HEADER LIGASE 14-DEC-21 7QI8 TITLE CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS COMPLEXED WITH L-LYSINE AND INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE--TRNA LIGASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSYL-TRNA SYNTHETASE 1,LYSRS 1; COMPND 5 EC: 6.1.1.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 GENE: LYSS1, LYSS, RV3598C, MTCY07H7B.24; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LIGASE, MYCOBACTERIUM TUBERCULOSIS, ATP BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.DAWSON,D.A.ROBINSON,J.TAMJAR,P.WYATT,S.GREEN REVDAT 3 07-FEB-24 7QI8 1 REMARK REVDAT 2 31-MAY-23 7QI8 1 SOURCE DBREF SEQADV REVDAT 1 19-OCT-22 7QI8 0 JRNL AUTH S.R.GREEN,S.H.DAVIS,S.DAMEROW,C.A.ENGELHART,M.MATHIESON, JRNL AUTH 2 B.BARAGANA,D.A.ROBINSON,J.TAMJAR,A.DAWSON,F.K.TAMAKI, JRNL AUTH 3 K.I.BUCHANAN,J.POST,K.DOWERS,S.M.SHEPHERD,C.JANSEN, JRNL AUTH 4 F.ZUCCOTTO,I.H.GILBERT,O.EPEMOLU,J.RILEY,L.STOJANOVSKI, JRNL AUTH 5 M.OSUNA-CABELLO,E.PEREZ-HERRAN,M.J.REBOLLO,L.GUIJARRO LOPEZ, JRNL AUTH 6 P.CASADO CASTRO,I.CAMINO,H.C.KIM,J.M.BEAN,N.NAHIYAAN, JRNL AUTH 7 K.Y.RHEE,Q.WANG,V.Y.TAN,H.I.M.BOSHOFF,P.J.CONVERSE,S.Y.LI, JRNL AUTH 8 Y.S.CHANG,N.FOTOUHI,A.M.UPTON,E.L.NUERMBERGER, JRNL AUTH 9 D.SCHNAPPINGER,K.D.READ,L.ENCINAS,R.H.BATES,P.G.WYATT, JRNL AUTH10 L.A.T.CLEGHORN JRNL TITL LYSYL-TRNA SYNTHETASE, A TARGET FOR URGENTLY NEEDED M. JRNL TITL 2 TUBERCULOSIS DRUGS. JRNL REF NAT COMMUN V. 13 5992 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36220877 JRNL DOI 10.1038/S41467-022-33736-5 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26375 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) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1393 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1878 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3970 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3591 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.03000 REMARK 3 B22 (A**2) : 3.03000 REMARK 3 B33 (A**2) : -6.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.308 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.255 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.310 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.634 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3689 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3575 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5010 ; 1.481 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8191 ; 1.216 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 457 ; 8.322 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;27.080 ;20.048 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 613 ;18.196 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;15.901 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 489 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4136 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 856 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7QI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-19 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27807 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 49.