HEADER LIGASE 19-JUL-22 8DQI TITLE CRYSTAL STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE FROM TITLE 2 METHANOMETHYLOPHILUS ALVUS ENGINEERED FOR ACRIDONE AMINO ACID (RS1) TITLE 3 BOUND TO ATP AND ACRIDONE AFTER 2- WEEKS OF CRYSTAL GROWTH COMPND MOL_ID: 1; COMPND 2 MOLECULE: AA_TRNA_LIGASE_II DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: D, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDATUS METHANOMETHYLOPHILUS ALVUS; SOURCE 3 ORGANISM_TAXID: 1291540; SOURCE 4 GENE: BKD89_05515; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GENETIC CODE EXPANSION, METHANOMETHYLOPHILUS ALVUS, PYRROLYSYL-TRNA KEYWDS 2 SYNTHETASE, ACRIDONE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR I.GOTTFRIED-LEE,P.A.KARPLUS,R.A.MEHL,R.B.COOLEY REVDAT 3 25-OCT-23 8DQI 1 REMARK REVDAT 2 28-DEC-22 8DQI 1 JRNL REVDAT 1 07-DEC-22 8DQI 0 JRNL AUTH I.GOTTFRIED-LEE,J.J.PERONA,P.A.KARPLUS,R.A.MEHL,R.B.COOLEY JRNL TITL STRUCTURES OF METHANOMETHYLOPHILUS ALVUS PYRROLYSINE JRNL TITL 2 TRNA-SYNTHETASES SUPPORT THE NEED FOR DE NOVO SELECTIONS JRNL TITL 3 WHEN ALTERING THE SUBSTRATE SPECIFICITY. JRNL REF ACS CHEM.BIOL. V. 17 3470 2022 JRNL REFN ESSN 1554-8937 JRNL PMID 36395426 JRNL DOI 10.1021/ACSCHEMBIO.2C00640 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 101115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 5083 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 45.4300 - 4.7900 1.00 3265 168 0.1730 0.1918 REMARK 3 2 4.7800 - 3.8000 1.00 3254 164 0.1317 0.1472 REMARK 3 3 3.8000 - 3.3200 1.00 3217 172 0.1434 0.1469 REMARK 3 4 3.3200 - 3.0100 1.00 3189 177 0.1556 0.1766 REMARK 3 5 3.0100 - 2.8000 1.00 3233 174 0.1638 0.1879 REMARK 3 6 2.8000 - 2.6300 1.00 3180 173 0.1612 0.1814 REMARK 3 7 2.6300 - 2.5000 1.00 3221 166 0.1607 0.1908 REMARK 3 8 2.5000 - 2.3900 1.00 3214 168 0.1561 0.1687 REMARK 3 9 2.3900 - 2.3000 1.00 3184 168 0.1551 0.1941 REMARK 3 10 2.3000 - 2.2200 1.00 3221 162 0.1497 0.1790 REMARK 3 11 2.2200 - 2.1500 1.00 3173 177 0.1578 0.1740 REMARK 3 12 2.1500 - 2.0900 1.00 3198 171 0.1588 0.1696 REMARK 3 13 2.0900 - 2.0400 1.00 3218 169 0.1579 0.2043 REMARK 3 14 2.0400 - 1.9900 1.00 3194 164 0.1800 0.1867 REMARK 3 15 1.9900 - 1.9400 1.00 3162 180 0.1776 0.2225 REMARK 3 16 1.9400 - 1.9000 1.00 3209 161 0.1784 0.1816 REMARK 3 17 1.9000 - 1.8600 1.00 3203 173 0.1744 0.1876 REMARK 3 18 1.8600 - 1.8300 1.00 3169 178 0.1786 0.1932 REMARK 3 19 1.8300 - 1.7900 1.00 3215 164 0.1792 0.2113 REMARK 3 20 1.7900 - 1.7600 1.00 3235 151 0.1931 0.1957 REMARK 3 21 1.7600 - 1.7300 1.00 3160 182 0.2085 0.2292 REMARK 3 22 1.7300 - 1.7100 1.00 3191 162 0.2265 0.2352 REMARK 3 23 1.7100 - 1.6800 1.00 3217 175 0.2485 0.2613 REMARK 3 24 1.6800 - 1.6600 1.00 3181 181 0.2696 0.2877 REMARK 3 25 1.6600 - 1.6400 1.00 3205 145 0.3026 0.3690 REMARK 3 26 1.6400 - 1.6200 1.00 3160 175 0.3194 0.3757 REMARK 3 27 1.6200 - 1.6000 1.00 3225 190 0.2773 0.2683 REMARK 3 28 1.6000 - 1.5800 1.00 3164 163 0.2741 0.2809 REMARK 3 29 1.5800 - 1.5600 1.00 