HEADER LIGASE/LIGASE INHIBITOR 26-MAY-21 7N11 TITLE CRYSTAL STRUCTURE OF THE M. ABSCESSUS LEURS EDITING DOMAIN IN COMPLEX TITLE 2 WITH EPETRABOROLE-AMP ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LEUCYL-TRNA SYNTHETASE,LEURS; COMPND 5 EC: 6.1.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTEROIDES ABSCESSUS; SOURCE 3 ORGANISM_TAXID: 36809; SOURCE 4 GENE: LEUS, D2E76_19720; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXABOROLE, INHIBITOR, COMPLEX, ANTIBIOTIC, LIGASE-LIGASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.KALTHOFF,M.SCHMEING REVDAT 3 18-OCT-23 7N11 1 REMARK REVDAT 2 27-OCT-21 7N11 1 JRNL REVDAT 1 06-OCT-21 7N11 0 JRNL AUTH J.R.SULLIVAN,A.LUPIEN,E.KALTHOFF,C.HAMELA,L.TAYLOR, JRNL AUTH 2 K.A.MUNRO,T.M.SCHMEING,L.KREMER,M.A.BEHR JRNL TITL EFFICACY OF EPETRABOROLE AGAINST MYCOBACTERIUM ABSCESSUS IS JRNL TITL 2 INCREASED WITH NORVALINE. JRNL REF PLOS PATHOG. V. 17 09965 2021 JRNL REFN ESSN 1553-7374 JRNL PMID 34637487 JRNL DOI 10.1371/JOURNAL.PPAT.1009965 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 14741 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 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 38.5700 - 4.3700 0.99 1467 163 0.1969 0.2069 REMARK 3 2 4.3700 - 3.4700 1.00 1386 154 0.1567 0.1900 REMARK 3 3 3.4700 - 3.0300 1.00 1362 151 0.1808 0.2339 REMARK 3 4 3.0300 - 2.7500 0.98 1334 149 0.1856 0.2393 REMARK 3 5 2.7500 - 2.5500 0.94 1273 141 0.1872 0.2074 REMARK 3 6 2.5500 - 2.4000 0.93 1273 141 0.1860 0.2484 REMARK 3 7 2.4000 - 2.2800 0.94 1244 139 0.1851 0.2462 REMARK 3 8 2.2800 - 2.1800 0.95 1278 142 0.1956 0.2688 REMARK 3 9 2.1800 - 2.1000 0.95 1281 142 0.2153 0.3124 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) : 0.226 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.703 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.02 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 : 0.008 1492 REMARK 3 ANGLE : 0.999 2040 REMARK 3 CHIRALITY : 0.059 226 REMARK 3 PLANARITY : 0.006 272 REMARK 3 DIHEDRAL : 23.398 521 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 7N11 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000257129. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V720 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V720 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25482 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.15.2_3472 REMARK 200 STARTING MODEL: 5AGR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 UL OF 10 MG/ML PROTEIN SOLUTION (50 REMARK 280 MM TRIS PH 7.5, 150 MM NACL, 2 MM BME) WERE MIXED WITH 2 UL OF REMARK 280 CRYSTALLIZATION SOLUTION (100 MM HEPES PH 7.0, 2.5 M AMMONIUM REMARK 280 SULFATE), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 1.000000 0.000000 0.000000 18.62450 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.07450 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.62450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.07450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 303 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 GLN A 304 CG CD OE1 NE2 REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 TYR A 421 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 435 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 458 CG CD CE NZ 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 TYR A 421 66.14 -111.24 REMARK 500 HIS A 432 22.13 -142.44 REMARK 500 ASP A 471 -124.73 46.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 DBREF1 7N11 A 303 498 UNP A0A0U0XQP3_9MYCO DBREF2 7N11 A A0A0U0XQP3 303 498 SEQADV 7N11 ALA A 315 UNP A0A0U0XQP VAL 315 CONFLICT SEQADV 7N11 THR A 355 UNP A0A0U0XQP ALA 355 CONFLICT SEQRES 1 A 196 SER GLN GLY ALA SER VAL LEU PHE GLY ALA PRO GLY ALA SEQRES 2 A 196 GLY ASP ILE GLU VAL PHE THR THR ARG PRO ASP THR LEU SEQRES 3 A 196 PHE GLY ALA THR TYR MET VAL LEU ALA PRO GLU HIS PRO SEQRES 4 A 196 LEU VAL ASP GLN LEU ALA ALA ASP VAL TRP PRO GLN ASP SEQRES 5 A 196 THR ASP PRO ARG TRP THR GLY GLY GLN ASP SER PRO ARG SEQRES 6 A 196 ALA ALA ILE GLU GLN TYR ARG ARG SER ILE ALA ALA LYS SEQRES 7 A 196 SER ASP LEU GLU ARG GLN GLU ASN LYS GLU LYS THR GLY SEQRES 8 A 196 VAL PHE THR GLY ALA TYR ALA THR ASN PRO VAL SER GLY SEQRES 9 A 196 LYS PRO VAL PRO VAL PHE ILE ALA ASP TYR VAL LEU LEU SEQRES 10 A 196 GLY TYR GLY THR GLY ALA ILE MET ALA VAL PRO GLY HIS SEQRES 11 A 196 ASP GLN ARG ASP TRP ASP PHE ALA ASN THR PHE GLY LEU SEQRES 12 A 196 PRO VAL GLN GLU VAL ILE SER GLY GLY ASP VAL THR LYS SEQRES 13 A 196 ALA ALA TYR THR GLY ASP GLY VAL LEU VAL ASN SER ASP SEQRES 14 A 196 TYR LEU ASP GLY LEU ASP ILE GLU ALA ALA LYS VAL GLU SEQRES 15 A 196 VAL THR ARG ARG LEU VAL LYS ASP GLY ARG GLY GLU SER SEQRES 16 A 196 ARG HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *131(H2 O) HELIX 1 AA1 ARG A 324 ALA A 331 5 8 HELIX 2 AA2 LEU A 342 ALA A 347 1 6 HELIX 3 AA3 ASP A 356 THR A 360 5 5 HELIX 4 AA4 SER A 365 ALA A 378 1 14 HELIX 5 AA5 SER A 381 GLU A 387 1 7 HELIX 6 AA6 ASP A 433 GLY A 444 1 12 HELIX 7 AA7 SER A 470 ASP A 474 5 5 HELIX 8 AA8 ASP A 477 ASP A 492 1 16 SHEET 1 AA1 3 ASP A 317 THR A 322 0 SHEET 2 AA1 3 ALA A 306 GLY A 311 -1 N PHE A 310 O ILE A 318 SHEET 3 AA1 3 GLY A 495 SER A 497 -1 O GLU A 496 N SER A 307 SHEET 1 AA2 4 VAL A 394 THR A 401 0 SHEET 2 AA2 4 PRO A 408 ILE A 413 -1 O VAL A 409 N ALA A 400 SHEET 3 AA2 4 TYR A 333 LEU A 336 1 N LEU A 336 O PHE A 412 SHEET 4 AA2 4 ALA A 425 ALA A 428 -1 O ILE A 426 N VAL A 335 SITE 1 AC1 4 THR A 322 THR A 323 HOH A 601 HOH A 603 SITE 1 AC2 2 ALA A 379 ARG A 498 SITE 1 AC3 2 SER A 365 THR A 457 CRYST1 37.249 51.597 116.149 90.00 90.00 90.00 P 21 2 21 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 0.026846 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008610 0.00000