HEADER LIGASE 04-MAR-14 4CS4 TITLE CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE MUTANT Y306A, TITLE 2 Y384F IN COMPLEX WITH AMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSYL-TRNA SYNTHETASE; 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, PYRROLYSYL-TRNA SYNTHETASE; 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_VARIANT: TOP10 KEYWDS LIGASE, AMINOACYL-TRNA SYNTHETASE, NONCANONICAL AMINO ACIDS EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHMIDT,A.WEBER,M.POTT,W.WELTE,D.SUMMERER REVDAT 3 27-AUG-14 4CS4 1 JRNL REVDAT 2 07-MAY-14 4CS4 1 HETATM REVDAT 1 30-APR-14 4CS4 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 2 REMARK 2 RESOLUTION. 1.35 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) : 1.349 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.100 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.34 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.41 REMARK 3 NUMBER OF REFLECTIONS : 62511 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1497 REMARK 3 R VALUE (WORKING SET) : 0.1483 REMARK 3 FREE R VALUE : 0.1756 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 3163 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 43.1219 - 3.8361 0.99 2671 160 0.1638 0.1699 REMARK 3 2 3.8361 - 3.0451 0.99 2610 134 0.1349 0.1466 REMARK 3 3 3.0451 - 2.6602 1.00 2615 132 0.1266 0.1499 REMARK 3 4 2.6602 - 2.4170 1.00 2612 129 0.1239 0.1761 REMARK 3 5 2.4170 - 2.2438 1.00 2605 129 0.1147 0.1457 REMARK 3 6 2.2438 - 2.1115 0.99 2581 142 0.1106 0.1353 REMARK 3 7 2.1115 - 2.0058 1.00 2579 129 0.1108 0.1321 REMARK 3 8 2.0058 - 1.9185 1.00 2594 140 0.1115 0.1612 REMARK 3 9 1.9185 - 1.8446 1.00 2603 142 0.1234 0.1836 REMARK 3 10 1.8446 - 1.7809 1.00 2569 128 0.1346 0.1580 REMARK 3 11 1.7809 - 1.7253 1.00 2588 163 0.1418 0.1766 REMARK 3 12 1.7253 - 1.6759 1.00 2574 136 0.1495 0.2175 REMARK 3 13 1.6759 - 1.6318 1.00 2549 135 0.1795 0.2209 REMARK 3 14 1.6318 - 1.5920 1.00 2583 138 0.1857 0.2440 REMARK 3 15 1.5920 - 1.5558 1.00 2624 139 0.1962 0.2332 REMARK 3 16 1.5558 - 1.5227 0.99 2554 136 0.2045 0.2442 REMARK 3 17 1.5227 - 1.4922 1.00 2581 139 0.2274 0.2441 REMARK 3 18 1.4922 - 1.4641 1.00 2557 136 0.2514 0.3312 REMARK 3 19 1.4641 - 1.4379 1.00 2565 137 0.2787 0.3313 REMARK 3 20 1.4379 - 1.4136 1.00 2610 138 0.3246 0.3802 REMARK 3 21 1.4136 - 1.3907 0.99 2506 133 0.3335 0.3876 REMARK 3 22 1.3907 - 1.3694 0.99 2560 137 0.3592 0.4168 REMARK 3 23 1.3694 - 1.3492 0.96 2458 131 0.4111 0.4318 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) : 0.22 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.50 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 : 0.022 2369 REMARK 3 ANGLE : 1.338 3146 REMARK 3 CHIRALITY : 0.080 334 REMARK 3 PLANARITY : 0.007 400 REMARK 3 DIHEDRAL : 14.565 915 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4CS4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAR-14. REMARK 100 THE PDBE ID CODE IS EBI-59666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : 62528 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.35 REMARK 200 RESOLUTION RANGE LOW (A) : 43.10 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 : 17.67 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.0 REMARK 200 R MERGE FOR SHELL (I) : 1.42 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.74 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 (%): 47.