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.20500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 1.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: 7QH8 REMARK 200 REMARK 200 REMARK: BLOCK REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR: 0.25 M NAOAC, 14% PEG 3350 REMARK 280 PROTEIN: 100 MM HEPES, 150 MM NACL, 5% GLYCEROL, PH 7.5, ~ 20 MG/ REMARK 280 ML, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 73.99200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.09800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.09800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.99600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.09800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.09800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 110.98800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.09800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.09800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.99600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.09800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.09800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 110.98800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.99200 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: 8220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 73.99200 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 -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 ASP A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 ASP A 9 REMARK 465 LEU A 10 REMARK 465 PRO A 11 REMARK 465 ARG A 128 REMARK 465 GLY A 129 REMARK 465 ALA A 151 REMARK 465 HIS A 152 REMARK 465 LYS A 153 REMARK 465 GLU A 154 REMARK 465 LEU A 354 REMARK 465 GLU A 355 REMARK 465 LYS A 356 REMARK 465 ASP A 357 REMARK 465 PRO A 358 REMARK 465 ALA A 359 REMARK 465 ILE A 360 REMARK 465 HIS A 361 REMARK 465 ASP A 362 REMARK 465 ASN A 363 REMARK 465 ARG A 364 REMARK 465 GLY A 365 REMARK 465 ALA A 447 REMARK 465 ALA A 448 REMARK 465 ALA A 449 REMARK 465 GLY A 450 REMARK 465 ASP A 451 REMARK 465 ASP A 452 REMARK 465 GLU A 453 REMARK 465 ALA A 454 REMARK 465 VAL A 500 REMARK 465 ARG A 501 REMARK 465 PRO A 502 REMARK 465 HIS A 503 REMARK 465 SER A 504 REMARK 465 ASN A 505 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 GLU A 157 CG CD OE1 OE2 REMARK 470 ARG A 378 CG CD NE CZ NH1 NH2 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 OH TYR A 313 O SER A 385 2.18 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 TYR A 32 75.77 -117.08 REMARK 500 PRO A 53 109.32 -45.81 REMARK 500 PHE A 70 140.82 -173.14 REMARK 500 SER A 74 51.54 -156.47 REMARK 500 ASP A 112 -163.35 -104.14 REMARK 500 GLN A 163 62.02 -151.38 REMARK 500 ALA A 233 146.52 -173.80 REMARK 500 LEU A 352 -83.24 -86.10 REMARK 500 THR A 379 -75.34 -106.47 REMARK 500 SER A 385 -56.70 -141.20 REMARK 500 ASP A 392 95.93 67.91 REMARK 500 THR A 398 59.86 -144.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 427 SER A 428 143.