HEADER TRANSFERASE/ANTIBIOTIC 11-JAN-19 6NMN TITLE TERNARY COMPLEX STRUCTURE OF THE T130K MUTANT OF ANT-4'' WITH NEOMYCIN TITLE 2 AND ATP (NO PYROPHOSPHATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: KANAMYCIN NUCLEOTIDYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_COMMON: BACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 6 PPPARG4; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS AMINOGLYCOSIDE NUCELOTIDYL TRANSFERASE (ANT) AMINOGLYCOSIDE MODIFYING KEYWDS 2 ENZYMES (AGMES) DNA POLYMERASE, ANTIBIOTIC, TRANSFERASE-ANTIBIOTIC KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.CUNEO,B.SELVARAJ REVDAT 4 13-MAR-24 6NMN 1 REMARK LINK REVDAT 3 26-FEB-20 6NMN 1 JRNL REVDAT 2 29-JAN-20 6NMN 1 JRNL REVDAT 1 15-JAN-20 6NMN 0 JRNL AUTH B.SELVARAJ,M.J.CUNEO JRNL TITL CATCH AND RELEASE: A NOVEL VARIATION OF THE ARCHETYPAL JRNL TITL 2 NUCLEOTIDYL TRANSFER REACTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 54657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2812 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 57.3525 - 4.8851 0.99 3120 182 0.1775 0.1989 REMARK 3 2 4.8851 - 3.8777 0.99 2931 147 0.1485 0.1763 REMARK 3 3 3.8777 - 3.3876 0.99 2884 149 0.1673 0.1918 REMARK 3 4 3.3876 - 3.0779 0.99 2838 136 0.1775 0.2335 REMARK 3 5 3.0779 - 2.8573 0.98 2816 152 0.1945 0.2052 REMARK 3 6 2.8573 - 2.6888 0.98 2778 148 0.1897 0.2179 REMARK 3 7 2.6888 - 2.5542 0.98 2757 139 0.1913 0.2198 REMARK 3 8 2.5542 - 2.4430 0.97 2714 147 0.1900 0.2340 REMARK 3 9 2.4430 - 2.3489 0.96 2687 135 0.1921 0.2327 REMARK 3 10 2.3489 - 2.2679 0.92 2588 149 0.1907 0.2191 REMARK 3 11 2.2679 - 2.1970 0.92 2574 145 0.1947 0.2496 REMARK 3 12 2.1970 - 2.1342 0.89 2440 144 0.1976 0.2221 REMARK 3 13 2.1342 - 2.0780 0.89 2476 136 0.2032 0.2659 REMARK 3 14 2.0780 - 2.0273 0.88 2439 142 0.2056 0.2393 REMARK 3 15 2.0273 - 1.9812 0.85 2374 143 0.2145 0.2459 REMARK 3 16 1.9812 - 1.9390 0.87 2340 135 0.2034 0.2734 REMARK 3 17 1.9390 - 1.9002 0.84 2335 130 0.2205 0.2650 REMARK 3 18 1.9002 - 1.8644 0.83 2280 110 0.2331 0.3108 REMARK 3 19 1.8644 - 1.8311 0.82 2271 131 0.2513 0.2713 REMARK 3 20 1.8311 - 1.8000 0.80 2203 112 0.2481 0.3038 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 4456 REMARK 3 ANGLE : 0.776 6080 REMARK 3 CHIRALITY : 0.047 677 REMARK 3 PLANARITY : 0.004 769 REMARK 3 DIHEDRAL : 4.082 3517 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 6NMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54803 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 60.