HEADER TRANSFERASE/ANTIBIOTIC 16-MAY-19 6P08 TITLE TERNARY STRUCTURE OF THE E52D MUTANT OF ANT-4'' WITH NEOMYCIN, AMP AND TITLE 2 PYROPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: KANAMYCIN NUCLEOTIDYLTRANSFERASE; COMPND 3 CHAIN: A, D; COMPND 4 EC: 2.7.7.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SP.; SOURCE 3 ORGANISM_TAXID: 1409; SOURCE 4 GENE: KNT, KAN; 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 KEYWDS 2 MODIFYING ENZYMES (AGMES), DNA POLYMERASE, ANTIBIOTIC, TRANSFERASE- KEYWDS 3 ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.SELVARAJ,M.J.CUNEO REVDAT 4 11-OCT-23 6P08 1 LINK REVDAT 3 20-MAY-20 6P08 1 JRNL REVDAT 2 06-MAY-20 6P08 1 JRNL REVDAT 1 29-JAN-20 6P08 0 JRNL AUTH B.SELVARAJ,S.KOCAMAN,M.TRIFAS,E.H.SERPERSU,M.J.CUNEO JRNL TITL "CATCH AND RELEASE": A VARIATION OF THE ARCHETYPAL JRNL TITL 2 NUCLEOTIDYL TRANSFER REACTION JRNL REF ACS CATALYSIS V. 10 3548 2020 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.9B05201 REMARK 2 REMARK 2 RESOLUTION. 2.27 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 30482 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1424 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 49.6626 - 4.8915 0.99 2856 151 0.1632 0.1840 REMARK 3 2 4.8915 - 3.8830 0.99 2724 163 0.1549 0.1650 REMARK 3 3 3.8830 - 3.3923 1.00 2689 169 0.1797 0.2091 REMARK 3 4 3.3923 - 3.0822 0.99 2693 113 0.2033 0.2496 REMARK 3 5 3.0822 - 2.8613 0.99 2654 163 0.2220 0.2797 REMARK 3 6 2.8613 - 2.6926 0.97 2607 130 0.2281 0.2310 REMARK 3 7 2.6926 - 2.5577 0.96 2594 128 0.2174 0.2812 REMARK 3 8 2.5577 - 2.4464 0.95 2540 132 0.2213 0.2736 REMARK 3 9 2.4464 - 2.3522 0.96 2548 140 0.2277 0.2668 REMARK 3 10 2.3522 - 2.2711 0.96 2532 132 0.2331 0.2735 REMARK 3 11 2.2711 - 2.2700 0.94 2496 128 0.2402 0.2899 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.390 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 : 0.006 4316 REMARK 3 ANGLE : 0.993 5874 REMARK 3 CHIRALITY : 0.079 658 REMARK 3 PLANARITY : 0.005 728 REMARK 3 DIHEDRAL : 8.840 3430 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 6P08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-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 : 23-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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30558 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 49.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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: 1KNY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8K, 0.1 M TRIS PH 8.0, 0.1 M REMARK 280 MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 29.87500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.74500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.74500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.87500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.65000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 10310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY D -2 REMARK 465 SER D -1 REMARK 465 HIS D 0 REMARK 465 MET D 1 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 OD1 ASP A 52 O HOH A 901 2.02 REMARK 500 O PRO A 47 O HOH A 902 2.13 REMARK 500 O22 PPV D 301 O HOH D 901 2.16 REMARK 