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7QH8 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH LYSINE ONLY REMARK 900 RELATED ID: 7QHN RELATED DB: PDB REMARK 900 SAME PROTEIN WITH LYSINE AND INHIBITOR DBREF 7QI8 A 1 505 UNP P9WFU9 SYK1_MYCTU 1 505 SEQADV 7QI8 MET A -20 UNP P9WFU9 INITIATING METHIONINE SEQADV 7QI8 GLY A -19 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 SER A -18 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 SER A -17 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 HIS A -16 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 HIS A -15 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 HIS A -14 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 HIS A -13 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 HIS A -12 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 HIS A -11 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 SER A -10 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 SER A -9 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 GLY A -8 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 GLU A -7 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 ASN A -6 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 LEU A -5 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 TYR A -4 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 PHE A -3 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 GLN A -2 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 GLY A -1 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 HIS A 0 UNP P9WFU9 EXPRESSION TAG SEQADV 7QI8 ALA A 455 UNP P9WFU9 MET 455 CONFLICT SEQRES 1 A 526 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 526 GLU ASN LEU TYR PHE GLN GLY HIS MET SER ALA ALA ASP SEQRES 3 A 526 THR ALA GLU ASP LEU PRO GLU GLN PHE ARG ILE ARG ARG SEQRES 4 A 526 ASP LYS ARG ALA ARG LEU LEU ALA GLN GLY ARG ASP PRO SEQRES 5 A 526 TYR PRO VAL ALA VAL PRO ARG THR HIS THR LEU ALA GLU SEQRES 6 A 526 VAL ARG ALA ALA HIS PRO ASP LEU PRO ILE ASP THR ALA SEQRES 7 A 526 THR GLU ASP ILE VAL GLY VAL ALA GLY ARG VAL ILE PHE SEQRES 8 A 526 ALA ARG ASN SER GLY LYS LEU CYS PHE ALA THR LEU GLN SEQRES 9 A 526 ASP GLY ASP GLY THR GLN LEU GLN VAL MET ILE SER LEU SEQRES 10 A 526 ASP LYS VAL GLY GLN ALA ALA LEU ASP ALA TRP LYS ALA SEQRES 11 A 526 ASP VAL ASP LEU GLY ASP ILE VAL TYR VAL HIS GLY ALA SEQRES 12 A 526 VAL ILE SER SER ARG ARG GLY GLU LEU SER VAL LEU ALA SEQRES 13 A 526 ASP CYS TRP ARG ILE ALA ALA LYS SER LEU ARG PRO LEU SEQRES 14 A 526 PRO VAL ALA HIS LYS GLU MET SER GLU GLU SER ARG VAL SEQRES 15 A 526 ARG GLN ARG TYR VAL ASP LEU ILE VAL ARG PRO GLU ALA SEQRES 16 A 526 ARG ALA VAL ALA ARG LEU ARG ILE ALA VAL VAL ARG ALA SEQRES 17 A 526 ILE ARG THR ALA LEU GLN ARG ARG GLY PHE LEU GLU VAL SEQRES 18 A 526 GLU THR PRO VAL LEU GLN THR LEU ALA GLY GLY ALA ALA SEQRES 19 A 526 ALA ARG PRO PHE ALA THR HIS SER ASN ALA LEU ASP ILE SEQRES 20 A 526 ASP LEU TYR LEU ARG ILE ALA PRO GLU LEU PHE LEU LYS SEQRES 21 A 526 ARG CYS ILE VAL GLY GLY PHE ASP LYS VAL PHE GLU LEU SEQRES 22 A 526 ASN ARG VAL PHE ARG ASN GLU GLY ALA ASP SER THR HIS SEQRES 23 A 526 SER PRO GLU PHE SER MET LEU GLU THR TYR GLN THR TYR SEQRES 24 A 526 GLY THR TYR ASP ASP SER ALA VAL VAL THR ARG GLU LEU SEQRES 25 A 526 ILE GLN GLU VAL ALA ASP GLU ALA ILE GLY THR ARG GLN SEQRES 26 A 526 LEU PRO LEU PRO ASP GLY SER VAL TYR ASP ILE ASP GLY SEQRES 27 A 526 GLU TRP ALA