188 REMARK 3 T TENSOR REMARK 3 T11: 0.1805 T22: 0.2469 REMARK 3 T33: 0.2939 T12: -0.0154 REMARK 3 T13: 0.0453 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 3.0651 L22: 1.2055 REMARK 3 L33: 0.8661 L12: -0.7451 REMARK 3 L13: 0.3800 L23: -0.3699 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: -0.1455 S13: -0.5956 REMARK 3 S21: 0.0687 S22: 0.0884 S23: 0.3441 REMARK 3 S31: 0.0202 S32: -0.1781 S33: -0.1076 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 243 THROUGH 265 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2156 71.5920 54.7499 REMARK 3 T TENSOR REMARK 3 T11: 0.2060 T22: 0.2556 REMARK 3 T33: 0.2073 T12: -0.0111 REMARK 3 T13: 0.0240 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 4.4243 L22: 1.6348 REMARK 3 L33: 1.0893 L12: -0.0340 REMARK 3 L13: 0.2896 L23: -0.6329 REMARK 3 S TENSOR REMARK 3 S11: 0.1232 S12: -0.1599 S13: 0.4741 REMARK 3 S21: -0.0140 S22: -0.0250 S23: 0.1939 REMARK 3 S31: -0.1427 S32: 0.0564 S33: 0.0277 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 266 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4043 63.2416 52.2971 REMARK 3 T TENSOR REMARK 3 T11: 0.1005 T22: 0.2394 REMARK 3 T33: 0.1796 T12: 0.0200 REMARK 3 T13: -0.0069 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 4.0671 L22: 4.4736 REMARK 3 L33: 3.4029 L12: 0.0313 REMARK 3 L13: -0.1357 L23: -0.1219 REMARK 3 S TENSOR REMARK 3 S11: 0.0285 S12: -0.2179 S13: 0.3119 REMARK 3 S21: 0.1428 S22: 0.2157 S23: 0.3392 REMARK 3 S31: 0.1124 S32: -0.3639 S33: -0.1113 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 8 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9955 28.6893 35.4591 REMARK 3 T TENSOR REMARK 3 T11: 0.1499 T22: 0.1089 REMARK 3 T33: 0.1195 T12: -0.0087 REMARK 3 T13: 0.0071 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.9210 L22: 2.1058 REMARK 3 L33: 1.2745 L12: -0.1563 REMARK 3 L13: 0.1058 L23: 0.4788 REMARK 3 S TENSOR REMARK 3 S11: 0.0019 S12: -0.0997 S13: -0.0030 REMARK 3 S21: 0.0472 S22: -0.0143 S23: 0.0231 REMARK 3 S31: -0.0192 S32: -0.0302 S33: 0.0072 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 95 THROUGH 170 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6646 32.0447 25.7281 REMARK 3 T TENSOR REMARK 3 T11: 0.1729 T22: 0.1188 REMARK 3 T33: 0.1881 T12: 0.0096 REMARK 3 T13: 0.0028 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 3.4441 L22: 3.8522 REMARK 3 L33: 2.7804 L12: 1.0107 REMARK 3 L13: 0.3438 L23: 0.2331 REMARK 3 S TENSOR REMARK 3 S11: 0.0421 S12: 0.1016 S13: 0.2431 