HEADER TRANSFERASE 09-OCT-21 7VMW TITLE CRYSTAL STRUCTURE OF LIMF PRENYLTRANSFERASE BOUND WITH A PEPTIDE TITLE 2 SUBSTRATE AND GSPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYNF/TRUF/PATF FAMILY PEPTIDE O-PRENYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SUBSTRATE PEPTIDE; COMPND 7 CHAIN: C; COMPND 8 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; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 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 7VMW 1 REMARK REVDAT 3 24-AUG-22 7VMW 1 JRNL REVDAT 2 10-AUG-22 7VMW 1 AUTHOR REVDAT 1 03-AUG-22 7VMW 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. 1.93 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 52411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 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 40.2400 - 4.6500 1.00 3736 153 0.1686 0.2183 REMARK 3 2 4.6500 - 3.6900 1.00 3643 141 0.1437 0.1766 REMARK 3 3 3.6900 - 3.2200 1.00 3613 139 0.1584 0.1823 REMARK 3 4 3.2200 - 2.9300 1.00 3640 138 0.1783 0.2488 REMARK 3 5 2.9300 - 2.7200 1.00 3595 139 0.1935 0.2759 REMARK 3 6 2.7200 - 2.5600 1.00 3584 140 0.1896 0.2240 REMARK 3 7 2.5600 - 2.4300 1.00 3586 146 0.1930 0.2690 REMARK 3 8 2.4300 - 2.3300 1.00 3579 151 0.2082 0.2774 REMARK 3 9 2.3300 - 2.2400 1.00 3558 148 0.2108 0.2643 REMARK 3 10 2.2400 - 2.1600 1.00 3615 138 0.2075 0.2551 REMARK 3 11 2.1600 - 2.0900 1.00 3555 137 0.2083 0.2544 REMARK 3 12 2.0900 - 2.0300 1.00 3566 140 0.2286 0.2773 REMARK 3 13 2.0300 - 1.9800 1.00 3571 148 0.2937 0.3775 REMARK 3 14 1.9800 - 1.9300 1.00 3564 148 0.3756 0.4111 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) : 0.285 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.241 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.92 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 5002 REMARK 3 ANGLE : 1.228 6784 REMARK 3 CHIRALITY : 0.074 736 REMARK 3 PLANARITY : 0.011 880 REMARK 3 DIHEDRAL : 11.583 672 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 7 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9139 13.7383 -32.3705 REMARK 3 T TENSOR REMARK 3 T11: 0.1424 T22: 0.1313 REMARK 3 T33: 0.1980 T12: 0.0064 REMARK 3 T13: -0.0078 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 2.1860 L22: 2.6183 REMARK 3 L33: 4.0399 L12: 0.8353 REMARK 3 L13: -1.1960 L23: -0.7063 REMARK 3 S TENSOR REMARK 3 S11: 0.0515 S12: -0.0310 S13: -0.0497 REMARK 3 S21: 0.0414 S22: -0.0179 S23: 0.2650 REMARK 3 S31: -0.0249 S32: -0.1205 S33: -0.0265 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0262 -1.1534 -28.5602 REMARK 3 T TENSOR REMARK 3 T11: 0.2167 T22: 0.1835 REMARK 3 T33: 0.2494 T12: 0.0047 REMARK 3 T13: 0.0262 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 2.9419 L22: 2.2230 REMARK 3 L33: 3.9825 L12: -0.3429 REMARK 3 L13: 0.1326 L23: -0.0843 REMARK 3 S TENSOR REMARK 3 S11: -0.0232 S12: -0.1892 S13: -0.2212 REMARK 3 S21: 0.0381 S22: 0.0522 S23: -0.0389 REMARK 3 S31: 0.1239 S32: 0.2357 S33: -0.0331 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 183 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8224 18.6271 -27.8234 REMARK 3 T TENSOR REMARK 3 T11: 0.2055 T22: 0.2381 REMARK 3 T33: 0.2060 T12: -0.0111 REMARK 3 T13: -0.0086 T23: -0.0576 REMARK 3 L TENSOR REMARK 3 L11: 2.2232 L22: 2.2935 REMARK 3 L33: 1.0732 L12: -0.5928 REMARK 3 L13: -0.1392 L23: 0.0444 REMARK 3 S TENSOR REMARK 3 S11: -0.0916 S12: -0.2915 S13: 0.2946 REMARK 3 S21: 0.2140 S22: 0.1374 S23: -0.2958 REMARK 3 S31: -0.1021 S32: 0.2006 S33: -0.0392 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 7 THROUGH 165 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.1249 16.0120 -62.6136 REMARK 3 T TENSOR REMARK 3 T11: 