500 OD2 ASP D 52 O HOH D 902 2.16 REMARK 500 O HOH D 903 O HOH D 1015 2.17 REMARK 500 NE2 GLN D 91 O HOH D 903 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 127 CA - CB - CG ANGL. DEV. = 17.7 DEGREES REMARK 500 ILE A 183 CG1 - CB - CG2 ANGL. DEV. = 15.2 DEGREES REMARK 500 GLU A 239 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 LYS D 14 CD - CE - NZ ANGL. DEV. = -18.2 DEGREES REMARK 500 LYS D 249 CD - CE - NZ ANGL. DEV. = -17.7 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 TYR A 37 -162.59 -121.72 REMARK 500 ASP A 50 -168.51 -104.83 REMARK 500 GLU A 63 96.56 -160.04 REMARK 500 SER A 105 49.03 -145.08 REMARK 500 ASP A 111 107.61 -160.86 REMARK 500 PRO A 252 34.31 -87.72 REMARK 500 TYR D 37 -162.70 -121.67 REMARK 500 ASP D 50 -168.40 -104.80 REMARK 500 GLU D 63 97.60 -160.04 REMARK 500 SER D 105 49.36 -145.16 REMARK 500 ASP D 111 106.58 -161.78 REMARK 500 GLU D 236 -72.00 -29.62 REMARK 500 PRO D 252 32.74 -86.48 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 GLN D 235 GLU D 236 132.52 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 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 50 OD2 REMARK 620 2 ASP A 52 OD1 110.4 REMARK 620 3 AMP A 306 O1P 115.8 95.8 REMARK 620 4 HOH A 901 O 162.7 53.0 74.3 REMARK 620 5 HOH A 911 O 111.4 84.4 129.2 65.6 REMARK 620 6 HOH A 913 O 68.9 62.3 156.6 96.2 60.7 REMARK 620 7 GLU D 145 OE2 85.1 164.0 72.9 111.9 93.9 130.2 REMARK 620 N 1 2 3 4 5 6 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 OD1 REMARK 620 2 ASP A 52 OD2 85.9 REMARK 620 3 PPV A 302 O31 162.6 101.5 REMARK 620 4 AMP A 306 O1P 97.4 77.7 99.5 REMARK 620 5 HOH A 927 O 86.7 80.6 79.2 157.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 308 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 145 OE1 REMARK 620 2 AMP A 305 O1P 74.7 REMARK 620 3 NMY A 307 O4 64.9 54.3 REMARK 620 4 ASP D 50 OD2 81.2 107.6 144.2 REMARK 620 5 ASP D 52 OD1 158.4 105.7 97.3 118.1 REMARK 620 6 ASP D 52 OD2 142.8 68.8 98.0 102.8 47.0 REMARK 620 7 HOH D 914 O 120.9 155.3 147.5 60.8 67.3 91.7 REMARK 620 8 HOH D 923 O 78.2 132.1 78.6 106.4 86.6 133.0 72.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AMP A 305 O1P REMARK 620 2 ASP D 50 OD1 100.6 REMARK 620 3 ASP D 52 OD2 79.0 82.7 REMARK 620 4 PPV D 301 O31 105.1 154.2 104.1 REMARK 620 5 HOH D 901 O 116.4 68.9 149.4 97.3 REMARK 620 6 HOH D 902 O 122.2 105.1 54.8 62.4 121.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NMY A 301 and AMP A REMARK 800 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues AMP A 305 and NMY A REMARK 800 307 DBREF 6P08 A 1 253 UNP P05058 KANU_BACSP 1 253 DBREF 6P08 D 1 253 UNP P05058 KANU_BACSP 1 253 SEQADV 6P08 GLY A -2 UNP P05058 EXPRESSION TAG SEQADV 6P08 SER A -1 UNP P05058 EXPRESSION TAG SEQADV 6P08 HIS A 0 UNP P05058 EXPRESSION TAG SEQADV 6P08 ASP A 52 UNP P05058 GLU 52 ENGINEERED MUTATION SEQADV 6P08 GLY D -2 UNP P05058 EXPRESSION TAG SEQADV 6P08 SER D -1 UNP P05058 EXPRESSION TAG SEQADV 6P08 HIS D 0 UNP P05058 EXPRESSION TAG SEQADV 6P08 ASP D 52 UNP P05058 GLU 52 ENGINEERED MUTATION 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 ASP 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 D 256 GLY SER HIS MET ASN GLY PRO ILE ILE MET THR ARG GLU