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.76000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.24800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZED IN 9-10% PEG 5K MME, 0.1 REMARK 280 M TRIS PH 7.5-8.0, 0.1-0.2 M CACL2. THE CRYSTALS WERE REMARK 280 TRANSFERRED TO A CRYOSOLUTION CONTAINING 9-10% PEG 5K MME, 0.1 M REMARK 280 TRIS PH 7.5-8.0, 10 MM MGCL2 AND 30% GLYCEROL FOR VARYING TIME REMARK 280 INTERVALS (3-30 MIN), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 285K 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 181.72500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.02500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 90.86250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.02500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.02500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 272.58750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.02500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.02500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 90.86250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.02500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.02500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 272.58750 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 181.72500 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: 8630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 B1134 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET B 171 N CA C O CB CG SD REMARK 480 MET B 171 CE 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 O HOH A 418 O HOH B 1031 2.14 REMARK 500 OE1 GLU B 52 O3 NMY B 900 2.15 REMARK 500 O HOH B 1004 O HOH B 1038 2.16 REMARK 500 O ASP A 45 O HOH A 401 2.17 REMARK 500 OE1 GLU B 60 O HOH B 1001 2.17 REMARK 500 OD2 ASP A 246 O HOH A 402 2.18 REMARK 500 O HOH B 1196 O HOH B 1218 2.19 REMARK 500 OE1 GLN B 156 O HOH B 1002 2.19 REMARK 500 O HOH B 1194 O HOH B 1204 2.19 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 ASP A 45 -111.19 -74.61 REMARK 500 GLU A 63 89.86 -160.28 REMARK 500 TYR B 37 -168.10 -122.48 REMARK 500 GLU B 63 89.94 -160.11 REMARK 500 REMARK 500 REMARK: NULL 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 A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 50 OD2 REMARK 620 2 GLU A 52 OE2 99.3 REMARK 620 3 A A 302 OP2 153.3 97.7 REMARK 620 4 HOH A 445 O 85.3 83.9 117.1 REMARK 620 5 HOH A 451 O 90.6 68.4 76.6 151.0 REMARK 620 6 GLU B 145 OE1 85.9 153.3 88.2 70.4 138.1 REMARK 620 7 GLU B 145 OE2 79.9 154.0 75.8 121.7 85.6 52.6 REMARK 620 N 1 2 3 4 5 6 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 145 OE1 REMARK 620 2 ASP B 50 OD1 103.6 REMARK 620 3 ASP B 50 OD2 88.7 49.2 REMARK 620 4 A B 901 OP1 97.6 107.2 156.4 REMARK 620 5 HOH B1016 O 143.6 53.5 92.6 69.