REMARK 3 S21: -0.0659 S22: -0.0245 S23: -0.4015 REMARK 3 S31: -0.1269 S32: 0.2006 S33: -0.0326 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 171 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0338 46.5857 27.0797 REMARK 3 T TENSOR REMARK 3 T11: 0.1845 T22: 0.1377 REMARK 3 T33: 0.1230 T12: -0.0016 REMARK 3 T13: -0.0040 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 1.2799 L22: 2.6315 REMARK 3 L33: 0.5909 L12: -0.4987 REMARK 3 L13: -0.5036 L23: 0.0482 REMARK 3 S TENSOR REMARK 3 S11: 0.0384 S12: -0.0135 S13: 0.1772 REMARK 3 S21: -0.0221 S22: 0.0264 S23: -0.0982 REMARK 3 S31: -0.1165 S32: -0.0030 S33: -0.0510 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 7VMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024959. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47519 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 31.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5TTY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MG(OAC)2, PEG 3350, BIS-TRIS, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 LYS A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 LYS A 8 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 LYS B 3 REMARK 465 ARG B 4 REMARK 465 LYS B 5 REMARK 465 SER B 6 REMARK 465 SER B 7 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 NH1 ARG B 257 OD1 ASP B 261 1.94 REMARK 500 O HOH A 641 O HOH A 644 2.01 REMARK 500 NH2 ARG B 21 O HOH B 501 2.03 REMARK 500 OD2 ASP A 87 NH2 ARG A 91 2.07 REMARK 500 O HOH B 528 O HOH B 688 2.07 REMARK 500 O HOH B 540 O HOH B 688 2.08 REMARK 500 O HOH B 512 O HOH B 688 2.09 REMARK 500 O HOH B 675 O HOH B 680 2.09 REMARK 500 O HOH A 528 O HOH A 640 2.10 REMARK 500 O HOH B 649 O HOH B 688 2.13 REMARK 500 O HOH B 506 O HOH B 547 2.19 REMARK 500 O HOH A 533 O HOH A 620 2.19 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 600 O HOH B 688 1666 2.13 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 ASP B 126 CB - CG - OD1 ANGL. DEV. = 6.3 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 PRO A 37 50.80 -107.53 REMARK 500 GLN A 61 -122.01 58.35 REMARK 500 PRO A 160 156.95 -45.58 REMARK 500 GLU A 161 -40.78 79.14 REMARK 500 LYS A 282 54.28 -96.28 REMARK 500 PRO B 37 52.79 -106.75 REMARK 500 GLN B 61 -112.55 57.55 REMARK 500 THR B 159 177.60 63.81 REMARK 500 SER B 162 -20.71 94.44 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 186 OE1 REMARK 620 2 GST A 402 O1A 89.3 REMARK 620 3 GST A 402 O3B 179.1 90.9 REMARK 620 4 HOH A 509 O 81.0 88.3 99.9 REMARK 620 5 HOH A 529 O 89.7 93.3 89.4 170.5 REMARK 620 6 HOH A 555 O 91.0 178.9 88.8 92.8 85.