HEADER TRANSFERASE 15-MAY-26 30XM TITLE ENGINEERED PYRROLYSYL-TRNA SYNTHETASE (PYLRS) FROM METHANOSARCINA TITLE 2 BARKERI (MB) IN COMPLEX WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSINE--TRNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYRROLYSINE--TRNA(PYL) LIGASE,PYRROLYSYL-TRNA SYNTHETASE, COMPND 5 PYLRS; COMPND 6 EC: 6.1.1.26; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA BARKERI; SOURCE 3 ORGANISM_TAXID: 2208; SOURCE 4 GENE: PYLS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETDUET-1 KEYWDS GENETIC CODE EXPANSION, SUBSTRATE RECOGNITION SPECIFICITY, BINDING KEYWDS 2 POCKET PLASTICITY, CATALYSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.WANKA,D.KVASHA,M.CIGLER,K.HEYMES-KRAUSKOPF,P.RUCKGABER,A.HEIDER, AUTHOR 2 M.FOTTNER,M.GROLL,K.LANG REVDAT 1 26-AUG-26 30XM 0 JRNL AUTH V.WANKA,D.KVASHA,M.CIGLER,K.HEYMES-KRAUSKOPF,P.RUCKGABER, JRNL AUTH 2 A.HEIDER,M.FOTTNER,M.GROLL,K.LANG JRNL TITL A GENETICALLY ENCODED ELECTROPHILIC LYSINE DERIVATIVE JRNL TITL 2 ENABLES SORTASE-MEDIATED ASSEMBLY OF SUMO ACTIVITY-BASED JRNL TITL 3 PROBES JRNL REF J.AM.CHEM.SOC. 2026 JRNL REFN ESSN 1520-5126 JRNL DOI 10.1021/JACS.6C10081 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 80923 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4259 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6032 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 317 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4155 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 301 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.09000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : 0.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.38000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.407 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4299 ; 0.003 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5801 ; 0.986 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 505 ; 6.257 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 248 ;27.820 ;21.371 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 796 ;11.570 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;13.081 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 541 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3228 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2038 ; 2.202 ; 2.909 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2537 ; 2.883 ; 4.362 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2261 ; 2.579 ; 3.172 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6468 ; 4.385 ;39.838 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4299 ; 1.313 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 30XM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1292157299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85191 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.77600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 10% ISOPROPANOL, PH 6.