HEADER LIGASE 04-MAR-14 4CS3 TITLE CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE MUTANT Y306A, TITLE 2 Y384F IN COMPLEX WITH AN ADENYLATED FURAN-BEARING TITLE 3 NONCANONICAL AMINO ACID AND PYROPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL FRAGMENT, RESIDUES 188-454; COMPND 5 SYNONYM: PYRROLYSINE--TRNA(PYL) LIGASE, PYRROLYSYL-TRNA SYNTHETASE, COMPND 6 PYLRS; COMPND 7 EC: 6.1.1.26; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 3 ORGANISM_TAXID: 2209; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TOP10 KEYWDS LIGASE, AMINOACYL-TRNA SYNTHETASE, PYRROLYSYL-TRNA-SYNTHETASE, KEYWDS 2 NONCANONICAL AMINO ACIDS, FURANS, CROSSLINKING REACTIONS EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHMIDT,A.WEBER,M.POTT,W.WELTE,D.SUMMERER REVDAT 2 27-AUG-14 4CS3 1 JRNL REVDAT 1 30-APR-14 4CS3 0 JRNL AUTH M.J.SCHMIDT,A.WEBER,M.POTT,W.WELTE,D.SUMMERER JRNL TITL STRUCTURAL BASIS OF FURAN-AMINO ACID RECOGNITION BY A JRNL TITL 2 POLYSPECIFIC AMINOACYL-TRNA-SYNTHETASE AND ITS GENETIC JRNL TITL 3 ENCODING IN HUMAN CELLS. JRNL REF CHEMBIOCHEM V. 15 1755 2014 JRNL REFN ISSN 1439-4227 JRNL PMID 24737732 JRNL DOI 10.1002/CBIC.201402006 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.SCHMIDT,D.SUMMERER REMARK 1 TITL RED-LIGHT-CONTROLLED PROTEIN-RNA CROSSLINKING WITH A REMARK 1 TITL 2 GENETICALLY ENCODED FURAN. REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 52 4690 2013 REMARK 1 REFN ISSN 1433-7851 REMARK 1 PMID 23512703 REMARK 1 DOI 10.1002/ANIE.201300754 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.499 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.489 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.35 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.40 REMARK 3 NUMBER OF REFLECTIONS : 45472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1565 REMARK 3 R VALUE (WORKING SET) : 0.1550 REMARK 3 FREE R VALUE : 0.1849 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 2300 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 36.4995 - 3.7750 0.99 2765 164 0.1383 0.1665 REMARK 3 2 3.7750 - 2.9967 0.99 2718 135 0.1409 0.1531 REMARK 3 3 2.9967 - 2.6181 0.99 2710 147 0.1488 0.1840 REMARK 3 4 2.6181 - 2.3787 0.99 2727 129 0.1408 0.1920 REMARK 3 5 2.3787 - 2.2083 1.00 2725 139 0.1344 0.1836 REMARK 3 6 2.2083 - 2.0781 1.00 2690 137 0.1376 0.1577 REMARK 3 7 2.0781 - 1.9740 1.00 2698 149 0.1398 0.1818 REMARK 3 8 1.9740 - 1.8881 1.00 2700 142 0.1477 0.1677 REMARK 3 9 1.8881 - 1.8154 1.00 2684 139 0.1718 0.2181 REMARK 3 10 1.8154 - 1.7528 1.00 2718 139 0.1918 0.2037 REMARK 3 11 1.7528 - 1.6980 1.00 2642 166 0.2163 0.2415 REMARK 3 12 1.6980 - 1.6494 1.00 2713 145 0.2256 0.2679 REMARK 3 13 1.6494 - 1.6060 1.00 2692 143 0.2372 0.2666 REMARK 3 14 1.6060 - 1.5668 1.00 2683 143 0.2604 0.3109 REMARK 3 15 1.5668 - 1.5312 1.00 2679 143 0.2925 0.3042 REMARK 3 16 1.5312 - 1.4986 0.98 2628 140 0.3415 0.3853 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) : 0.20 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.00 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 : 0.019 2316 REMARK 3 ANGLE : 1.342 3106 REMARK 3 CHIRALITY : 0.075 332 REMARK 3 PLANARITY : 0.007 398 REMARK 3 DIHEDRAL : 18.106 898 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 189 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.3142 