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 186 OE1 REMARK 620 2 GST B 402 O2B 175.3 REMARK 620 3 GST B 402 O2A 90.1 94.4 REMARK 620 4 HOH B 527 O 84.1 97.0 90.7 REMARK 620 5 HOH B 554 O 85.1 93.7 91.0 169.0 REMARK 620 6 HOH B 579 O 90.1 85.3 177.6 91.8 86.6 REMARK 620 N 1 2 3 4 5 DBREF1 7VMY A 1 302 UNP A0A372DCN7_9CYAN DBREF2 7VMY A A0A372DCN7 1 302 DBREF1 7VMY B 1 302 UNP A0A372DCN7_9CYAN DBREF2 7VMY B A0A372DCN7 1 302 SEQRES 1 A 302 MET LYS LYS ARG LYS SER SER LYS VAL PHE LYS SER THR SEQRES 2 A 302 ILE ALA PRO GLU GLU LYS LEU ARG TYR ILE GLY ASN HIS SEQRES 3 A 302 LYS GLN ALA PHE ASP ILE GLU PRO LEU TYR PRO LEU ALA SEQRES 4 A 302 LEU PHE GLU GLU PHE VAL ALA THR THR GLY ASP CYS ILE SEQRES 5 A 302 ILE GLU CYS SER GLY LYS ILE LYS GLN ASP GLN LEU TYR SEQRES 6 A 302 PRO ALA ARG ILE ASP LEU GLN PHE SER ASP LYS HIS HIS SEQRES 7 A 302 PHE HIS ASN ILE HIS THR SER ILE ASP PHE LEU LYS ARG SEQRES 8 A 302 ALA ALA SER ARG THR ASP VAL ASN LEU ASN LEU ASP ILE SEQRES 9 A 302 LEU ALA THR PHE LEU ALA GLY ASN PHE ASP TYR SER LYS SEQRES 10 A 302 VAL GLN ASN ILE LEU ALA GLY ILE ASP LEU ARG GLN ASN SEQRES 11 A 302 LEU GLY GLU SER LYS LEU LYS LEU PHE ILE ARG ILE GLY SEQRES 12 A 302 ASP TYR PRO ALA LYS MET ALA VAL ALA LYS HIS LEU CYS SEQRES 13 A 302 ASN ILE THR PRO GLU SER GLU ALA MET LEU ARG SER ASP SEQRES 14 A 302 THR LEU HIS ILE GLY PHE ASP PHE TYR LEU ASP GLY ARG SEQRES 15 A 302 SER ALA ILE GLU LEU TYR PRO GLU LEU LYS LYS ASP GLU SEQRES 16 A 302 PHE ASN HIS PRO PHE ILE TYR ASN GLN LEU LYS THR ILE SEQRES 17 A 302 LEU SER PRO GLU ALA LEU LYS PRO LEU PRO LEU CYS ASN SEQRES 18 A 302 LEU PHE GLY ILE GLY LEU SER PRO ALA ASN GLU ALA ASN SEQRES 19 A 302 VAL LEU TYR TYR HIS LEU GLU ASN ILE GLU ASP PHE LEU SEQRES 20 A 302 SER TYR PHE PRO ILE ASN ASP THR ALA ARG ARG VAL HIS SEQRES 21 A 302 ASP PHE TYR LEU GLN GLN GLU GLY SER ARG ARG MET TRP SEQRES 22 A 302 VAL ALA LEU SER GLU SER GLU MET LYS ALA GLY ARG ILE SEQRES 23 A 302 ASN ASN VAL ASN LEU TYR TYR SER LYS ALA PHE THR SER SEQRES 24 A 302 GLN ASN PRO SEQRES 1 B 302 MET LYS LYS ARG LYS SER SER LYS VAL PHE LYS SER THR SEQRES 2 B 302 ILE ALA PRO GLU GLU LYS LEU ARG TYR ILE GLY ASN HIS SEQRES 3 B 302 LYS GLN ALA PHE ASP ILE GLU PRO LEU TYR PRO LEU ALA SEQRES 4 B 302 LEU PHE GLU GLU PHE VAL ALA THR THR GLY ASP CYS ILE SEQRES 5 B 302 ILE GLU CYS SER GLY LYS ILE LYS GLN ASP GLN LEU TYR SEQRES 6 B 302 PRO