3164 166 0.2841 0.2727 REMARK 3 30 1.5600 - 1.5400 1.00 3211 164 0.2933 0.3068 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.188 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.668 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.60 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 : 0.010 4320 REMARK 3 ANGLE : 1.081 5862 REMARK 3 CHIRALITY : 0.059 652 REMARK 3 PLANARITY : 0.010 751 REMARK 3 DIHEDRAL : 14.114 1605 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 8DQI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000266939. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101122 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 45.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : 2.79000 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: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: 6JP2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 55.39750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.39750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.88700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.39750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.39750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.88700 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 55.39750 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 55.39750 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.88700 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 55.39750 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 55.39750 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.88700 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: 7440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 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 D 0 REMARK 465 HIS D 154 REMARK 465 SER A 0 REMARK 465 GLY A 1 REMARK 465 THR A 2 REMARK 465 SER A 153 REMARK 465 HIS A 154 REMARK 465 SER A 155 REMARK 465 GLY A 156 REMARK 465 GLU A 201 REMARK 465 GLU A 202 REMARK 465 SER A 203 REMARK 465 ASP A 204 REMARK 465 VAL A 205 REMARK 465 TYR A 206 REMARK 465 LYS A 207 REMARK 465 GLU A 208 REMARK 465 LEU A 229 REMARK 465 ASP A 230 REMARK 465 ALA A 231 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS D 38 CG CD CE NZ REMARK 470 LYS D 49 CG CD CE NZ REMARK 470 GLU D 100 CG CD OE1 OE2 REMARK 470 ASP D 101 CG OD1 OD2 REMARK 470 LYS D 106 CG CD CE NZ REMARK 470 SER D 153 OG REMARK 470 ARG D 173 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 202 CG CD OE1 OE2 REMARK 470 LYS D 207 CG CD CE NZ REMARK 470 GLU D 208 CG CD OE1 OE2 REMARK 470 GLN A 23 CG CD OE1 NE2 REMARK 470 ILE A 98 CG1 CG2 CD1 REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 ASP A 101 CB CG OD1 OD2 REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 LYS A 106 CG CD CE NZ REMARK 470 GLU A 113 CG CD OE1 OE2 REMARK 470 ARG A 130 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 158 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 173 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 TYR A 228 CG CD1 CD2 CE1 CE2 CZ OH 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 THR D 20 77.94 -109.75 REMARK 500 MET D 157 18.61 59.52 REMARK 500 LYS D 207 -62.66 75.62 REMARK 500 HIS A 227 7.38 -67.