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 145 OE1 REMARK 620 2 GLU A 145 OE2 50.1 REMARK 620 3 NMY B 900 O4 112.6 77.2 REMARK 620 4 HOH B1003 O 74.3 122.9 120.9 REMARK 620 5 HOH B1005 O 75.1 81.7 141.6 97.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide NMY A 301 and A A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide NMY B 900 and A B REMARK 800 901 DBREF 6NMN A 1 253 UNP Q57514 Q57514_GEOSE 1 253 DBREF 6NMN B 1 253 UNP Q57514 Q57514_GEOSE 1 253 SEQADV 6NMN GLY A -2 UNP Q57514 EXPRESSION TAG SEQADV 6NMN SER A -1 UNP Q57514 EXPRESSION TAG SEQADV 6NMN HIS A 0 UNP Q57514 EXPRESSION TAG SEQADV 6NMN ASP A 80 UNP Q57514 TYR 80 CONFLICT SEQADV 6NMN GLY B -2 UNP Q57514 EXPRESSION TAG SEQADV 6NMN SER B -1 UNP Q57514 EXPRESSION TAG SEQADV 6NMN HIS B 0 UNP Q57514 EXPRESSION TAG SEQADV 6NMN ASP B 80 UNP Q57514 TYR 80 CONFLICT SEQRES 1 A 256 GLY SER HIS MET ASN GLY PRO ILE ILE MET THR ARG GLU SEQRES 2 A 256 GLU ARG MET LYS ILE VAL HIS GLU ILE LYS GLU ARG ILE SEQRES 3 A 256 LEU ASP LYS TYR GLY ASP ASP VAL LYS ALA ILE GLY VAL SEQRES 4 A 256 TYR GLY SER LEU GLY ARG GLN THR ASP GLY PRO TYR SER SEQRES 5 A 256 ASP ILE GLU MET MET CYS VAL MET SER THR GLU GLU ALA SEQRES 6 A 256 GLU PHE SER HIS GLU TRP THR THR GLY GLU TRP LYS VAL SEQRES 7 A 256 GLU VAL ASN PHE ASP SER GLU GLU ILE LEU LEU ASP TYR SEQRES 8 A 256 ALA SER GLN VAL GLU SER ASP TRP PRO LEU THR HIS GLY SEQRES 9 A 256 GLN PHE PHE SER ILE LEU PRO ILE TYR ASP SER GLY GLY SEQRES 10 A 256 TYR LEU GLU LYS VAL TYR GLN THR ALA LYS SER VAL GLU SEQRES 11 A 256 ALA GLN LYS PHE HIS ASP ALA ILE CYS ALA LEU ILE VAL SEQRES 12 A 256 GLU GLU LEU PHE GLU TYR ALA GLY LYS TRP ARG ASN ILE SEQRES 13 A 256 ARG VAL GLN GLY PRO THR THR PHE LEU PRO SER LEU THR SEQRES 14 A 256 VAL GLN VAL ALA MET ALA GLY ALA MET LEU ILE GLY LEU SEQRES 15 A 256 HIS HIS ARG ILE CYS TYR THR THR SER ALA SER VAL LEU SEQRES 16 A 256 THR GLU ALA VAL LYS GLN SER ASP LEU PRO SER GLY TYR SEQRES 17 A 256 ASP HIS LEU CYS GLN PHE VAL MET SER GLY GLN LEU SER SEQRES 18 A 256 ASP SER GLU LYS LEU LEU GLU SER LEU GLU ASN PHE TRP SEQRES 19 A 256 ASN GLY ILE GLN GLU TRP THR GLU ARG HIS GLY TYR ILE SEQRES 20 A 256 VAL ASP VAL SER LYS ARG ILE PRO PHE SEQRES 1 B 256 GLY SER HIS MET ASN GLY PRO ILE ILE MET THR ARG GLU SEQRES 2 B 256 GLU ARG MET LYS ILE VAL HIS GLU ILE LYS GLU ARG ILE SEQRES 3 B 256 LEU ASP LYS TYR GLY ASP ASP VAL LYS ALA ILE GLY VAL SEQRES 4 B 256 TYR GLY SER