HEADER DNA BINDING PROTEIN 02-JUL-19 6KDU 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 ATCC: 25618; SOURCE 6 GENE: LIGA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS LIGASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.RAMACHANDRAN,A.SHUKLA,M.AFSAR REVDAT 3 22-NOV-23 6KDU 1 REMARK REVDAT 2 09-JUN-21 6KDU 1 JRNL REVDAT 1 01-JUL-20 6KDU 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. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28693 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1420 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 48.0840 - 4.7384 1.00 2965 163 0.2063 0.2182 REMARK 3 2 4.7384 - 3.7615 1.00 2792 148 0.1713 0.2004 REMARK 3 3 3.7615 - 3.2861 1.00 2749 137 0.2059 0.2421 REMARK 3 4 3.2861 - 2.9857 1.00 2716 140 0.2388 0.3175 REMARK 3 5 2.9857 - 2.7718 1.00 2693 138 0.2377 0.2556 REMARK 3 6 2.7718 - 2.6084 1.00 2683 145 0.2260 0.2917 REMARK 3 7 2.6084 - 2.4777 1.00 2676 136 0.2260 0.2635 REMARK 3 8 2.4777 - 2.3699 1.00 2684 133 0.2217 0.2865 REMARK 3 9 2.3699 - 2.2786 1.00 2658 139 0.2269 0.2879 REMARK 3 10 2.2786 - 2.2000 1.00 2657 141 0.2584 0.2855 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.72 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 6KDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9784 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI111 WITH LN2 REMARK 200 CLOSED LOOP COOLING REMARK 200 OPTICS : CILINDRICAL MIRROR WITH 50 NM PT REMARK 200 -COATING REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28776 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 48.084 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.4000 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 : 16.40 REMARK 200 R MERGE FOR SHELL (I) : 0.93900 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 REMARK 200 STARTING MODEL: 1ZAU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES NA PH=7.6 0.1M NACL 1.5 M 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 66.94500 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 133.89000 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 100.41750 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 167.36250 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 33.47250 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 66.94500 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 133.89000 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 167.36250 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 100.41750 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 33.47250 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: 850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 583 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 601 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 603 LIES ON A SPECIAL POSITION. 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 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 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 8 CG CD OE1 NE2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 201 CG CD OE1 OE2 REMARK 470 LYS A 221 CG CD CE NZ REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 ARG A 309 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 315 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 HZ3 LYS A 123 O1P AMP A 401 1.31 REMARK 500 NZ LYS A 123 O1P AMP A 401 1.33 REMARK 500 CE LYS A 123 O1P AMP A 401 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 182 CZ ARG A 182 NH1 -0.079 REMARK 500 GLU A 184 CD GLU A 184 OE1 -0.076 REMARK 500 GLU A 184 CD GLU A 184 OE2 -0.074 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 ARG A 230 52.11 -90.48 REMARK 500 HIS A 236 24.88 -144.99 REMARK 500 PHE A 244 112.09 -167.12 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 AMP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NMN 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDEU5 RELATED DB: SASBDB REMARK 900 ADENYLATION DOMAIN OF