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 7.5, 10 % REMARK 280 (W/V) PEG 2000 MONOMETHYL ETHER 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 51.03750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.26650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.03750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.26650 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: 7160 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 23800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48 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 -10.79952 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.44644 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 457 REMARK 465 HIS A 458 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 O HOH A 2012 O HOH A 2030 2.07 REMARK 500 O HOH A 2052 O HOH A 2053 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 SER A 209 -67.62 -137.87 REMARK 500 GLU A 237 -100.18 -102.44 REMARK 500 ASP A 292 -161.92 45.20 REMARK 500 ASN A 453 76.90 -101.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 AXZ A 1480 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 A1478 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2104 O REMARK 620 2 SER A 399 OG 76.5 REMARK 620 3 ANP A1457 O2A 155.9 100.1 REMARK 620 4 HOH A2107 O 52.9 83.6 103.2 REMARK 620 5 GLU A 396 OE2 102.9 95.7 101.1 155.4 REMARK 620 6 ANP A1457 O1B 94.8 168.3 84.7 84.9 93.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1479 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A1457 O2G REMARK 620 2 HOH A2121 O 93.8 REMARK 620 3 ANP A1457 O2B 84.8 89.4 REMARK 620 4 HOH A2056 O 172.0 80.0 90.1 REMARK 620 5 HOH A2057 O 93.4 91.3 178.1 91.7 REMARK 620 6 HOH A2074 O 92.4 173.2 93.9 94.1 85.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A1457 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1458 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1459 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1466 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1467 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1468 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1469 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1470 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1471 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1472 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1474 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1475 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1476 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1477 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1478 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1479 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AXZ A1480 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1481 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: 4CS3 RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE MUTANT REMARK 900 Y306A, Y384F IN COMPLEX WITH AN ADENYLATED FURAN- REMARK 900 BEARING NONCANONICAL AMINO ACID AND PYROPHOSPHATE DBREF 4CS4 A 188 454 UNP Q8PWY1 PYLS_METMA 188 454 SEQADV 4CS4 MET A 187 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS4 HIS A 455 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS4 HIS A 456 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS4 HIS A 457 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS4 HIS A 458 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS4 HIS A 459 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS4 HIS A 460 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CS4 ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 4CS4 PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION 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 ANP A1457 44 HET EDO A1458 10 HET EDO A1459 10 HET EDO A1460 10 HET EDO A1461 10 HET EDO A1462 10 HET EDO A1463 10 HET EDO A1464 10 HET EDO A1465 10 HET EDO A1466 10 HET EDO A1467 10 HET EDO