LEU GLY ARG GLN THR ASP GLY PRO TYR SER SEQRES 5 B 256 ASP ILE GLU MET MET CYS VAL MET SER THR GLU GLU ALA SEQRES 6 B 256 GLU PHE SER HIS GLU TRP THR THR GLY GLU TRP LYS VAL SEQRES 7 B 256 GLU VAL ASN PHE ASP SER GLU GLU ILE LEU LEU ASP TYR SEQRES 8 B 256 ALA SER GLN VAL GLU SER ASP TRP PRO LEU THR HIS GLY SEQRES 9 B 256 GLN PHE PHE SER ILE LEU PRO ILE TYR ASP SER GLY GLY SEQRES 10 B 256 TYR LEU GLU LYS VAL TYR GLN THR ALA LYS SER VAL GLU SEQRES 11 B 256 ALA GLN LYS PHE HIS ASP ALA ILE CYS ALA LEU ILE VAL SEQRES 12 B 256 GLU GLU LEU PHE GLU TYR ALA GLY LYS TRP ARG ASN ILE SEQRES 13 B 256 ARG VAL GLN GLY PRO THR THR PHE LEU PRO SER LEU THR SEQRES 14 B 256 VAL GLN VAL ALA MET ALA GLY ALA MET LEU ILE GLY LEU SEQRES 15 B 256 HIS HIS ARG ILE CYS TYR THR THR SER ALA SER VAL LEU SEQRES 16 B 256 THR GLU ALA VAL LYS GLN SER ASP LEU PRO SER GLY TYR SEQRES 17 B 256 ASP HIS LEU CYS GLN PHE VAL MET SER GLY GLN LEU SER SEQRES 18 B 256 ASP SER GLU LYS LEU LEU GLU SER LEU GLU ASN PHE TRP SEQRES 19 B 256 ASN GLY ILE GLN GLU TRP THR GLU ARG HIS GLY TYR ILE SEQRES 20 B 256 VAL ASP VAL SER LYS ARG ILE PRO PHE HET NMY A 301 42 HET A A 302 22 HET MG A 303 1 HET MG A 304 1 HET MG A 305 1 HET NMY B 900 42 HET A B 901 22 HETNAM NMY NEOMYCIN HETNAM A ADENOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN NMY MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN FORMUL 3 NMY 2(C23 H46 N6 O13) FORMUL 4 A 2(C10 H14 N5 O7 P) FORMUL 5 MG 3(MG 2+) FORMUL 10 HOH *507(H2 O) HELIX 1 AA1 THR A 8 GLY A 28 1 21 HELIX 2 AA2 GLU A 82 SER A 90 1 9 HELIX 3 AA3 ASP A 95 HIS A 100 1 6 HELIX 4 AA4 GLY A 101 SER A 105 5 5 HELIX 5 AA5 GLY A 114 SER A 125 1 12 HELIX 6 AA6 GLU A 127 GLU A 142 1 16 HELIX 7 AA7 GLU A 142 GLY A 157 1 16 HELIX 8 AA8 PRO A 158 THR A 160 5 3 HELIX 9 AA9 PHE A 161 ARG A 182 1 22 HELIX 10 AB1 SER A 190 VAL A 196 1 7 HELIX 11 AB2 GLY A 204 GLY A 215 1 12 HELIX 12 AB3 ASP A 219 GLY A 242 1 24 HELIX 13 AB4 THR B 8 GLY B 28 1 21 HELIX 14 AB5 GLU B 82 SER B 90 1 9 HELIX 15 AB6 ASP B 95 HIS B 100 1 6 HELIX 16 AB7 GLY B 101 SER B 105 5 5 HELIX 17 AB8 GLY B 114 SER B 125 1 12 HELIX 18 AB9 GLU B 127 GLU B 142 1 16 HELIX 19 AC1 GLU B 142 GLY B 157 1 16 HELIX 20 AC2 PRO B 158 THR B 160 5 3 HELIX 21 AC3 PHE B 161 ARG B 182 1 22 HELIX 22 AC4 THR B 187 ALA B 189 5 3 HELIX 23 AC5 SER B 190 VAL B 196 1 7 HELIX 24 AC6 GLY B 204 GLY B 215 1 12 HELIX 25 AC7 ASP B 219 GLY B 242 1 24 SHEET 1 AA1 5 GLU A 63 THR A 69 0 SHEET 2 AA1 5 LYS A 74 SER A 81 -1 O PHE A 79 N PHE A 64 SHEET 3 AA1 5 ILE A 51 MET A 57 1 N CYS A 55 O ASP A 80 SHEET 4 AA1 5 VAL A 31 VAL A 36 -1 