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 601 DISTANCE = 6.35 ANGSTROMS 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 D 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 218 OE2 REMARK 620 2 SER D 221 OG 84.5 REMARK 620 3 ATP D 301 O1B 95.0 178.4 REMARK 620 4 ATP D 301 O2A 99.1 90.3 91.2 REMARK 620 5 HOH D 439 O 90.2 85.1 93.4 169.2 REMARK 620 6 HOH D 528 O 169.1 85.0 95.4 83.8 86.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 218 OE1 REMARK 620 2 ATP D 301 O1G 93.2 REMARK 620 3 ATP D 301 O1B 96.8 88.0 REMARK 620 4 HOH D 439 O 75.2 161.7 79.5 REMARK 620 5 HOH D 625 O 87.2 104.3 166.8 89.4 REMARK 620 6 HOH D 626 O 164.0 97.5 95.6 97.1 78.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP D 301 O2G REMARK 620 2 ATP D 301 O2B 90.2 REMARK 620 3 HOH D 418 O 94.8 95.0 REMARK 620 4 HOH D 533 O 171.8 82.4 89.2 REMARK 620 5 HOH D 563 O 96.0 173.5 86.6 91.4 REMARK 620 6 HOH D 567 O 81.5 93.5 170.7 95.5 85.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 218 OE2 REMARK 620 2 ATP A 302 O1B 118.7 REMARK 620 3 ATP A 302 O2A 128.0 85.8 REMARK 620 4 ATP A 302 O3A 95.9 57.3 57.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 302 O3G REMARK 620 2 ATP A 302 O2B 95.2 REMARK 620 3 HOH A 453 O 95.7 101.8 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8DQH RELATED DB: PDB REMARK 900 RELATED ID: 8DQG RELATED DB: PDB REMARK 900 RELATED ID: 8DQJ RELATED DB: PDB DBREF1 8DQI D 2 275 UNP A0A3G3IHP7_9ARCH DBREF2 8DQI D A0A3G3IHP7 2 275 DBREF1 8DQI A 2 275 UNP A0A3G3IHP7_9ARCH DBREF2 8DQI A A0A3G3IHP7 2 275 SEQADV 8DQI SER D 0 UNP A0A3G3IHP EXPRESSION TAG SEQADV 8DQI GLY D 1 UNP A0A3G3IHP EXPRESSION TAG SEQADV 8DQI ALA D 166 UNP A0A3G3IHP ASN 166 CONFLICT SEQADV 8DQI GLY D 168 UNP A0A3G3IHP VAL 168 CONFLICT SEQADV 8DQI CYS D 239 UNP A0A3G3IHP TRP 239 CONFLICT SEQADV 8DQI SER A 0 UNP A0A3G3IHP EXPRESSION TAG SEQADV 8DQI GLY A 1 UNP A0A3G3IHP EXPRESSION TAG SEQADV 8DQI ALA A 166 UNP A0A3G3IHP ASN 166 CONFLICT SEQADV 8DQI GLY A 168 UNP A0A3G3IHP VAL 168 CONFLICT SEQADV 8DQI CYS A 239 UNP A0A3G3IHP TRP 239 CONFLICT SEQRES 1 D 276 SER GLY THR VAL LYS TYR THR ASP ALA GLN ILE GLN ARG SEQRES 2 D 276 LEU ARG GLU TYR GLY ASN GLY THR TYR GLU GLN LYS VAL SEQRES 3 D 276 PHE GLU ASP LEU ALA SER ARG ASP ALA ALA PHE SER LYS SEQRES 4 D 276 GLU MET SER VAL ALA SER THR ASP ASN GLU LYS LYS ILE SEQRES 5 D 276 LYS GLY MET ILE ALA ASN PRO SER ARG HIS GLY LEU THR SEQRES 6 D 276 GLN LEU MET ASN ASP ILE ALA ASP ALA LEU VAL ALA GLU SEQRES 7 D 276 GLY PHE ILE GLU VAL ARG THR PRO ILE PHE ILE SER LYS SEQRES 8 D 276 ASP ALA LEU ALA ARG MET THR ILE THR GLU ASP LYS PRO SEQRES 9 D 276 LEU PHE LYS GLN VAL PHE TRP ILE ASP GLU LYS ARG ALA SEQRES 10 D 276 LEU ARG PRO MET LEU ALA PRO ASN LEU TYR SER VAL MET SEQRES 11 D 276 ARG ASP LEU