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 31.61000 REMARK 290 SMTRY3 2 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: 7800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A 153 REMARK 465 LYS A 172 REMARK 465 ILE A 173 REMARK 465 SER A 174 REMARK 465 LEU A 175 REMARK 465 ASN A 176 REMARK 465 MET A 177 REMARK 465 ALA A 178 REMARK 465 SER B 153 REMARK 465 SER B 154 REMARK 465 ASP B 171 REMARK 465 LYS B 172 REMARK 465 ILE B 173 REMARK 465 SER B 174 REMARK 465 LEU B 175 REMARK 465 ASN B 176 REMARK 465 ASN B 245 REMARK 465 ASP B 246 REMARK 465 THR B 247 REMARK 465 SER B 298 REMARK 465 ASP B 299 REMARK 465 GLY B 300 REMARK 465 LYS B 301 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 ASP A 203 -83.11 -128.36 REMARK 500 ARG A 204 -4.27 83.18 REMARK 500 ASP A 257 -145.79 52.24 REMARK 500 CYS A 319 64.38 -101.61 REMARK 500 ASP A 379 39.59 -146.20 REMARK 500 PRO B 169 72.82 -64.59 REMARK 500 ASP B 203 -86.54 -129.67 REMARK 500 ARG B 204 -0.93 85.34 REMARK 500 ASP B 257 -140.61 58.19 REMARK 500 CYS B 319 55.39 -109.99 REMARK 500 MET B 347 35.47 -90.55 REMARK 500 VAL B 348 -49.05 -133.23 REMARK 500 ASP B 379 31.36 -145.88 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 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 361 OE2 REMARK 620 2 ATP A 501 O1G 88.0 REMARK 620 3 ATP A 501 O2B 94.3 87.0 REMARK 620 4 HOH A 620 O 78.7 159.5 78.6 REMARK 620 5 HOH A 707 O 169.2 101.6 81.4 90.7 REMARK 620 6 HOH A 734 O 91.5 91.9 174.0 103.9 93.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 361 OE1 REMARK 620 2 SER A 364 OG 86.6 REMARK 620 3 ATP A 501 O2B 88.8 175.4 REMARK 620 4 ATP A 501 O1A 93.5 88.8 90.8 REMARK 620 5 HOH A 620 O 93.8 92.2 88.8 172.7 REMARK 620 6 HOH A 716 O 176.7 90.1 94.5 85.9 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 406 O REMARK 620 2 SER A 408 O 105.9 REMARK 620 3 TYR A 411 O 154.6 77.5 REMARK 620 4 HOH A 631 O 79.8 135.3 80.6 REMARK 620 5 HOH B 620 O 104.8 60.9 98.8 162.0 REMARK 620 6 HOH B 675 O 83.4 129.5 114.3 95.1 68.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 501 O3G REMARK 620 2 ATP A 501 O1B 86.8 REMARK 620 3 HOH A 604 O 94.2 91.6 REMARK 620 4 HOH A 612 O 95.5 176.1 85.1 REMARK 620 5 HOH A 662 O 168.0 81.9 90.2 96.0 REMARK 620 6 HOH A 678 O 84.7 90.1 177.9 93.2 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 630 O REMARK 620 2 SER B 406 O 102.7 REMARK 620 3 SER B 408 O 63.1 102.8 REMARK 620 4 TYR B 411 O 103.7 150.8 78.3 REMARK 620 5 HOH B 654 O 163.2 78.1 133.4 80.3 REMARK 620 6 HOH B 679 O 70.0 84.6 133.0 116.3 93.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 361 OE2 REMARK 620 2 ATP B 501 O1G 91.3 REMARK 620 3 ATP B 501 O2B 94.5 87.1 REMARK 620 4 HOH B 608 O 69.8 157.9 83.3 REMARK 620 5 HOH B 706 O 88.9 94.5 176.2 96.3 REMARK 620 6 HOH B 712 O 163.9 102.4 94.5 98.1 81.