0.1909 T22: 0.1993 REMARK 3 T33: 0.1588 T12: -0.0126 REMARK 3 T13: 0.0155 T23: -0.0335 REMARK 3 L TENSOR REMARK 3 L11: 1.8966 L22: 2.6746 REMARK 3 L33: 1.7381 L12: -0.7953 REMARK 3 L13: 0.5219 L23: -0.4230 REMARK 3 S TENSOR REMARK 3 S11: 0.1035 S12: 0.1842 S13: -0.0134 REMARK 3 S21: 0.0504 S22: -0.1147 S23: 0.0540 REMARK 3 S31: -0.0669 S32: 0.1013 S33: 0.0250 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 166 THROUGH 225 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0969 10.3462 -80.9988 REMARK 3 T TENSOR REMARK 3 T11: 0.4945 T22: 0.5950 REMARK 3 T33: 0.2973 T12: -0.0502 REMARK 3 T13: -0.0100 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 0.1538 L22: 3.9765 REMARK 3 L33: 6.5391 L12: 0.4845 REMARK 3 L13: 0.2418 L23: 1.3477 REMARK 3 S TENSOR REMARK 3 S11: 0.0300 S12: 0.2582 S13: -0.1220 REMARK 3 S21: -0.9207 S22: 0.0097 S23: 0.0028 REMARK 3 S31: 0.4052 S32: -0.6779 S33: -0.0406 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 226 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.2937 -0.4406 -70.6339 REMARK 3 T TENSOR REMARK 3 T11: 0.3332 T22: 0.3483 REMARK 3 T33: 0.2779 T12: -0.0014 REMARK 3 T13: 0.0052 T23: -0.0542 REMARK 3 L TENSOR REMARK 3 L11: 6.0216 L22: 4.5786 REMARK 3 L33: 4.6362 L12: 0.2730 REMARK 3 L13: -1.2284 L23: 0.2155 REMARK 3 S TENSOR REMARK 3 S11: -0.1448 S12: 0.8743 S13: -0.1976 REMARK 3 S21: -0.6117 S22: 0.0742 S23: -0.2491 REMARK 3 S31: 0.1963 S32: 0.2426 S33: 0.0933 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8236 12.3808 -20.9722 REMARK 3 T TENSOR REMARK 3 T11: 0.5332 T22: 0.7892 REMARK 3 T33: 0.4827 T12: 0.0766 REMARK 3 T13: 0.0115 T23: 0.0345 REMARK 3 L TENSOR REMARK 3 L11: 3.7041 L22: 4.2012 REMARK 3 L33: 4.6184 L12: -3.9383 REMARK 3 L13: 4.1100 L23: -4.3427 REMARK 3 S TENSOR REMARK 3 S11: 0.1949 S12: -1.2678 S13: 0.3920 REMARK 3 S21: 1.3036 S22: 1.1637 S23: 0.8063 REMARK 3 S31: 0.2019 S32: -0.8422 S33: -1.3486 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 7VMW 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_1300024952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-21 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 : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52412 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 40.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 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 (%): 50.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, PCB (NA PROPIONATE, NA REMARK 280 CACODYLATE, BIS-TRIS PROPANE) BUFFER, MAGNESIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.21500 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 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: 500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 ASN B 301 REMARK 465 PRO B 302 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 OD1 ASP B 126 NH1 ARG B 128 2.02 REMARK 500 O HOH A 694 O HOH A 754 2.07 REMARK 500 OE2 GLU B 33 O HOH B 501 2.10 REMARK 500 O HOH A 707 O HOH A 714 2.14 REMARK 500 O HOH A 676 O HOH A 733 2.16 REMARK 500 O HOH A 623 O HOH A 648 2.18 REMARK 500 O HOH A 506 O HOH A 666 2.18 REMARK 500 O HOH A 538 O HOH A 709 2.18 REMARK 500 O HOH B 640 O HOH B 654 2.19 REMARK 500 O GLU B 212 O HOH B 502 2.19 REMARK 500 O PRO A 199 O HOH A 501 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 NH1 ARG A 21 OE2 GLU B 18 2454 2.09 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 LEU A 240 CA - CB - CG ANGL. DEV. = 14.2 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 57.28 -110.51 REMARK 500 GLN A 61 -116.50 50.56 REMARK 500 ASP A 144 63.45 35.28 REMARK 500 PRO B 37 56.66 -108.45 REMARK 500 GLN B 61 -105.03 41.45 REMARK 500 PHE B 196 