HEADER LIGASE 23-AUG-19 6KSD TITLE STRUCTURAL BASIS FOR DOMAIN ROTATION DURING ADENYLATION OF ACTIVE SITE TITLE 2 K123 AND FRAGMENT LIBRARY SCREENING AGAINST NAD+ -DEPENDENT DNA TITLE 3 LIGASE FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LIGA,POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD(+)]; COMPND 5 EC: 6.5.1.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: LIGA, LIG, RV3014C, MTV012.28C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR R.RAMACHANDRAN,A.SHUKLA,M.AFSAR REVDAT 3 22-NOV-23 6KSD 1 REMARK REVDAT 2 09-JUN-21 6KSD 1 JRNL REVDAT 1 26-AUG-20 6KSD 0 JRNL AUTH M.AFSAR,A.SHUKLA,N.KUMAR,R.RAMACHANDRAN JRNL TITL SALT BRIDGES AT THE SUBDOMAIN INTERFACES OF THE ADENYLATION JRNL TITL 2 DOMAIN AND ACTIVE-SITE RESIDUES OF MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS NAD + -DEPENDENT DNA LIGASE A (MTBLIGA) ARE JRNL TITL 4 IMPORTANT FOR THE INITIAL STEPS OF NICK-SEALING ACTIVITY. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 77 776 2021 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 34076591 JRNL DOI 10.1107/S2059798321003107 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 19315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.266 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 955 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 46.5570 - 4.7811 0.99 2815 151 0.2549 0.2730 REMARK 3 2 4.7811 - 3.7955 0.98 2637 127 0.2217 0.2226 REMARK 3 3 3.7955 - 3.3159 0.98 2574 147 0.2661 0.2815 REMARK 3 4 3.3159 - 3.0127 1.00 2582 148 0.3007 0.3516 REMARK 3 5 3.0127 - 2.7968 0.99 2574 148 0.3202 0.3985 REMARK 3 6 2.7968 - 2.6320 1.00 2593 122 0.3198 0.4155 REMARK 3 7 2.6320 - 2.5002 1.00 2585 112 0.3145 0.3981 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.44 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6KSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : WATER-COOLED DCM WITH SI (111) REMARK 200 OR SI(220) CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19550 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 46.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.85300 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 REMARK 200 STARTING MODEL: 1ZAU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES NA PH=7.6 0.1M NACL 1.5M REMARK 280 AMMONIUM SULFATE, PH 7.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.60067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 133.20133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 99.90100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 166.50167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.30033 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 66.60067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 133.20133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 166.50167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 99.90100 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 33.30033 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 TOTAL BURIED SURFACE AREA: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 520 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 538 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 570 LIES ON A SPECIAL POSITION. 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 VAL A 13 CG1 CG2 REMARK 470 LEU A 14 CG CD1 CD2 REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 16 CG CD OE1 NE2 REMARK 470 LEU A 20 CG CD1 CD2 REMARK 470 GLU A 22 CG CD OE1 OE2 REMARK 470 VAL A 24 CG1 CG2 REMARK 470 SER A 40 OG REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 LEU A 51 CG CD1 CD2 REMARK 470 LEU A 54 CG CD1 CD2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 GLN A 57 CG CD OE1 NE2 REMARK 470 GLU A 60 CG CD OE1 OE2 REMARK 470 ARG A 62 CG CD NE CZ NH1 NH2 REMARK 470 THR A 68 OG1 CG2 REMARK 470 GLN A 69 CG CD OE1 NE2 REMARK 470 LEU A 70 CG CD1 CD2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 96 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 107 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 VAL A 112 CG1 CG2 REMARK 470 ARG A 140 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 171 CG OD1 OD2 REMARK 470 ASP A 172 CG OD1 OD2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 LYS A 204 CG CD CE NZ REMARK 470 ARG A 230 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 244 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 249 CG CD1 CD2 REMARK 470 VAL A 