8.0600 50.4138 REMARK 3 T TENSOR REMARK 3 T11: 0.1791 T22: 0.3486 REMARK 3 T33: 0.3080 T12: 0.0559 REMARK 3 T13: 0.0111 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.1603 L22: 0.3152 REMARK 3 L33: 0.0745 L12: 0.0274 REMARK 3 L13: -0.1149 L23: -0.0346 REMARK 3 S TENSOR REMARK 3 S11: -0.1015 S12: 0.1255 S13: -0.2062 REMARK 3 S21: -0.1906 S22: -0.0147 S23: 0.3530 REMARK 3 S31: -0.0041 S32: -0.2087 S33: 0.0032 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 216 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.8697 0.8829 54.1998 REMARK 3 T TENSOR REMARK 3 T11: 0.1971 T22: 0.2946 REMARK 3 T33: 0.2724 T12: 0.0598 REMARK 3 T13: 0.0623 T23: 0.0931 REMARK 3 L TENSOR REMARK 3 L11: 0.3257 L22: 0.0663 REMARK 3 L33: 0.0904 L12: -0.1645 REMARK 3 L13: 0.0546 L23: -0.0589 REMARK 3 S TENSOR REMARK 3 S11: -0.2231 S12: -0.4766 S13: -0.5248 REMARK 3 S21: 0.0957 S22: 0.2156 S23: 0.2660 REMARK 3 S31: 0.0673 S32: -0.0424 S33: 0.0346 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 237 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2743 -4.0856 31.9159 REMARK 3 T TENSOR REMARK 3 T11: 0.2125 T22: 0.1680 REMARK 3 T33: 0.2192 T12: -0.0077 REMARK 3 T13: 0.0140 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: -0.0151 L22: 0.0424 REMARK 3 L33: 0.0953 L12: 0.0144 REMARK 3 L13: 0.0508 L23: 0.0827 REMARK 3 S TENSOR REMARK 3 S11: -0.0685 S12: -0.0266 S13: -0.1853 REMARK 3 S21: 0.0389 S22: -0.0176 S23: 0.0258 REMARK 3 S31: 0.1285 S32: -0.0893 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 257 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.7583 14.4828 18.6232 REMARK 3 T TENSOR REMARK 3 T11: 0.2334 T22: 0.1635 REMARK 3 T33: 0.1938 T12: -0.0117 REMARK 3 T13: -0.0231 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.7735 L22: 0.2015 REMARK 3 L33: 0.7056 L12: 0.1221 REMARK 3 L13: -0.1646 L23: 0.1676 REMARK 3 S TENSOR REMARK 3 S11: -0.0783 S12: 0.1411 S13: 0.0968 REMARK 3 S21: -0.0631 S22: 0.0489 S23: 0.0537 REMARK 3 S31: -0.1633 S32: -0.0474 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESID 330 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1008 5.2532 20.2189 REMARK 3 T TENSOR REMARK 3 T11: 0.2025 T22: 0.2126 REMARK 3 T33: 0.1926 T12: -0.0125 REMARK 3 T13: -0.0101 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.5394 L22: 0.0625 REMARK 3 L33: 0.3476 L12: 0.2509 REMARK 3 L13: 0.1473 L23: 0.0044 REMARK 3 S TENSOR REMARK 3 S11: -0.0445 S12: 0.1075 S13: 0.0389 REMARK 3 S21: 0.0172 S22: 0.0528 S23: 0.0194 REMARK 3 S31: -0.0462 S32: -0.2201 S33: 0.0012 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND (RESID 371 THROUGH 384 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.1421 7.9058 16.7461 REMARK 3 T TENSOR REMARK 3 T11: 0.2751 T22: 0.3407 REMARK 3 T33: 0.3341 T12: -0.0383 REMARK 3 T13: -0.0476 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.0911 L22: 0.0278 REMARK 3 L33: 0.0716 L12: 0.0043 REMARK 3 L13: -0.0264 L23: 0.0380 REMARK 3 S TENSOR REMARK 3 S11: -0.1030 S12: 0.0668 S13: 0.2213 REMARK 3 S21: 0.0285 S22: -0.0433 S23: 0.1033 REMARK 3 S31: -0.1136 S32: -0.0910 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN A AND (RESID 385 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.1368 7.7097 17.9535 REMARK 3 T TENSOR REMARK 3 T11: 0.2020 T22: 0.3463 REMARK 3 T33: 