ALA ARG ILE ASP LEU GLN PHE SER ASP LYS HIS HIS SEQRES 7 B 302 PHE HIS ASN ILE HIS THR SER ILE ASP PHE LEU LYS ARG SEQRES 8 B 302 ALA ALA SER ARG THR ASP VAL ASN LEU ASN LEU ASP ILE SEQRES 9 B 302 LEU ALA THR PHE LEU ALA GLY ASN PHE ASP TYR SER LYS SEQRES 10 B 302 VAL GLN ASN ILE LEU ALA GLY ILE ASP LEU ARG GLN ASN SEQRES 11 B 302 LEU GLY GLU SER LYS LEU LYS LEU PHE ILE ARG ILE GLY SEQRES 12 B 302 ASP TYR PRO ALA LYS MET ALA VAL ALA LYS HIS LEU CYS SEQRES 13 B 302 ASN ILE THR PRO GLU SER GLU ALA MET LEU ARG SER ASP SEQRES 14 B 302 THR LEU HIS ILE GLY PHE ASP PHE TYR LEU ASP GLY ARG SEQRES 15 B 302 SER ALA ILE GLU LEU TYR PRO GLU LEU LYS LYS ASP GLU SEQRES 16 B 302 PHE ASN HIS PRO PHE ILE TYR ASN GLN LEU LYS THR ILE SEQRES 17 B 302 LEU SER PRO GLU ALA LEU LYS PRO LEU PRO LEU CYS ASN SEQRES 18 B 302 LEU PHE GLY ILE GLY LEU SER PRO ALA ASN GLU ALA ASN SEQRES 19 B 302 VAL LEU TYR TYR HIS LEU GLU ASN ILE GLU ASP PHE LEU SEQRES 20 B 302 SER TYR PHE PRO ILE ASN ASP THR ALA ARG ARG VAL HIS SEQRES 21 B 302 ASP PHE TYR LEU GLN GLN GLU GLY SER ARG ARG MET TRP SEQRES 22 B 302 VAL ALA LEU SER GLU SER GLU MET LYS ALA GLY ARG ILE SEQRES 23 B 302 ASN ASN VAL ASN LEU TYR TYR SER LYS ALA PHE THR SER SEQRES 24 B 302 GLN ASN PRO HET MG A 401 1 HET GST A 402 19 HET BTB A 403 14 HET MG B 401 1 HET GST B 402 19 HET BTB B 403 14 HETNAM MG MAGNESIUM ION HETNAM GST GERANYL S-THIOLODIPHOSPHATE HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETSYN GST S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN HETSYN 2 GST THIODIPHOSPHATE HETSYN BTB BIS-TRIS BUFFER FORMUL 3 MG 2(MG 2+) FORMUL 4 GST 2(C10 H20 O6 P2 S) FORMUL 5 BTB 2(C8 H19 N O5) FORMUL 9 HOH *360(H2 O) HELIX 1 AA1 ALA A 15 ASP A 31 1 17 HELIX 2 AA2 PRO A 37 THR A 47 1 11 HELIX 3 AA3 HIS A 77 ALA A 93 1 17 HELIX 4 AA4 LEU A 102 ALA A 110 1 9 HELIX 5 AA5 ASP A 114 SER A 116 5 3 HELIX 6 AA6 ASN A 130 GLU A 133 5 4 HELIX 7 AA7 TYR A 145 CYS A 156 1 12 HELIX 8 AA8 SER A 162 LEU A 166 5 5 HELIX 9 AA9 LYS A 193 ASN A 197 1 5 HELIX 10 AB1 HIS A 198 LEU A 209 1 12 HELIX 11 AB2 SER A 210 LYS A 215 1 6 HELIX 12 AB3 PRO A 216 PRO A 218 5 3 HELIX 13 AB4 ASN A 242 GLU A 244 5 3 HELIX 14 AB5 ASP A 245 PHE A 250 1 6 HELIX 15 AB6 ASN A 253 LEU A 264 1 12 HELIX 16 AB7 SER A 279 LYS A 282 5 4 HELIX 17 AB8 ALA B 15 PHE B 30 1 16 HELIX 18 AB9 PRO B 37 THR B 48 1 12 HELIX 19 AC1 HIS B 77 ALA B 93 1 17 HELIX 20 AC2 LEU B 102 ALA B 110 1 9 HELIX 21 AC3 ASP B 114 SER B 116 5 3 HELIX 22 AC4 ASN B 130 GLU B 133 5 4 HELIX 