263 CG1 CG2 REMARK 470 LEU A 269 CG CD1 CD2 REMARK 470 LEU A 273 CG CD1 CD2 REMARK 470 ASP A 281 CG OD1 OD2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 ARG A 309 CG CD NE CZ NH1 NH2 REMARK 470 SER A 312 OG REMARK 470 ARG A 315 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 327 CG CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 101 CB - CA - C ANGL. DEV. = 25.2 DEGREES REMARK 500 LEU A 167 CB - CG - CD1 ANGL. DEV. = -10.9 DEGREES 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 ALA A 36 79.58 -150.76 REMARK 500 LEU A 70 -6.60 84.41 REMARK 500 ALA A 115 42.90 -85.59 REMARK 500 TYR A 133 58.69 -114.72 REMARK 500 PHE A 244 -59.57 -121.76 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 NMN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 DBREF 6KSD A 8 328 UNP P9WNV1 DNLJ_MYCTU 8 328 SEQADV 6KSD ALA A 123 UNP P9WNV1 LYS 123 ENGINEERED MUTATION SEQRES 1 A 321 GLN THR ALA PRO GLU VAL LEU ARG GLN TRP GLN ALA LEU SEQRES 2 A 321 ALA GLU GLU VAL ARG GLU HIS GLN PHE ARG TYR TYR VAL SEQRES 3 A 321 ARG ASP ALA PRO ILE ILE SER ASP ALA GLU PHE ASP GLU SEQRES 4 A 321 LEU LEU ARG ARG LEU GLU ALA LEU GLU GLU GLN HIS PRO SEQRES 5 A 321 GLU LEU ARG THR PRO ASP SER PRO THR GLN LEU VAL GLY SEQRES 6 A 321 GLY ALA GLY PHE ALA THR ASP PHE GLU PRO VAL ASP HIS SEQRES 7 A 321 LEU GLU ARG MET LEU SER LEU ASP ASN ALA PHE THR ALA SEQRES 8 A 321 ASP GLU LEU ALA ALA TRP ALA GLY ARG ILE HIS ALA GLU SEQRES 9 A 321 VAL GLY ASP ALA ALA HIS TYR LEU CYS GLU LEU ALA ILE SEQRES 10 A 321 ASP GLY VAL ALA LEU SER LEU VAL TYR ARG GLU GLY ARG SEQRES 11 A 321 LEU THR ARG ALA SER THR ARG GLY ASP GLY ARG THR GLY SEQRES 12 A 321 GLU ASP VAL THR LEU ASN ALA ARG THR ILE ALA ASP VAL SEQRES 13 A 321 PRO GLU ARG LEU THR PRO GLY ASP ASP TYR PRO VAL PRO SEQRES 14 A 321 GLU VAL LEU GLU VAL ARG GLY GLU VAL PHE PHE ARG LEU SEQRES 15 A 321 ASP ASP PHE GLN ALA LEU ASN ALA SER LEU VAL GLU GLU SEQRES 16 A 321 GLY LYS ALA PRO PHE ALA ASN PRO ARG ASN SER ALA ALA SEQRES 17 A 321 GLY SER LEU ARG GLN LYS ASP PRO ALA VAL THR ALA ARG SEQRES 18 A 321 ARG ARG LEU ARG MET ILE CYS HIS GLY LEU GLY HIS VAL SEQRES 19 A 321 GLU GLY PHE ARG PRO ALA THR LEU HIS GLN ALA TYR LEU SEQRES 20 A 321 ALA LEU ARG ALA TRP GLY LEU PRO VAL SER GLU HIS THR SEQRES 21 A 321 THR LEU ALA THR ASP LEU ALA GLY VAL ARG GLU ARG ILE SEQRES 22 A 321 ASP TYR TRP GLY GLU HIS ARG HIS GLU VAL ASP HIS GLU SEQRES 23 A 321 ILE ASP GLY VAL VAL VAL LYS VAL ASP GLU VAL ALA LEU SEQRES 24 A 321 GLN ARG ARG LEU GLY SER THR SER ARG ALA PRO ARG TRP SEQRES 25 A 321 ALA ILE ALA TYR LYS TYR PRO PRO GLU HET NMN A 401 72 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE HETNAM SO4 SULFATE ION HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE FORMUL 2 NMN C11 H16 N2 O8 P 1+ FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *72(H2 O) HELIX 1 AA1 ALA A 10 VAL A 33 1 24 HELIX 2 AA2 SER A 40 HIS A 58 1 19 HELIX 3 AA3 PRO A 59 ARG A 62 5 4 HELIX 4 AA4 THR A 97 VAL A 112 1 16 HELIX 5 AA5 ARG A 134 ARG A 137 5 4 HELIX 6 AA6 VAL A 153 ILE A 160 1 8 HELIX 7 AA7 ARG A 188 GLU A 202 1 15 HELIX 8 AA8 ASN A 209 ARG A 219 1 11 HELIX 9 AA9 ASP A 222 ARG A 229 1 8 HELIX 10 AB1 THR A 248 TRP A 259 1 12 HELIX 11 AB2 ASP A 272 ARG A 287 1 16 HELIX 12 AB3 HIS A 288 VAL A 290 5 3 HELIX 13 AB4 GLU A 303 GLY A 311 1 9 SHEET 1 AA1 2 PRO A 82 ASP A 84 0 SHEET 2 AA1 2 THR A 149 GLU A 151 -1 O GLY A 150 N VAL A 83 SHEET 1 AA2 5 ASP A 93 ALA A 95 0 SHEET 2 AA2 5 ALA A 320 LYS A 324 1 O ALA A 322 N ALA A 95 SHEET 3 AA2 5 ILE A 294 VAL A 301 -1 N VAL A 297 O TYR A 323 SHEET 4 AA2 5 TYR A 118 ILE A 124 -1 N GLU A 121 O VAL A 298 SHEET 5 AA2 5 THR A 268 ALA A 270 -1 O ALA A 270 N TYR A 118 SHEET 1 AA3 4 ARG A 140 THR A 143 0 SHEET 2 AA3 4 VAL A 127 VAL A 132 -1 N SER A 130 O SER A 142 SHEET 3 AA3 4 LEU A 179 PHE A 186 -1 O GLY A 183 N LEU A 129 SHEET 4 AA3 4 ARG A 232 VAL A 241 -1 O GLY A 239 N GLU A 180 SITE 1 AC1 9 HIS A 27 TYR A 31 TYR A 32 PRO A 37 SITE 2 AC1 9 ILE A 39 ASP A 41 PHE A 44 ASP A 45 SITE 3 AC1 9 HOH A 534 SITE 1 AC2 4 ARG A 30 ARG A 34 VAL A 163 GLU A 165 SITE 1 AC3 4 VAL A 127 ALA A 128 ARG A 144 HOH A 511 SITE 1 AC4 4 SER A 264 GLU A 265 HIS A 266 HIS A 292 CRYST1 95.750 95.750 199.802 90.00 90.00 120.00 P 61 2 2 12 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 0.010444 0.006030 0.000000 0.00000 SCALE2 0.000000 0.012060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005005 0.00000