0.2567 T12: -0.0024 REMARK 3 T13: -0.0245 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.0478 L22: 0.1025 REMARK 3 L33: 0.0821 L12: 0.0298 REMARK 3 L13: 0.0435 L23: 0.0967 REMARK 3 S TENSOR REMARK 3 S11: -0.0705 S12: 0.0478 S13: 0.2140 REMARK 3 S21: -0.1106 S22: 0.0304 S23: 0.1597 REMARK 3 S31: -0.0633 S32: -0.2838 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN A AND (RESID 403 THROUGH 416 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3501 13.6051 4.7680 REMARK 3 T TENSOR REMARK 3 T11: 0.3171 T22: 0.3020 REMARK 3 T33: 0.2114 T12: -0.0611 REMARK 3 T13: -0.0218 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 0.0430 L22: 0.0327 REMARK 3 L33: 0.0284 L12: 0.0203 REMARK 3 L13: -0.0051 L23: -0.0294 REMARK 3 S TENSOR REMARK 3 S11: -0.1774 S12: 0.3804 S13: 0.1196 REMARK 3 S21: -0.2302 S22: 0.1007 S23: 0.1059 REMARK 3 S31: -0.0329 S32: -0.0637 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN A AND (RESID 417 THROUGH 458 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.3076 6.8807 37.9208 REMARK 3 T TENSOR REMARK 3 T11: 0.1749 T22: 0.2247 REMARK 3 T33: 0.1991 T12: 0.0185 REMARK 3 T13: 0.0112 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.5029 L22: 0.1647 REMARK 3 L33: 0.2222 L12: -0.0545 REMARK 3 L13: -0.0149 L23: -0.0563 REMARK 3 S TENSOR REMARK 3 S11: -0.0908 S12: -0.0780 S13: -0.0039 REMARK 3 S21: 0.0185 S22: -0.0002 S23: 0.0665 REMARK 3 S31: -0.0541 S32: -0.1721 S33: -0.0000 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 4CS3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAR-14. REMARK 100 THE PDBE ID CODE IS EBI-59665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 2M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45483 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.50 REMARK 200 RESOLUTION RANGE LOW (A) : 36.49 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NONE REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.3 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.12 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.2 REMARK 200 R MERGE FOR SHELL (I) : 0.99 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.19 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL PH 8.5, 200 MM REMARK 280 CALCIUM CHLORIDE, 18 % (W/V) PEG4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.16750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.17250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.16750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.17250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.1 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 BIOMT1 2 -1.000000 0.000000 0.000000 -10.97667 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.21914 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 187 REMARK 465 PRO A 188 REMARK 465 HIS A 459 REMARK 465 HIS A 460 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 OD2 ASP A 389 O HOH A 2195 2.05 REMARK 500 O3 POP A 1462 O HOH A 2208 2.17 REMARK 500 O HOH A 2050 O HOH A 2223 2.16 REMARK 500 O HOH A 2145 O HOH A 2149 2.17 REMARK 500 O HOH A 2149 O HOH A 2151 2.16 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 GLU A 207 69.90 -117.21 REMARK 500 GLU A 237 -82.69 -104.12 REMARK 500 ASP A 292 -146.00 53.36 REMARK 500 ASP A 334 -114.69 60.22 REMARK 500 ASP A 414 25.65 -140.