2.88 -69.61 REMARK 500 ALA B 283 73.17 -108.10 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 O3A 178.4 REMARK 620 3 GST A 402 O2B 89.7 91.7 REMARK 620 4 HOH A 530 O 85.3 93.9 88.8 REMARK 620 5 HOH A 544 O 86.5 92.1 176.2 91.4 REMARK 620 6 HOH A 586 O 89.2 91.6 90.0 174.3 89.4 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 PPV B 402 O11 REMARK 620 2 PPV B 402 OPP 58.0 REMARK 620 3 PPV B 402 O22 89.5 58.2 REMARK 620 4 HOH B 513 O 82.0 54.0 104.0 REMARK 620 5 HOH B 520 O 57.2 90.6 67.0 137.3 REMARK 620 6 HOH B 628 O 110.2 135.5 80.7 167.2 55.5 REMARK 620 N 1 2 3 4 5 DBREF1 7VMW A 1 302 UNP A0A372DCN7_9CYAN DBREF2 7VMW A A0A372DCN7 1 302 DBREF1 7VMW B 1 302 UNP A0A372DCN7_9CYAN DBREF2 7VMW B A0A372DCN7 1 302 DBREF 7VMW C 0 6 PDB 7VMW 7VMW 0 6 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 SEQRES 1 C 7 ACE GLY ALA HIS THR ILE NH2 HET ACE C 0 3 HET NH2 C 6 1 HET MG A 401 1 HET GST A 402 19 HET MG B 401 1 HET PPV B 402 9 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM MG MAGNESIUM ION HETNAM GST GERANYL S-THIOLODIPHOSPHATE HETNAM PPV PYROPHOSPHATE HETSYN GST S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN HETSYN 2 GST THIODIPHOSPHATE FORMUL 3 ACE C2 H4 O FORMUL 3 NH2 H2 N FORMUL 4 MG 2(MG 2+) FORMUL 5 GST C10 H20 O6 P2 S FORMUL 7 PPV H4 O7 P2 FORMUL 8 HOH *423(H2 O) HELIX 1 AA1 ALA A 15 PHE A 30 1 16 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 ASN A 157 1 13 HELIX 8 AA8 THR A 159 MET A 165 1 7 HELIX 9 AA9 LYS A 193 ASN A 197 1 5 HELIX 10 AB1 HIS A 198 LYS A 206 1 9 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 GLU A 278 LYS A 282 1 5 HELIX 17 AB8 PRO B 16 PHE B 30 1 15 HELIX 18 AB9 PRO B 37 THR B 47 1 11 HELIX 19 AC1 HIS B 77 SER B 94 1 18 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 HIS B 198 LEU B 209 1 12 HELIX 26 AC8 SER B 210 LYS B 215 1 6 HELIX 27 AC9 PRO B 216 PRO B 218 5 3 HELIX 28 AD1 ASN B 242 GLU B 244 5 3 HELIX 29 AD2 ASP B 245 PHE B 250 1 6 HELIX 30 AD3 ASN B 253 GLN B 265 1 13 HELIX 31 AD4 SER B 279 ALA B 283 5 5 SHEET 1 AA111 SER A 183 TYR A 188 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 136 O PHE A 177 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 PHE A 297 N CYS A 51 SHEET 8 AA111 MET A 272 SER A 277 -1 N ALA A 275 O ASN A 290 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 224 O TYR A 237 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 138 O PHE B 175 SHEET 4 AA211 VAL B 118 ASP B 126 -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 ILE B 52 O GLN B 72 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 TRP B 273 O TYR B 292 SHEET 9 AA211 VAL B 235 LEU B 240 -1 N LEU B 236 O LEU B 276 SHEET 10 AA211 CYS B 220 ILE B 225 -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 C ACE C 0 N GLY C 1 1555 1555 1.33 LINK C ILE C 5 N NH2 C 6 1555 1555 1.33 LINK OE1 GLU A 186 MG MG A 401 1555 1555 2.09 LINK MG MG A 401 O3A GST A 402 1555 1555 2.05 LINK MG MG A 401 O2B GST A 402 1555 1555 2.06 LINK MG MG A 401 O HOH A 530 1555 1555 2.12 LINK MG MG A 401 O HOH A 544 1555 1555 2.16 LINK MG MG A 401 O HOH A 586 1555 1555 2.10 LINK MG MG B 401 O11 PPV B 402 1555 1555 2.34 LINK MG MG B 401 OPP PPV B 402 1555 1555 2.98 LINK MG MG B 401 O22 PPV B 402 1555 1555 2.32 LINK MG MG B 401 O HOH B 513 1555 1555 2.06 LINK MG MG B 401 O HOH B 520 1555 1555 2.89 LINK MG MG B 401 O HOH B 628 1555 1555 2.67 CISPEP 1 TYR A 36 PRO A 37 0 -1.68 CISPEP 2 TYR B 36 PRO B 37 0 0.54 CRYST1 89.660 48.430 91.040 90.00 117.87 90.00 P 1 21 1 4 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 0.011153 0.000000 0.005898 0.00000 SCALE2 0.000000 0.020648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012425 0.00000