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 361 OE1 REMARK 620 2 SER B 364 OG 86.5 REMARK 620 3 ATP B 501 O2B 89.3 174.7 REMARK 620 4 ATP B 501 O1A 95.3 89.6 94.0 REMARK 620 5 HOH B 608 O 90.0 90.9 85.9 174.7 REMARK 620 6 HOH B 682 O 171.9 89.6 94.1 91.7 83.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B 501 O3G REMARK 620 2 ATP B 501 O1B 94.3 REMARK 620 3 HOH B 613 O 92.9 94.3 REMARK 620 4 HOH B 632 O 89.8 175.9 85.8 REMARK 620 5 HOH B 674 O 175.6 88.1 90.6 87.8 REMARK 620 6 HOH B 691 O 86.6 88.8 176.8 91.0 89.8 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q7G RELATED DB: PDB REMARK 900 PYRROLYSINE TRNA SYNTHETASE BOUND TO A PYRROLYSINE ANALOGUE (CYC) REMARK 900 AND ATP DBREF 30XM A 154 419 UNP Q6WRH6 PYLS_METBA 154 419 DBREF 30XM B 154 419 UNP Q6WRH6 PYLS_METBA 154 419 SEQADV 30XM SER A 153 UNP Q6WRH6 EXPRESSION TAG SEQADV 30XM ALA A 271 UNP Q6WRH6 TYR 271 CONFLICT SEQADV 30XM GLN A 311 UNP Q6WRH6 ASN 311 CONFLICT SEQADV 30XM SER A 313 UNP Q6WRH6 CYS 313 CONFLICT SEQADV 30XM TRP A 349 UNP Q6WRH6 TYR 349 CONFLICT SEQADV 30XM SER B 153 UNP Q6WRH6 EXPRESSION TAG SEQADV 30XM ALA B 271 UNP Q6WRH6 TYR 271 CONFLICT SEQADV 30XM GLN B 311 UNP Q6WRH6 ASN 311 CONFLICT SEQADV 30XM SER B 313 UNP Q6WRH6 CYS 313 CONFLICT SEQADV 30XM TRP B 349 UNP Q6WRH6 TYR 349 CONFLICT SEQRES 1 A 267 SER SER LEU THR ARG SER GLN LEU ASP ARG VAL GLU ALA SEQRES 2 A 267 LEU LEU SER PRO GLU ASP LYS ILE SER LEU ASN MET ALA SEQRES 3 A 267 LYS PRO PHE ARG GLU LEU GLU PRO GLU LEU VAL THR ARG SEQRES 4 A 267 ARG LYS ASN ASP PHE GLN ARG LEU TYR THR ASN ASP ARG SEQRES 5 A 267 GLU ASP TYR LEU GLY LYS LEU GLU ARG ASP ILE THR LYS SEQRES 6 A 267 PHE PHE VAL ASP ARG GLY PHE LEU GLU ILE LYS SER PRO SEQRES 7 A 267 ILE LEU ILE PRO ALA GLU TYR VAL GLU ARG MET GLY ILE SEQRES 8 A 267 ASN ASN ASP THR GLU LEU SER LYS GLN ILE PHE ARG VAL SEQRES 9 A 267 ASP LYS ASN LEU CYS LEU ARG PRO MET LEU ALA PRO THR SEQRES 10 A 267 LEU ALA ASN TYR LEU ARG LYS LEU ASP ARG ILE LEU PRO SEQRES 11 A 267 GLY PRO ILE LYS ILE PHE GLU VAL GLY PRO CYS TYR ARG SEQRES 12 A 267 LYS GLU SER ASP GLY LYS GLU HIS LEU GLU GLU PHE THR SEQRES 13 A 267 MET VAL GLN PHE SER GLN MET GLY SER GLY CYS THR ARG SEQRES 14 A 267 GLU ASN LEU GLU ALA LEU ILE LYS GLU PHE LEU ASP TYR SEQRES 15 A 267 LEU GLU ILE ASP PHE GLU ILE VAL GLY ASP SER CYS MET SEQRES 16 A 267 VAL TRP GLY ASP THR LEU ASP ILE MET HIS GLY ASP LEU SEQRES 17 A 267 GLU LEU SER SER ALA VAL VAL GLY PRO VAL SER LEU ASP SEQRES 18 A 267 ARG GLU TRP GLY ILE ASP LYS PRO TRP ILE GLY ALA GLY SEQRES 19 A 267 PHE GLY LEU GLU ARG LEU LEU LYS VAL MET HIS GLY PHE SEQRES 20 A 267 LYS ASN ILE LYS ARG ALA SER ARG SER GLU SER TYR TYR SEQRES 21 A 267 ASN GLY ILE SER THR ASN LEU SEQRES 1 B 267 SER SER LEU THR ARG SER GLN LEU ASP ARG VAL GLU ALA SEQRES 2 B 267 LEU LEU SER PRO GLU ASP LYS ILE SER LEU ASN MET ALA SEQRES 3 B 267 LYS PRO PHE ARG GLU LEU GLU PRO GLU LEU VAL THR ARG