MTBLIGA DBREF 6KDU A 8 328 UNP P9WNV1 DNLJ_MYCTU 8 328 SEQADV 6KDU ALA A 22 UNP P9WNV1 GLU 22 ENGINEERED MUTATION SEQADV 6KDU HIS A 329 UNP P9WNV1 EXPRESSION TAG SEQADV 6KDU HIS A 330 UNP P9WNV1 EXPRESSION TAG SEQADV 6KDU HIS A 331 UNP P9WNV1 EXPRESSION TAG SEQADV 6KDU HIS A 332 UNP P9WNV1 EXPRESSION TAG SEQADV 6KDU HIS A 333 UNP P9WNV1 EXPRESSION TAG SEQADV 6KDU HIS A 334 UNP P9WNV1 EXPRESSION TAG SEQRES 1 A 327 GLN THR ALA PRO GLU VAL LEU ARG GLN TRP GLN ALA LEU SEQRES 2 A 327 ALA ALA GLU VAL ARG GLU HIS GLN PHE ARG TYR TYR VAL SEQRES 3 A 327 ARG ASP ALA PRO ILE ILE SER ASP ALA GLU PHE ASP GLU SEQRES 4 A 327 LEU LEU ARG ARG LEU GLU ALA LEU GLU GLU GLN HIS PRO SEQRES 5 A 327 GLU LEU ARG THR PRO ASP SER PRO THR GLN LEU VAL GLY SEQRES 6 A 327 GLY ALA GLY PHE ALA THR ASP PHE GLU PRO VAL ASP HIS SEQRES 7 A 327 LEU GLU ARG MET LEU SER LEU ASP ASN ALA PHE THR ALA SEQRES 8 A 327 ASP GLU LEU ALA ALA TRP ALA GLY ARG ILE HIS ALA GLU SEQRES 9 A 327 VAL GLY ASP ALA ALA HIS TYR LEU CYS GLU LEU LYS ILE SEQRES 10 A 327 ASP GLY VAL ALA LEU SER LEU VAL TYR ARG GLU GLY ARG SEQRES 11 A 327 LEU THR ARG ALA SER THR ARG GLY ASP GLY ARG THR GLY SEQRES 12 A 327 GLU ASP VAL THR LEU ASN ALA ARG THR ILE ALA ASP VAL SEQRES 13 A 327 PRO GLU ARG LEU THR PRO GLY ASP ASP TYR PRO VAL PRO SEQRES 14 A 327 GLU VAL LEU GLU VAL ARG GLY GLU VAL PHE PHE ARG LEU SEQRES 15 A 327 ASP ASP PHE GLN ALA LEU ASN ALA SER LEU VAL GLU GLU SEQRES 16 A 327 GLY LYS ALA PRO PHE ALA ASN PRO ARG ASN SER ALA ALA SEQRES 17 A 327 GLY SER LEU ARG GLN LYS ASP PRO ALA VAL THR ALA ARG SEQRES 18 A 327 ARG ARG LEU ARG MET ILE CYS HIS GLY LEU GLY HIS VAL SEQRES 19 A 327 GLU GLY PHE ARG PRO ALA THR LEU HIS GLN ALA TYR LEU SEQRES 20 A 327 ALA LEU ARG ALA TRP GLY LEU PRO VAL SER GLU HIS THR SEQRES 21 A 327 THR LEU ALA THR ASP LEU ALA GLY VAL ARG GLU ARG ILE SEQRES 22 A 327 ASP TYR TRP GLY GLU HIS ARG HIS GLU VAL ASP HIS GLU SEQRES 23 A 327 ILE ASP GLY VAL VAL VAL LYS VAL ASP GLU VAL ALA LEU SEQRES 24 A 327 GLN ARG ARG LEU GLY SER THR SER ARG ALA PRO ARG TRP SEQRES 25 A 327 ALA ILE ALA TYR LYS TYR PRO PRO GLU HIS HIS HIS HIS SEQRES 26 A 327 HIS HIS HET AMP A 401 35 HET NMN A 402 36 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE HETNAM SO4 SULFATE ION HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 NMN C11 H16 N2 O8 P 1+ FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 HOH *103(H2 O) HELIX 1 AA1 THR A 9 VAL A 33 1 25 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 SER A 66 LEU A 70 5 5 HELIX 5 AA5 THR A 97 GLY A 113 1 17 HELIX 6 AA6 ASP A 114 ALA A 116 5 3 HELIX 7 AA7 VAL A 153 ARG A 158 1 6 HELIX 8 AA8 ARG A 188 GLU A 202 1 15 HELIX 9 AA9 ASN A 209 ARG A 219 1 11 HELIX 10 AB1 ASP A 222 ARG A 228 1 7 HELIX 11 AB2 THR A 248 GLY A 260 1 13 HELIX 12 AB3 ASP A 272 ARG A 287 1 16 HELIX 13 AB4 HIS A 288 VAL A 290 5 3 HELIX 14 AB5 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 ASN A 94 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 LEU A 119 O LYS A 300 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 137 SER A 142 0 SHEET 2 AA3 4 VAL A 127 ARG A 134 -1 N ARG A 134 O ARG A 137 SHEET 3 AA3 4 VAL A 178 PHE A 186 -1 O VAL A 185 N VAL A 127 SHEET 4 AA3 4 ARG A 232 GLU A 242 -1 O GLY A 239 N GLU A 180 SITE 1 AC1 13 SER A 91 LEU A 92 ASN A 94 GLU A 121 SITE 2 AC1 13 LEU A 122 LYS A 123 ILE A 124 ARG A 144 SITE 3 AC1 13 GLU A 184 HIS A 236 ASP A 295 LYS A 300 SITE 4 AC1 13 LYS A 324 SITE 1 AC2 10 HIS A 27 TYR A 31 TYR A 32 PRO A 37 SITE 2 AC2 10 ILE A 39 SER A 40 ASP A 41 PHE A 44 SITE 3 AC2 10 ASP A 45 HOH A 560 SITE 1 AC3 6 VAL A 127 ALA A 128 ARG A 144 HOH A 501 SITE 2 AC3 6 HOH A 510 HOH A 525 SITE 1 AC4 5 ARG A 30 ARG A 34 VAL A 163 GLU A 165 SITE 2 AC4 5 HOH A 515 SITE 1 AC5 2 GLY A 243 PHE A 244 CRYST1 96.168 96.168 200.835 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 0.010398 0.006004 0.000000 0.00000 SCALE2 0.000000 0.012007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004979 0.00000