N LYS A 32 O VAL A 56 SHEET 5 AA1 5 LEU A 107 ASP A 111 -1 O TYR A 110 N ILE A 34 SHEET 1 AA2 5 GLU B 63 THR B 69 0 SHEET 2 AA2 5 LYS B 74 SER B 81 -1 O PHE B 79 N PHE B 64 SHEET 3 AA2 5 ILE B 51 MET B 57 1 N MET B 57 O ASP B 80 SHEET 4 AA2 5 VAL B 31 VAL B 36 -1 N LYS B 32 O VAL B 56 SHEET 5 AA2 5 LEU B 107 ASP B 111 -1 O TYR B 110 N ILE B 34 LINK O4 NMY A 301 P A A 302 1555 1555 1.56 LINK O4 NMY B 900 P A B 901 1555 1555 1.56 LINK OD2 ASP A 50 MG MG A 304 1555 1555 2.16 LINK OE2AGLU A 52 MG MG A 304 1555 1555 2.22 LINK OE1 GLU A 145 MG MG A 303 1555 1555 2.56 LINK OE1 GLU A 145 MG MG A 305 1555 1555 2.77 LINK OE2 GLU A 145 MG MG A 305 1555 1555 2.34 LINK OP2 A A 302 MG MG A 304 1555 1555 2.30 LINK MG MG A 303 OD1 ASP B 50 1555 1555 2.89 LINK MG MG A 303 OD2 ASP B 50 1555 1555 2.00 LINK MG MG A 303 OP1 A B 901 1555 1555 2.29 LINK MG MG A 303 O HOH B1016 1555 1555 2.29 LINK MG MG A 304 O HOH A 445 1555 1555 2.60 LINK MG MG A 304 O HOH A 451 1555 1555 2.57 LINK MG MG A 304 OE1 GLU B 145 1555 1555 2.65 LINK MG MG A 304 OE2 GLU B 145 1555 1555 2.27 LINK MG MG A 305 O4 NMY B 900 1555 1555 2.15 LINK MG MG A 305 O HOH B1003 1555 1555 2.30 LINK MG MG A 305 O HOH B1005 1555 1555 2.28 CISPEP 1 GLY A 157 PRO A 158 0 -1.72 CISPEP 2 GLY B 157 PRO B 158 0 -1.50 SITE 1 AC1 7 GLU A 145 MG A 305 ASP B 50 NMY B 900 SITE 2 AC1 7 A B 901 HOH B1003 HOH B1016 SITE 1 AC2 7 ASP A 50 GLU A 52 NMY A 301 A A 302 SITE 2 AC2 7 HOH A 445 HOH A 451 GLU B 145 SITE 1 AC3 7 GLU A 145 MG A 303 GLU B 76 NMY B 900 SITE 2 AC3 7 A B 901 HOH B1003 HOH B1005 SITE 1 AC4 32 GLU A 52 GLU A 63 GLU A 67 GLU A 76 SITE 2 AC4 32 ASP A 80 TYR A 88 LEU A 98 THR A 99 SITE 3 AC4 32 GLN A 102 THR A 187 SER A 188 MG A 304 SITE 4 AC4 32 HOH A 409 HOH A 410 HOH A 418 HOH A 429 SITE 5 AC4 32 HOH A 434 HOH A 451 HOH A 466 HOH A 472 SITE 6 AC4 32 HOH A 481 HOH A 498 HOH A 509 HOH A 525 SITE 7 AC4 32 HOH A 590 GLU B 141 GLU B 145 LYS B 149 SITE 8 AC4 32 HOH B1031 HOH B1040 HOH B1075 HOH B1090 SITE 1 AC5 27 GLU A 141 GLU A 145 LYS A 149 MG A 303 SITE 2 AC5 27 MG A 305 HOH A 427 TYR B 37 GLU B 52 SITE 3 AC5 27 GLU B 63 GLU B 67 GLU B 76 ASP B 80 SITE 4 AC5 27 TYR B 88 LEU B 98 THR B 99 THR B 186 SITE 5 AC5 27 THR B 187 SER B 188 HOH B1005 HOH B1013 SITE 6 AC5 27 HOH B1016 HOH B1019 HOH B1028 HOH B1029 SITE 7 AC5 27 HOH B1037 HOH B1116 HOH B1199 CRYST1 58.050 58.050 363.450 90.00 90.00 90.00 P 41 21 2 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 0.017227 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017227 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002751 0.00000