SEQRES 4 B 267 ARG LYS ASN ASP PHE GLN ARG LEU TYR THR ASN ASP ARG SEQRES 5 B 267 GLU ASP TYR LEU GLY LYS LEU GLU ARG ASP ILE THR LYS SEQRES 6 B 267 PHE PHE VAL ASP ARG GLY PHE LEU GLU ILE LYS SER PRO SEQRES 7 B 267 ILE LEU ILE PRO ALA GLU TYR VAL GLU ARG MET GLY ILE SEQRES 8 B 267 ASN ASN ASP THR GLU LEU SER LYS GLN ILE PHE ARG VAL SEQRES 9 B 267 ASP LYS ASN LEU CYS LEU ARG PRO MET LEU ALA PRO THR SEQRES 10 B 267 LEU ALA ASN TYR LEU ARG LYS LEU ASP ARG ILE LEU PRO SEQRES 11 B 267 GLY PRO ILE LYS ILE PHE GLU VAL GLY PRO CYS TYR ARG SEQRES 12 B 267 LYS GLU SER ASP GLY LYS GLU HIS LEU GLU GLU PHE THR SEQRES 13 B 267 MET VAL GLN PHE SER GLN MET GLY SER GLY CYS THR ARG SEQRES 14 B 267 GLU ASN LEU GLU ALA LEU ILE LYS GLU PHE LEU ASP TYR SEQRES 15 B 267 LEU GLU ILE ASP PHE GLU ILE VAL GLY ASP SER CYS MET SEQRES 16 B 267 VAL TRP GLY ASP THR LEU ASP ILE MET HIS GLY ASP LEU SEQRES 17 B 267 GLU LEU SER SER ALA VAL VAL GLY PRO VAL SER LEU ASP SEQRES 18 B 267 ARG GLU TRP GLY ILE ASP LYS PRO TRP ILE GLY ALA GLY SEQRES 19 B 267 PHE GLY LEU GLU ARG LEU LEU LYS VAL MET HIS GLY PHE SEQRES 20 B 267 LYS ASN ILE LYS ARG ALA SER ARG SER GLU SER TYR TYR SEQRES 21 B 267 ASN GLY ILE SER THR ASN LEU HET ATP A 501 31 HET MG A 502 1 HET MG A 503 1 HET MG A 504 1 HET NA A 505 1 HET ATP B 501 31 HET MG B 502 1 HET MG B 503 1 HET MG B 504 1 HET NA B 505 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 3 ATP 2(C10 H16 N5 O13 P3) FORMUL 4 MG 6(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 13 HOH *301(H2 O) HELIX 1 AA1 THR A 156 LEU A 167 1 12 HELIX 2 AA2 PRO A 180 ASP A 203 1 24 HELIX 3 AA3 ASP A 206 ASP A 221 1 16 HELIX 4 AA4 ALA A 235 MET A 241 1 7 HELIX 5 AA5 GLY A 242 ASP A 246 5 5 HELIX 6 AA6 GLU A 248 GLN A 252 5 5 HELIX 7 AA7 LEU A 266 ASP A 278 1 13 HELIX 8 AA8 THR A 320 GLU A 336 1 17 HELIX 9 AA9 VAL A 370 GLY A 377 5 8 HELIX 10 AB1 LEU A 389 GLY A 398 1 10 HELIX 11 AB2 ASN A 401 SER A 406 5 6 HELIX 12 AB3 THR B 156 LEU B 167 1 12 HELIX 13 AB4 PRO B 180 ASP B 203 1 24 HELIX 14 AB5 ASP B 206 ASP B 221 1 16 HELIX 15 AB6 ALA B 235 MET B 241 1 7 HELIX 16 AB7 LEU B 249 ILE B 253 5 5 HELIX 17 AB8 LEU B 266 ASP B 278 1 13 HELIX 18 AB9 THR B 320 GLU B 336 1 17 HELIX 19 AC1 VAL B 370 GLY B 377 5 8 HELIX 20 AC2 LEU B 389 GLY B 398 1 10 HELIX 21 AC3 ASN B 401 SER B 406 5 6 SHEET 1 AA1 7 LEU A 225 GLU A 226 0 SHEET 2 AA1 7 ILE A 285 TYR A 294 1 O LYS A 286 N LEU A 225 SHEET 3 AA1 7 GLU A 306 MET A 315 -1 O MET A 315 N ILE A 285 SHEET 4 AA1 7 TRP A 382 GLY A 388 -1 O PHE A 387 N VAL A 310 SHEET 5 AA1 7 LEU A 360 VAL A 367 -1 N VAL A 366 O GLY A 384 SHEET 6 AA1 7 GLY A 350 HIS A 357 -1 N ILE A 355 O LEU A 362 SHEET 7 AA1 7 GLU A 340 CYS A 346 -1 N GLU A 340 O MET A 356 SHEET 1 AA2 3 LEU A 232 PRO A 234 0 SHEET 2 AA2 3 LEU A 260 LEU A 262 -1 O CYS A 261 N ILE A 233 SHEET 3 AA2 3 ARG A 255 VAL A 256 -1 N VAL A 256 O LEU A 260 SHEET 1 AA3 2 TYR A 411 TYR A 