23 AC5 TYR B 145 CYS B 156 1 12 HELIX 24 AC6 THR B 159 ALA B 164 1 6 HELIX 25 AC7 LYS B 193 ASN B 197 1 5 HELIX 26 AC8 HIS B 198 LEU B 209 1 12 HELIX 27 AC9 SER B 210 LYS B 215 1 6 HELIX 28 AD1 PRO B 216 PRO B 218 5 3 HELIX 29 AD2 ASN B 242 GLU B 244 5 3 HELIX 30 AD3 ASP B 245 PHE B 250 1 6 HELIX 31 AD4 ASN B 253 LEU B 264 1 12 HELIX 32 AD5 GLU B 278 LYS B 282 1 5 SHEET 1 AA111 SER A 183 LEU A 187 0 SHEET 2 AA111 LEU A 171 TYR A 178 -1 N GLY A 174 O GLU A 186 SHEET 3 AA111 LYS A 135 ILE A 142 -1 N LEU A 138 O PHE A 175 SHEET 4 AA111 VAL A 118 ASP A 126 -1 N GLN A 119 O ARG A 141 SHEET 5 AA111 GLN A 63 PHE A 73 -1 N LEU A 71 O ALA A 123 SHEET 6 AA111 CYS A 51 LYS A 60 -1 N ILE A 52 O GLN A 72 SHEET 7 AA111 ASN A 288 PHE A 297 -1 O VAL A 289 N ILE A 59 SHEET 8 AA111 MET A 272 SER A 277 -1 N TRP A 273 O TYR A 292 SHEET 9 AA111 VAL A 235 LEU A 240 -1 N LEU A 236 O LEU A 276 SHEET 10 AA111 CYS A 220 GLY A 226 -1 N GLY A 226 O VAL A 235 SHEET 11 AA111 GLU A 190 LYS A 192 -1 N LEU A 191 O PHE A 223 SHEET 1 AA211 SER B 183 LEU B 187 0 SHEET 2 AA211 LEU B 171 TYR B 178 -1 N GLY B 174 O GLU B 186 SHEET 3 AA211 LYS B 135 ILE B 142 -1 N LEU B 136 O PHE B 177 SHEET 4 AA211 VAL B 118 LEU B 127 -1 N GLN B 119 O ARG B 141 SHEET 5 AA211 GLN B 63 PHE B 73 -1 N LEU B 71 O ALA B 123 SHEET 6 AA211 CYS B 51 LYS B 60 -1 N LYS B 58 O TYR B 65 SHEET 7 AA211 ASN B 288 PHE B 297 -1 O PHE B 297 N CYS B 51 SHEET 8 AA211 MET B 272 SER B 277 -1 N ALA B 275 O ASN B 290 SHEET 9 AA211 VAL B 235 LEU B 240 -1 N LEU B 236 O LEU B 276 SHEET 10 AA211 CYS B 220 GLY B 226 -1 N GLY B 224 O TYR B 237 SHEET 11 AA211 GLU B 190 LYS B 192 -1 N LEU B 191 O PHE B 223 LINK OE1 GLU A 186 MG MG A 401 1555 1555 2.08 LINK MG MG A 401 O1A GST A 402 1555 1555 2.10 LINK MG MG A 401 O3B GST A 402 1555 1555 2.00 LINK MG MG A 401 O HOH A 509 1555 1555 2.27 LINK MG MG A 401 O HOH A 529 1555 1555 2.08 LINK MG MG A 401 O HOH A 555 1555 1555 2.10 LINK OE1 GLU B 186 MG MG B 401 1555 1555 2.13 LINK MG MG B 401 O2B GST B 402 1555 1555 1.99 LINK MG MG B 401 O2A GST B 402 1555 1555 2.11 LINK MG MG B 401 O HOH B 527 1555 1555 2.21 LINK MG MG B 401 O HOH B 554 1555 1555 2.13 LINK MG MG B 401 O HOH B 579 1555 1555 2.15 CISPEP 1 TYR A 36 PRO A 37 0 1.57 CISPEP 2 TYR B 36 PRO B 37 0 -0.34 CRYST1 47.280 47.520 61.190 100.12 104.69 96.68 P 1 2 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 0.021151 0.002477 0.006219 0.00000 SCALE2 0.000000 0.021188 0.004634 0.00000 SCALE3 0.000000 0.000000 0.017294 0.00000