A1468 10 HET EDO A1469 10 HET EDO A1470 10 HET EDO A1471 10 HET EDO A1472 10 HET EDO A1473 10 HET EDO A1474 10 HET EDO A1475 10 HET EDO A1476 10 HET EDO A1477 10 HET MG A1478 1 HET MG A1479 1 HET AXZ A1480 30 HET PO4 A1481 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM AXZ 2-{[DIHYDROXY(4-AMINOETHYLPHENYL)-{4}-SULFANYL]AMINO}-3- HETNAM 2 AXZ HYDROXYPROPANOIC ACID HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 20(C2 H6 O2) FORMUL 3 AXZ C11 H18 N2 O5 S FORMUL 4 ANP C10 H17 N6 O12 P3 FORMUL 5 PO4 O4 P 3- FORMUL 6 MG 2(MG 2+) FORMUL 7 HOH *122(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 THR A 282 ILE A 288 5 7 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 O2A ANP A1457 MG MG A1478 1555 1555 2.39 LINK O1B ANP A1457 MG MG A1478 1555 1555 2.43 LINK O2B ANP A1457 MG MG A1479 1555 1555 2.14 LINK O2G ANP A1457 MG MG A1479 1555 1555 2.12 LINK MG MG A1478 O HOH A2104 1555 1555 2.35 LINK MG MG A1478 OG SER A 399 1555 1555 2.19 LINK MG MG A1478 O HOH A2107 1555 1555 2.58 LINK MG MG A1478 OE2 GLU A 396 1555 1555 2.45 LINK MG MG A1479 O HOH A2056 1555 1555 2.17 LINK MG MG A1479 O HOH A2057 1555 1555 2.13 LINK MG MG A1479 O HOH A2074 1555 1555 2.05 LINK MG MG A1479 O HOH A2121 1555 1555 1.99 CISPEP 1 ASP A 318 PRO A 319 0 -6.16 CISPEP 2 GLY A 403 PRO A 404 0 -2.31 SITE 1 AC1 24 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC1 24 PHE A 342 MET A 344 GLU A 396 LEU A 397 SITE 3 AC1 24 SER A 398 SER A 399 GLY A 421 GLY A 423 SITE 4 AC1 24 ARG A 426 EDO A1477 MG A1478 MG A1479 SITE 5 AC1 24 AXZ A1480 HOH A2056 HOH A2057 HOH A2074 SITE 6 AC1 24 HOH A2106 HOH A2109 HOH A2120 HOH A2121 SITE 1 AC2 6 GLU A 247 LYS A 263 THR A 343 ARG A 442 SITE 2 AC2 6 HOH A2032 HOH A2034 SITE 1 AC3 6 TYR A 242 LYS A 245 GLU A 249 LYS A 431 SITE 2 AC3 6 HIS A 432 HOH A2031 SITE 1 AC4 4 ALA A 302 ALA A 306 EDO A1461 EDO A1462 SITE 1 AC5 5 MET A 276 ASP A 408 TRP A 411 ILE A 413 SITE 2 AC5 5 EDO A1460 SITE 1 AC6 2 ASN A 346 EDO A1460 SITE 1 AC7 5 GLU A 274 ILE A 278 ASP A 279 ASN A 280 SITE 2 AC7 5 SER A 285 SITE 1 AC8 4 VAL A 383 PRO A 406 LEU A 407 HOH A2102 SITE 1 AC9 5 MET A 300 LEU A 301 ALA A 302 ASN A 346 SITE 2 AC9 5 AXZ A1480 SITE 1 BC1 4 ASP A 386 THR A 387 VAL A 401 VAL A 402 SITE 1 BC2 8 GLU A 240 LYS A 245 ARG A 248 GLU A 249 SITE 2 BC2 8 ARG A 252 LYS A 293 EDO A1471 HOH A2036 SITE 1 BC3 4 LYS A 429 ASP A 433 PHE A 434 LYS A 435 SITE 1 BC4 4 TYR A 235 GLY A 258 HOH A2072 HOH A2073 SITE 1 BC5 6 GLY A 351 SER A 352 GLY A 353 CYS A 354 SITE 2 BC5 6 PRO A 416 HOH A2085 SITE 1 BC6 5 GLU A 238 LYS A 245 LYS A 293 EDO A1467 SITE 2 BC6 5 HOH A2036 SITE 1 BC7 5 VAL A 200 SER A 445 TYR A 446 SER A 451 SITE 2 BC7 5 ASN A 453 SITE 1 BC8 4 LEU A 339 GLU A 340 GLU A 341 HOH A2080 SITE 1 BC9 5 SER A 221 SER A 225 LYS A 228 PRO A 416 SITE 2 BC9 5 HIS A 456 SITE 1 CC1 8 ARG A 257 PHE A 259 LYS A 321 GLN A 349 SITE 2 CC1 8 ASN A 358 ILE A 362 HOH A2054 HOH A2082 SITE 1 CC2 7 ASN A 241 ARG A 439 ALA A 440 ALA A 441 SITE 2 CC2 7 ASN A 448 GLY A 449 HOH A2115 SITE 1 CC3 4 HIS A 338 ASP A 394 GLU A 396 ANP A1457 SITE 1 CC4 5 GLU A 396 SER A 399 ANP A1457 HOH A2104 SITE 2 CC4 5 HOH A2107 SITE 1 CC5 5 ANP A1457 HOH A2056 HOH A2057 HOH A2074 SITE 2 CC5 5 HOH A2121 SITE 1 CC6 11 ILE A 278 LEU A 284 GLN A 287 ILE A 288 SITE 2 CC6 11 PRO A 299 MET A 300 ARG A 330 CYS A 381 SITE 3 CC6 11 VAL A 383 ANP A1457 EDO A1465 SITE 1 CC7 5 ARG A 310 LYS A 311 ARG A 314 ASN A 453 SITE 2 CC7 5 HIS A 455 CRYST1 102.075 44.533 64.359 90.00 99.66 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 0.009797 0.000000 0.001668 0.00000 SCALE2 0.000000 0.022455 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015761 0.00000