412 0 SHEET 2 AA3 2 ILE A 415 SER A 416 -1 O ILE A 415 N TYR A 412 SHEET 1 AA4 7 LEU B 225 GLU B 226 0 SHEET 2 AA4 7 ILE B 285 TYR B 294 1 O LYS B 286 N LEU B 225 SHEET 3 AA4 7 GLU B 306 MET B 315 -1 O SER B 313 N ILE B 287 SHEET 4 AA4 7 TRP B 382 GLY B 388 -1 O PHE B 387 N VAL B 310 SHEET 5 AA4 7 LEU B 360 VAL B 367 -1 N VAL B 366 O GLY B 384 SHEET 6 AA4 7 GLY B 350 HIS B 357 -1 N ILE B 355 O LEU B 362 SHEET 7 AA4 7 GLU B 340 CYS B 346 -1 N VAL B 342 O ASP B 354 SHEET 1 AA5 3 LEU B 232 PRO B 234 0 SHEET 2 AA5 3 LEU B 260 LEU B 262 -1 O CYS B 261 N ILE B 233 SHEET 3 AA5 3 ARG B 255 VAL B 256 -1 N VAL B 256 O LEU B 260 SHEET 1 AA6 2 TYR B 411 TYR B 412 0 SHEET 2 AA6 2 ILE B 415 SER B 416 -1 O ILE B 415 N TYR B 412 LINK OE2 GLU A 361 MG MG A 503 1555 1555 2.30 LINK OE1 GLU A 361 MG MG A 504 1555 1555 2.26 LINK OG SER A 364 MG MG A 504 1555 1555 2.14 LINK O SER A 406 NA NA A 505 1555 1555 2.33 LINK O SER A 408 NA NA A 505 1555 1555 2.57 LINK O TYR A 411 NA NA A 505 1555 1555 2.25 LINK O3G ATP A 501 MG MG A 502 1555 1555 2.26 LINK O1B ATP A 501 MG MG A 502 1555 1555 2.20 LINK O1G ATP A 501 MG MG A 503 1555 1555 2.23 LINK O2B ATP A 501 MG MG A 503 1555 1555 2.30 LINK O2B ATP A 501 MG MG A 504 1555 1555 2.20 LINK O1A ATP A 501 MG MG A 504 1555 1555 2.23 LINK MG MG A 502 O HOH A 604 1555 1555 2.13 LINK MG MG A 502 O HOH A 612 1555 1555 2.13 LINK MG MG A 502 O HOH A 662 1555 1555 2.07 LINK MG MG A 502 O HOH A 678 1555 1555 2.12 LINK MG MG A 503 O HOH A 620 1555 1555 2.36 LINK MG MG A 503 O HOH A 707 1555 1555 2.18 LINK MG MG A 503 O HOH A 734 1555 1555 2.19 LINK MG MG A 504 O HOH A 620 1555 1555 2.01 LINK MG MG A 504 O HOH A 716 1555 1555 2.16 LINK NA NA A 505 O HOH A 631 1555 1555 2.56 LINK NA NA A 505 O HOH B 620 1555 1555 2.92 LINK NA NA A 505 O HOH B 675 1555 1555 2.39 LINK O HOH A 630 NA NA B 505 1555 1555 3.00 LINK OE2 GLU B 361 MG MG B 503 1555 1555 2.43 LINK OE1 GLU B 361 MG MG B 504 1555 1555 2.28 LINK OG SER B 364 MG MG B 504 1555 1555 2.12 LINK O SER B 406 NA NA B 505 1555 1555 2.31 LINK O SER B 408 NA NA B 505 1555 1555 2.53 LINK O TYR B 411 NA NA B 505 1555 1555 2.30 LINK O3G ATP B 501 MG MG B 502 1555 1555 2.23 LINK O1B ATP B 501 MG MG B 502 1555 1555 2.18 LINK O1G ATP B 501 MG MG B 503 1555 1555 2.23 LINK O2B ATP B 501 MG MG B 503 1555 1555 2.20 LINK O2B ATP B 501 MG MG B 504 1555 1555 2.21 LINK O1A ATP B 501 MG MG B 504 1555 1555 2.22 LINK MG MG B 502 O HOH B 613 1555 1555 2.08 LINK MG MG B 502 O HOH B 632 1555 1555 2.15 LINK MG MG B 502 O HOH B 674 1555 1555 2.11 LINK MG MG B 502 O HOH B 691 1555 1555 2.06 LINK MG MG B 503 O HOH B 608 1555 1555 2.28 LINK MG MG B 503 O HOH B 706 1555 1555 1.93 LINK MG MG B 503 O HOH B 712 1555 1555 2.11 LINK MG MG B 504 O HOH B 608 1555 1555 2.16 LINK MG MG B 504 O HOH B 682 1555 1555 1.95 LINK NA NA B 505 O HOH B 654 1555 1555 2.55 LINK NA NA B 505 O HOH B 679 1555 1555 2.44 CISPEP 1 GLY A 