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 AMP-ESTER OF N-EPSILON-[2-(FURAN-2-YL)ETHOXY]CARBONYL REMARK 600 LYSINE: NEW NONCANONICAL AMINO ACID REMARK 600 N-EPSILON-2-FURAN-2-YL ETHOXYCARBONYL LYSINE BOUND TO REMARK 600 ADENOSINE-MONOPHOSPHATE 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 A1463 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 POP A1462 O1 REMARK 620 2 POP A1462 O6 76.1 REMARK 620 3 HOH A2100 O 173.3 98.4 REMARK 620 4 HOH A2101 O 99.8 175.9 85.7 REMARK 620 5 HOH A2140 O 95.2 93.9 81.2 85.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1464 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2202 O REMARK 620 2 GLU A 396 OE1 62.9 REMARK 620 3 GLU A 396 OE2 113.4 50.8 REMARK 620 4 POP A1462 O5 106.6 103.3 95.0 REMARK 620 5 SER A 399 OG 79.0 85.7 89.3 170.8 REMARK 620 6 AMP A1459 O1P 156.8 136.0 85.6 83.8 88.4 REMARK 620 7 HOH A2209 O 75.5 138.2 171.0 83.0 91.5 85.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR LINKED RESIDUES A 1459 TO 1461 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CS2 RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE MUTANT REMARK 900 Y306A, Y384F IN ITS APO FORM REMARK 900 RELATED ID: 4CS4 RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE MUTANT REMARK 900 Y306A, Y384F IN COMPLEX WITH AMPPNP DBREF 4CS3 A 188 454 UNP Q8PWY1 PYLS_METMA 188 454 SEQADV 4CS3 MET A 187 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS3 ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 4CS3 PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION SEQADV 4CS3 HIS A 455 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS3 HIS A 456 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS3 HIS A 457 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS3 HIS A 458 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS3 HIS A 459 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS3 HIS A 460 UNP Q8PWY1 EXPRESSION TAG SEQRES 1 A 274 MET PRO ALA LEU THR LYS SER GLN THR ASP ARG LEU GLU SEQRES 2 A 274 VAL LEU LEU ASN PRO LYS ASP GLU ILE SER LEU ASN SER SEQRES 3 A 274 GLY LYS PRO PHE ARG GLU LEU GLU SER GLU LEU LEU SER SEQRES 4 A 274 ARG ARG LYS LYS ASP LEU GLN GLN ILE TYR ALA GLU GLU SEQRES 5 A 274 ARG GLU ASN TYR LEU GLY LYS LEU GLU ARG GLU ILE THR SEQRES 6 A 274 ARG PHE PHE VAL ASP ARG GLY PHE LEU GLU ILE LYS SER SEQRES 7 A 274 PRO ILE LEU ILE PRO LEU GLU TYR ILE GLU ARG MET GLY SEQRES 8 A 274 ILE ASP ASN ASP THR GLU LEU SER LYS GLN ILE PHE ARG SEQRES 9 A 274 VAL ASP LYS ASN PHE CYS LEU ARG PRO MET LEU ALA PRO SEQRES 10 A 274 ASN LEU ALA ASN TYR LEU ARG LYS LEU ASP ARG ALA LEU SEQRES 11 A 274 PRO ASP PRO ILE LYS ILE PHE GLU ILE GLY PRO CYS TYR SEQRES 12 A 274 ARG LYS GLU SER ASP GLY LYS GLU HIS LEU GLU GLU PHE SEQRES 13 A 274 THR MET LEU ASN PHE CYS GLN MET GLY SER GLY CYS THR SEQRES 14 A 274 ARG GLU ASN LEU GLU SER ILE ILE THR ASP PHE LEU ASN SEQRES 15 A 274 HIS LEU GLY ILE ASP PHE LYS ILE VAL GLY ASP SER CYS SEQRES 16 A 274 MET VAL PHE GLY ASP THR LEU ASP VAL MET HIS GLY ASP SEQRES 17 A 274 LEU GLU LEU SER SER ALA VAL VAL GLY PRO ILE PRO LEU SEQRES 18 A 274 ASP ARG GLU TRP GLY ILE ASP LYS PRO TRP ILE GLY ALA SEQRES 19 A 274 GLY PHE GLY LEU GLU ARG LEU LEU LYS VAL LYS HIS ASP SEQRES 20 A 274 PHE LYS ASN ILE LYS ARG ALA ALA ARG SER GLU SER TYR SEQRES 21 A 274 TYR