THR ILE GLN MET TYR PRO SER LEU SER VAL SEQRES 28 A 526 ALA LEU GLY GLU GLU ILE THR PRO GLN THR THR VAL ASP SEQRES 29 A 526 ARG LEU ARG GLY ILE ALA ASP SER LEU GLY LEU GLU LYS SEQRES 30 A 526 ASP PRO ALA ILE HIS ASP ASN ARG GLY PHE GLY HIS GLY SEQRES 31 A 526 LYS LEU ILE GLU GLU LEU TRP GLU ARG THR VAL GLY LYS SEQRES 32 A 526 SER LEU SER ALA PRO THR PHE VAL LYS ASP PHE PRO VAL SEQRES 33 A 526 GLN THR THR PRO LEU THR ARG GLN HIS ARG SER ILE PRO SEQRES 34 A 526 GLY VAL THR GLU LYS TRP ASP LEU TYR LEU ARG GLY ILE SEQRES 35 A 526 GLU LEU ALA THR GLY TYR SER GLU LEU SER ASP PRO VAL SEQRES 36 A 526 VAL GLN ARG GLU ARG PHE ALA ASP GLN ALA ARG ALA ALA SEQRES 37 A 526 ALA ALA GLY ASP ASP GLU ALA ALA VAL LEU ASP GLU ASP SEQRES 38 A 526 PHE LEU ALA ALA LEU GLU TYR GLY MET PRO PRO CYS THR SEQRES 39 A 526 GLY THR GLY MET GLY ILE ASP ARG LEU LEU MET SER LEU SEQRES 40 A 526 THR GLY LEU SER ILE ARG GLU THR VAL LEU PHE PRO ILE SEQRES 41 A 526 VAL ARG PRO HIS SER ASN HET LYS A 601 10 HET DD0 A 602 23 HETNAM LYS LYSINE HETNAM DD0 2-AZANYL-6-[(1~{S},7~{S})-2,2-BIS(FLUORANYL)-7- HETNAM 2 DD0 OXIDANYL-CYCLOHEPTYL]-4-METHOXY-7~{H}-PYRROLO[3,4- HETNAM 3 DD0 D]PYRIMIDIN-5-ONE FORMUL 2 LYS C6 H15 N2 O2 1+ FORMUL 3 DD0 C14 H18 F2 N4 O3 FORMUL 4 HOH *69(H2 O) HELIX 1 AA1 GLU A 12 ALA A 26 1 15 HELIX 2 AA2 THR A 41 HIS A 49 1 9 HELIX 3 AA3 GLY A 100 VAL A 111 1 12 HELIX 4 AA4 SER A 156 VAL A 161 1 6 HELIX 5 AA5 GLN A 163 ARG A 171 1 9 HELIX 6 AA6 ARG A 171 ARG A 195 1 25 HELIX 7 AA7 PRO A 234 GLY A 244 1 11 HELIX 8 AA8 THR A 280 GLY A 301 1 22 HELIX 9 AA9 MET A 324 GLY A 333 1 10 HELIX 10 AB1 THR A 341 GLY A 353 1 13 HELIX 11 AB2 GLY A 367 VAL A 380 1 14 HELIX 12 AB3 GLY A 381 LEU A 384 5 4 HELIX 13 AB4 GLN A 396 THR A 398 5 3 HELIX 14 AB5 ASP A 432 ALA A 446 1 15 HELIX 15 AB6 ASP A 458 TYR A 467 1 10 HELIX 16 AB7 ILE A 479 GLY A 488 1 10 HELIX 17 AB8 SER A 490 VAL A 495 1 6 SHEET 1 AA1 7 ARG A 139 ALA A 142 0 SHEET 2 AA1 7 ASP A 115 SER A 125 -1 N TYR A 118 O ARG A 139 SHEET 3 AA1 7 LEU A 131 ALA A 135 -1 O LEU A 134 N ALA A 122 SHEET 4 AA1 7 GLN A 89 SER A 95 1 N GLN A 91 O LEU A 131 SHEET 5 AA1 7 LEU A 77 GLN A 83 -1 N CYS A 78 O ILE A 94 SHEET 6 AA1 7 ALA A 57 ASN A 73 -1 N ARG A 72 O PHE A 79 SHEET 7 AA1 7 ASP A 115 SER A 125 -1 O VAL A 119 N VAL A 64 SHEET 1 AA2 8 LEU A 198 GLU A 199 0 SHEET 2 AA2 8 LYS A 248 PHE A 256 1 O LYS A 248 N LEU A 198 SHEET 3 AA2 8 GLU A 268 THR A 277 -1 O TYR A 275 N VAL A 249 SHEET 4 AA2 8 CYS A 472 GLY A 478 -1 O MET A 477 N LEU A 272 SHEET 5 AA2 8 ILE A 421 SER A 428 -1 N TYR A 427 O GLY A 474 SHEET 6 AA2 8 VAL A 410 LEU A 418 -1 N LEU A 416 O ALA A 424 SHEET 7 AA2 8 THR A 388 PRO A 394 -1 N VAL A 390 O ASP A 415 SHEET 8 AA2 8 ALA A 320 GLN A 323 1 N ALA A 320 O PHE A 389 SHEET 1 AA3 3 LEU A 205 GLN A 206 0 SHEET 2 AA3 3 ASP A 227 LEU A 230 -1 O TYR A 229 N GLN A 206 SHEET 3 AA3 3 ALA A 218 HIS A 220 -1 N THR A 219 O LEU A 228 SHEET 1 AA4 2 GLN A 304 PRO A 306 0 SHEET 2 AA4 2 VAL A 312 ASP A 314 -1 O TYR A 313 N LEU A 305 CRYST1 84.196 84.196 147.984 90.00 90.00 90.00 P 41 21 2 8 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 0.011877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006757 0.00000