283 PRO A 284 0 -2.27 CISPEP 2 GLY A 368 PRO A 369 0 -0.77 CISPEP 3 GLY B 283 PRO B 284 0 1.02 CISPEP 4 GLY B 368 PRO B 369 0 2.41 CRYST1 60.670 63.220 81.640 90.00 95.05 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 0.016483 0.000000 0.001457 0.00000 SCALE2 0.000000 0.015818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012297 0.00000 CONECT 1648 4191 CONECT 1649 4190 CONECT 1669 4191 CONECT 1995 4192 CONECT 2012 4192 CONECT 2033 4192 CONECT 3701 4226 CONECT 3702 4225 CONECT 3722 4226 CONECT 4048 4227 CONECT 4065 4227 CONECT 4086 4227 CONECT 4158 4159 4160 4161 4165 CONECT 4159 4158 4190 CONECT 4160 4158 CONECT 4161 4158 4189 CONECT 4162 4163 4164 4165 4169 CONECT 4163 4162 4189 CONECT 4164 4162 4190 4191 CONECT 4165 4158 4162 CONECT 4166 4167 4168 4169 4170 CONECT 4167 4166 4191 CONECT 4168 4166 CONECT 4169 4162 4166 CONECT 4170 4166 4171 CONECT 4171 4170 4172 CONECT 4172 4171 4173 4174 CONECT 4173 4172 4178 CONECT 4174 4172 4175 4176 CONECT 4175 4174 CONECT 4176 4174 4177 4178 CONECT 4177 4176 CONECT 4178 4173 4176 4179 CONECT 4179 4178 4180 4188 CONECT 4180 4179 4181 CONECT 4181 4180 4182 CONECT 4182 4181 4183 4188 CONECT 4183 4182 4184 4185 CONECT 4184 4183 CONECT 4185 4183 4186 CONECT 4186 4185 4187 CONECT 4187 4186 4188 CONECT 4188 4179 4182 4187 CONECT 4189 4161 4163 4231 4239 CONECT 4189 4289 4305 CONECT 4190 1649 4159 4164 4247 CONECT 4190 4334 4361 CONECT 4191 1648 1669 4164 4167 CONECT 4191 4247 4343 CONECT 4192 1995 2012 2033 4258 CONECT 4192 4409 4464 CONECT 4193 4194 4195 4196 4200 CONECT 4194 4193 4225 CONECT 4195 4193 CONECT 4196 4193 4224 CONECT 4197 4198 4199 4200 4204 CONECT 4198 4197 4224 CONECT 4199 4197 4225 4226 CONECT 4200 4193 4197 CONECT 4201 4202 4203 4204 4205 CONECT 4202 4201 4226 CONECT 4203 4201 CONECT 4204 4197 4201 CONECT 4205 4201 4206 CONECT 4206 4205 4207 CONECT 4207 4206 4208 4209 CONECT 4208 4207 4213 CONECT 4209 4207 4210 4211 CONECT 4210 4209 CONECT 4211 4209 4212 4213 CONECT 4212 4211 CONECT 4213 4208 4211 4214 CONECT 4214 4213 4215 4223 CONECT 4215 4214 4216 CONECT 4216 4215 4217 CONECT 4217 4216 4218 4223 CONECT 4218 4217 4219 4220 CONECT 4219 4218 CONECT 4220 4218 4221 CONECT 4221 4220 4222 CONECT 4222 4221 4223 CONECT 4223 4214 4217 4222 CONECT 4224 4196 4198 4402 4421 CONECT 4224 4463 4480 CONECT 4225 3702 4194 4199 4397 CONECT 4225 4495 4501 CONECT 4226 3701 3722 4199 4202 CONECT 4226 4397 4471 CONECT 4227 4048 4065 4086 4257 CONECT 4227 4443 4468 CONECT 4231 4189 CONECT 4239 4189 CONECT 4247 4190 4191 CONECT 4257 4227 CONECT 4258 4192 CONECT 4289 4189 CONECT 4305 4189 CONECT 4334 4190 CONECT 4343 4191 CONECT 4361 4190 CONECT 4397 4225 4226 CONECT 4402 4224 CONECT 4409 4192 CONECT 4421 4224 CONECT 4443 4227 CONECT 4463 4224 CONECT 4464 4192 CONECT 4468 4227 CONECT 4471 4226 CONECT 4480 4224 CONECT 4495 4225 CONECT 4501 4225 MASTER 388 0 10 21 24 0 0 6 4526 2 112 42 END