ARG ASP HIS THR ASP GLY PRO VAL LYS ILE SEQRES 12 D 276 PHE GLU MET GLY SER CYS PHE ARG LYS GLU SER HIS SER SEQRES 13 D 276 GLY MET HIS LEU GLU GLU PHE THR MET LEU ALA LEU GLY SEQRES 14 D 276 ASP MET GLY PRO ARG GLY ASP ALA THR GLU VAL LEU LYS SEQRES 15 D 276 ASN TYR ILE SER VAL VAL MET LYS ALA ALA GLY LEU PRO SEQRES 16 D 276 ASP TYR ASP LEU VAL GLN GLU GLU SER ASP VAL TYR LYS SEQRES 17 D 276 GLU THR ILE ASP VAL GLU ILE ASN GLY GLN GLU VAL CYS SEQRES 18 D 276 SER ALA ALA VAL GLY PRO HIS TYR LEU ASP ALA ALA HIS SEQRES 19 D 276 ASP VAL HIS GLU PRO CYS SER GLY ALA GLY PHE GLY LEU SEQRES 20 D 276 GLU ARG LEU LEU THR ILE ARG GLU LYS TYR SER THR VAL SEQRES 21 D 276 LYS LYS GLY GLY ALA SER ILE SER TYR LEU ASN GLY ALA SEQRES 22 D 276 LYS ILE ASN SEQRES 1 A 276 SER GLY THR VAL LYS TYR THR ASP ALA GLN ILE GLN ARG SEQRES 2 A 276 LEU ARG GLU TYR GLY ASN GLY THR TYR GLU GLN LYS VAL SEQRES 3 A 276 PHE GLU ASP LEU ALA SER ARG ASP ALA ALA PHE SER LYS SEQRES 4 A 276 GLU MET SER VAL ALA SER THR ASP ASN GLU LYS LYS ILE SEQRES 5 A 276 LYS GLY MET ILE ALA ASN PRO SER ARG HIS GLY LEU THR SEQRES 6 A 276 GLN LEU MET ASN ASP ILE ALA ASP ALA LEU VAL ALA GLU SEQRES 7 A 276 GLY PHE ILE GLU VAL ARG THR PRO ILE PHE ILE SER LYS SEQRES 8 A 276 ASP ALA LEU ALA ARG MET THR ILE THR GLU ASP LYS PRO SEQRES 9 A 276 LEU PHE LYS GLN VAL PHE TRP ILE ASP GLU LYS ARG ALA SEQRES 10 A 276 LEU ARG PRO MET LEU ALA PRO ASN LEU TYR SER VAL MET SEQRES 11 A 276 ARG ASP LEU ARG ASP HIS THR ASP GLY PRO VAL LYS ILE SEQRES 12 A 276 PHE GLU MET GLY SER CYS PHE ARG LYS GLU SER HIS SER SEQRES 13 A 276 GLY MET HIS LEU GLU GLU PHE THR MET LEU ALA LEU GLY SEQRES 14 A 276 ASP MET GLY PRO ARG GLY ASP ALA THR GLU VAL LEU LYS SEQRES 15 A 276 ASN TYR ILE SER VAL VAL MET LYS ALA ALA GLY LEU PRO SEQRES 16 A 276 ASP TYR ASP LEU VAL GLN GLU GLU SER ASP VAL TYR LYS SEQRES 17 A 276 GLU THR ILE ASP VAL GLU ILE ASN GLY GLN GLU VAL CYS SEQRES 18 A 276 SER ALA ALA VAL GLY PRO HIS TYR LEU ASP ALA ALA HIS SEQRES 19 A 276 ASP VAL HIS GLU PRO CYS SER GLY ALA GLY PHE GLY LEU SEQRES 20 A 276 GLU ARG LEU LEU THR ILE ARG GLU LYS TYR SER THR VAL SEQRES 21 A 276 LYS LYS GLY GLY ALA SER ILE SER TYR LEU ASN GLY ALA SEQRES 22 A 276 LYS ILE ASN HET ATP D 301 42 HET T7Q D 302 34 HET PG4 D 303 30 HET MG D 304 1 HET MG D 305 1 HET MG D 306 1 HET GOL A 301 14 HET ATP A 302 43 HET MG A 303 1 HET MG A 304 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM T7Q (2~{S})-2-AZANYL-3-(9-OXIDANYLIDENE-10~{H}-ACRIDIN-2- HETNAM 2 T7Q YL)PROPANOIC ACID HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN T7Q ACRIDONE AMINO ACID (RS1) HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ATP 2(C10 H16 N5 O13 P3) FORMUL 4 T7Q C16 H15 N2 O3 1+ FORMUL 5 PG4 C8 H18 O5 FORMUL 6 MG 5(MG 2+) FORMUL 9 GOL C3 H8 O3 FORMUL 13 HOH *470(H2 O) HELIX 1 AA1 THR D 6 GLY D 17 1 12 HELIX 2 AA2 THR D 20 LYS D 24 5 5 HELIX 3 AA3 ASP D 28 ASN D 57 1 30 HELIX 4 AA4 HIS D 61 GLU D 77 1 17 HELIX 5 AA5 LYS D 90 MET D 96 1 7 HELIX 6 AA6 LYS D 102 VAL