ASN GLY ILE SER THR ASN LEU HIS HIS HIS HIS HIS SEQRES 22 A 274 HIS HET AMP A1459 35 HET LYS A1460 21 HET FU0 A1461 17 HET POP A1462 9 HET MG A1463 1 HET MG A1464 1 HET EDO A1465 10 HETNAM EDO 1,2-ETHANEDIOL HETNAM FU0 2-(FURAN-2-YL)ETHYL HYDROGEN CARBONATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM LYS LYSINE HETNAM MG MAGNESIUM ION HETNAM POP PYROPHOSPHATE 2- HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 FU0 C7 H8 O4 FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 3 LYS C6 H15 N2 O2 1+ FORMUL 4 MG 2(MG 2+) FORMUL 5 POP H2 O7 P2 2- FORMUL 6 HOH *250(H2 O) HELIX 1 1 THR A 191 LEU A 202 1 12 HELIX 2 2 PRO A 215 GLU A 237 1 23 HELIX 3 3 ASN A 241 ARG A 257 1 17 HELIX 4 4 LEU A 270 MET A 276 1 7 HELIX 5 5 LEU A 284 ILE A 288 5 5 HELIX 6 6 LEU A 301 ASP A 313 1 13 HELIX 7 7 THR A 355 GLY A 371 1 17 HELIX 8 8 ILE A 405 GLY A 412 5 8 HELIX 9 9 LEU A 424 ASP A 433 1 10 HELIX 10 10 ASN A 436 ALA A 441 5 6 SHEET 1 AA 7 LEU A 260 ILE A 262 0 SHEET 2 AA 7 ILE A 320 TYR A 329 1 O LYS A 321 N LEU A 260 SHEET 3 AA 7 GLU A 341 MET A 350 -1 O PHE A 342 N CYS A 328 SHEET 4 AA 7 TRP A 417 GLY A 423 -1 O ILE A 418 N GLN A 349 SHEET 5 AA 7 LEU A 395 VAL A 402 -1 O LEU A 397 N GLY A 423 SHEET 6 AA 7 GLY A 385 HIS A 392 -1 O LEU A 388 N ALA A 400 SHEET 7 AA 7 LYS A 375 CYS A 381 -1 O LYS A 375 N MET A 391 SHEET 1 AB 3 LEU A 267 PRO A 269 0 SHEET 2 AB 3 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268 SHEET 3 AB 3 ARG A 290 VAL A 291 -1 O VAL A 291 N PHE A 295 SHEET 1 AC 2 TYR A 446 TYR A 447 0 SHEET 2 AC 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447 LINK O1P AMP A1459 MG MG A1464 1555 1555 2.28 LINK O3P AMP A1459 C LYS A1460 1555 1555 1.40 LINK NZ LYS A1460 C FU0 A1461 1555 1555 1.40 LINK MG MG A1463 O1 POP A1462 1555 1555 2.36 LINK MG MG A1463 O6 POP A1462 1555 1555 2.18 LINK MG MG A1463 O HOH A2100 1555 1555 2.13 LINK MG MG A1463 O HOH A2101 1555 1555 2.10 LINK MG MG A1463 O HOH A2140 1555 1555 2.06 LINK MG MG A1464 OE1 GLU A 396 1555 1555 2.61 LINK MG MG A1464 OE2 GLU A 396 1555 1555 2.31 LINK MG MG A1464 O5 POP A1462 1555 1555 1.91 LINK MG MG A1464 OG SER A 399 1555 1555 2.29 LINK MG MG A1464 O HOH A2209 1555 1555 2.10 LINK MG MG A1464 O HOH A2202 1555 1555 2.14 CISPEP 1 ASP A 318 PRO A 319 0 -1.88 CISPEP 2 GLY A 403 PRO A 404 0 2.97 SITE 1 AC1 10 ARG A 330 HIS A 338 GLU A 396 ARG A 426 SITE 2 AC1 10 AMP A1459 MG A1463 MG A1464 HOH A2140 SITE 3 AC1 10 HOH A2208 HOH A2209 SITE 1 AC2 4 POP A1462 HOH A2100 HOH A2101 HOH A2140 SITE 1 AC3 7 GLU A 396 SER A 399 AMP A1459 POP A1462 SITE 2 AC3 7 HOH A2202 HOH A2208 HOH A2209 SITE 1 AC4 8 ASN A 241 ARG A 439 ALA A 440 ALA A 441 SITE 2 AC4 8 ASN A 448 GLY A 449 HOH A2049 HOH A2233 SITE 1 AC5 27 MET A 300 ARG A 330 GLU A 332 HIS A 338 SITE 2 AC5 27 LEU A 339 PHE A 342 MET A 344 ASN A 346 SITE 3 AC5 27 PHE A 384 GLU A 396 LEU A 397 SER A 398 SITE 4 AC5 27 SER A 399 ASP A 408 ILE A 413 TRP A 417 SITE 5 AC5 27 GLY A 419 GLY A 421 GLY A 423 ARG A 426 SITE 6 AC5 27 POP A1462 MG A1464 HOH A2117 HOH A2140 SITE 7 AC5 27 HOH A2209 HOH A2220 HOH A2250 CRYST1 102.335 44.345 64.165 90.00 99.85 90.00 C 1 2 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 0.009772 0.000000 0.001697 0.00000 SCALE2 0.000000 0.022550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015818 0.00000