D 108 5 7 HELIX 7 AA7 LEU D 121 ASP D 134 1 14 HELIX 8 AA8 ASP D 175 ALA D 191 1 17 HELIX 9 AA9 PRO D 226 HIS D 233 1 8 HELIX 10 AB1 LEU D 246 LYS D 255 1 10 HELIX 11 AB2 THR A 6 GLY A 17 1 12 HELIX 12 AB3 ASP A 28 ASN A 57 1 30 HELIX 13 AB4 HIS A 61 GLU A 77 1 17 HELIX 14 AB5 LYS A 90 MET A 96 1 7 HELIX 15 AB6 LEU A 104 VAL A 108 5 5 HELIX 16 AB7 LEU A 121 ASP A 134 1 14 HELIX 17 AB8 ASP A 175 ALA A 191 1 17 HELIX 18 AB9 LEU A 246 LYS A 255 1 10 SHEET 1 AA1 7 ILE D 80 GLU D 81 0 SHEET 2 AA1 7 VAL D 140 PHE D 149 1 O LYS D 141 N ILE D 80 SHEET 3 AA1 7 GLU D 161 MET D 170 -1 O MET D 170 N VAL D 140 SHEET 4 AA1 7 CYS D 239 GLY D 245 -1 O PHE D 244 N LEU D 165 SHEET 5 AA1 7 GLN D 217 VAL D 224 -1 N ALA D 223 O GLY D 241 SHEET 6 AA1 7 LYS D 207 ILE D 214 -1 N VAL D 212 O VAL D 219 SHEET 7 AA1 7 ASP D 197 SER D 203 -1 N VAL D 199 O ASP D 211 SHEET 1 AA2 2 PHE D 87 SER D 89 0 SHEET 2 AA2 2 ARG D 115 LEU D 117 -1 O ALA D 116 N ILE D 88 SHEET 1 AA3 2 TYR D 268 LEU D 269 0 SHEET 2 AA3 2 ALA D 272 LYS D 273 -1 O ALA D 272 N LEU D 269 SHEET 1 AA4 7 ILE A 80 GLU A 81 0 SHEET 2 AA4 7 VAL A 140 PHE A 149 1 O LYS A 141 N ILE A 80 SHEET 3 AA4 7 GLU A 161 MET A 170 -1 O PHE A 162 N CYS A 148 SHEET 4 AA4 7 CYS A 239 GLY A 245 -1 O PHE A 244 N LEU A 165 SHEET 5 AA4 7 GLN A 217 VAL A 224 -1 N SER A 221 O GLY A 243 SHEET 6 AA4 7 ILE A 210 ILE A 214 -1 N ILE A 210 O ALA A 222 SHEET 7 AA4 7 ASP A 197 VAL A 199 -1 N VAL A 199 O ASP A 211 SHEET 1 AA5 2 PHE A 87 SER A 89 0 SHEET 2 AA5 2 ARG A 115 LEU A 117 -1 O ALA A 116 N ILE A 88 SHEET 1 AA6 2 TYR A 268 LEU A 269 0 SHEET 2 AA6 2 ALA A 272 LYS A 273 -1 O ALA A 272 N LEU A 269 LINK OE2 GLU D 218 MG MG D 305 1555 1555 2.22 LINK OE1 GLU D 218 MG MG D 306 1555 1555 2.43 LINK OG SER D 221 MG MG D 305 1555 1555 2.13 LINK O2G ATP D 301 MG MG D 304 1555 1555 2.25 LINK O2B ATP D 301 MG MG D 304 1555 1555 2.12 LINK O1B ATP D 301 MG MG D 305 1555 1555 2.10 LINK O2A ATP D 301 MG MG D 305 1555 1555 2.15 LINK O1G ATP D 301 MG MG D 306 1555 1555 2.46 LINK O1B ATP D 301 MG MG D 306 1555 1555 2.42 LINK MG MG D 304 O HOH D 418 1555 1555 2.15 LINK MG MG D 304 O HOH D 533 1555 1555 2.14 LINK MG MG D 304 O HOH D 563 1555 1555 2.14 LINK MG MG D 304 O HOH D 567 1555 1555 2.18 LINK MG MG D 305 O HOH D 439 1555 1555 2.19 LINK MG MG D 305 O HOH D 528 1555 1555 2.03 LINK MG MG D 306 O HOH D 439 1555 1555 2.47 LINK MG MG D 306 O HOH D 625 1555 1555 2.50 LINK MG MG D 306 O HOH D 626 1555 1555 2.21 LINK OE2 GLU A 218 MG MG A 303 1555 1555 2.55 LINK O1B ATP A 302 MG MG A 303 1555 1555 2.28 LINK O2A ATP A 302 MG MG A 303 1555 1555 2.09 LINK O3A ATP A 302 MG MG A 303 1555 1555 2.90 LINK O3G ATP A 302 MG MG A 304 1555 1555 2.41 LINK O2B ATP A 302 MG MG A 304 1555 1555 2.07 LINK MG MG A 304 O HOH A 453 1555 1555 2.26 CISPEP 1 GLY D 225 PRO D 226 0 3.98 CRYST1 110.795 110.795 113.774 90.00 90.00 90.00 I 4 16 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 0.009026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008789 0.00000