SEQRES 2 D 256 GLU ARG MET LYS ILE VAL HIS GLU ILE LYS GLU ARG ILE SEQRES 3 D 256 LEU ASP LYS TYR GLY ASP ASP VAL LYS ALA ILE GLY VAL SEQRES 4 D 256 TYR GLY SER LEU GLY ARG GLN THR ASP GLY PRO TYR SER SEQRES 5 D 256 ASP ILE ASP MET MET CYS VAL MET SER THR GLU GLU ALA SEQRES 6 D 256 GLU PHE SER HIS GLU TRP THR THR GLY GLU TRP LYS VAL SEQRES 7 D 256 GLU VAL ASN PHE ASP SER GLU GLU ILE LEU LEU ASP TYR SEQRES 8 D 256 ALA SER GLN VAL GLU SER ASP TRP PRO LEU THR HIS GLY SEQRES 9 D 256 GLN PHE PHE SER ILE LEU PRO ILE TYR ASP SER GLY GLY SEQRES 10 D 256 TYR LEU GLU LYS VAL TYR GLN THR ALA LYS SER VAL GLU SEQRES 11 D 256 ALA GLN LYS PHE HIS ASP ALA ILE CYS ALA LEU ILE VAL SEQRES 12 D 256 GLU GLU LEU PHE GLU TYR ALA GLY LYS TRP ARG ASN ILE SEQRES 13 D 256 ARG VAL GLN GLY PRO THR THR PHE LEU PRO SER LEU THR SEQRES 14 D 256 VAL GLN VAL ALA MET ALA GLY ALA MET LEU ILE GLY LEU SEQRES 15 D 256 HIS HIS ARG ILE CYS TYR THR THR SER ALA SER VAL LEU SEQRES 16 D 256 THR GLU ALA VAL LYS GLN SER ASP LEU PRO SER GLY TYR SEQRES 17 D 256 ASP HIS LEU CYS GLN PHE VAL MET SER GLY GLN LEU SER SEQRES 18 D 256 ASP SER GLU LYS LEU LEU GLU SER LEU GLU ASN PHE TRP SEQRES 19 D 256 ASN GLY ILE GLN GLU TRP THR GLU ARG HIS GLY TYR ILE SEQRES 20 D 256 VAL ASP VAL SER LYS ARG ILE PRO PHE HET NMY A 301 42 HET PPV A 302 9 HET MG A 303 1 HET MG A 304 1 HET AMP A 305 22 HET AMP A 306 22 HET NMY A 307 42 HET MG A 308 1 HET PPV D 301 9 HET MG D 302 1 HETNAM NMY NEOMYCIN HETNAM PPV PYROPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETSYN NMY MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN FORMUL 3 NMY 2(C23 H46 N6 O13) FORMUL 4 PPV 2(H4 O7 P2) FORMUL 5 MG 4(MG 2+) FORMUL 7 AMP 2(C10 H14 N5 O7 P) FORMUL 13 HOH *228(H2 O) HELIX 1 AA1 THR A 8 GLY A 28 1 21 HELIX 2 AA2 GLY A 38 ARG A 42 1 5 HELIX 3 AA3 GLU A 82 SER A 90 1 9 HELIX 4 AA4 ASP A 95 HIS A 100 1 6 HELIX 5 AA5 GLY A 101 PHE A 104 5 4 HELIX 6 AA6 GLY A 114 SER A 125 1 12 HELIX 7 AA7 GLU A 127 GLU A 142 1 16 HELIX 8 AA8 GLU A 142 GLY A 157 1 16 HELIX 9 AA9 PRO A 158 THR A 160 5 3 HELIX 10 AB1 PHE A 161 ARG A 182 1 22 HELIX 11 AB2 THR A 187 ALA A 189 5 3 HELIX 12 AB3 SER A 190 VAL A 196 1 7 HELIX 13 AB4 GLY A 204 GLY A 215 1 12 HELIX 14 AB5 ASP A 219 GLY A 242 1 24 HELIX 15 AB6 THR D 8 GLY D 28 1 21 HELIX 16 AB7 GLY D 38 ARG D 42 1 5 HELIX 17 AB8 GLU D 82 SER D 90 1 9 HELIX 18 AB9 ASP D 95 HIS D 100 1 6 HELIX 19 AC1 GLY D 101 PHE D 104 5 4 HELIX 20 AC2 GLY D 114 SER D 125 1 12 HELIX 21 AC3 GLU D 127 GLU D 142 1 16 HELIX 22 AC4 GLU D 142 GLY D 157 1 16 HELIX 23 AC5 PRO D 158 THR D 160 5 3 HELIX 24 AC6 PHE D 161 ARG D 182 1 22 HELIX 25 AC7 THR D 187 ALA D 189 5 3 HELIX 26 AC8 SER D 190 VAL D 196 1 7 HELIX 27 AC9 GLY D 204 GLY D 215 1 12 HELIX 28 AD1 ASP D 219 GLY D 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 MET A 57 O ASP A 80 SHEET 4 AA1 5 VAL A 31 TYR A 37 -1 N LYS A 32 O VAL A 56 SHEET 5 AA1 5 LEU A 107 ASP A 111 -1 O LEU A 107 N VAL A 36 SHEET 1 AA2 5 GLU D 63 THR D 69 0 SHEET 2 AA2 5 LYS D 74 SER D 81 -1 O PHE D 79 N PHE D 64 SHEET 3 AA2 5 ILE D 51 MET D 57 1 N MET D 57 O ASP D 80 SHEET 4 AA2 5 VAL D 31 TYR D 37 -1 N LYS D 32 O VAL D 56 SHEET 5 AA2 5 LEU D 107 ASP D 111 -1 O TYR D 110 N ILE D 34 LINK O4 NMY A 301 P AMP A 306 1555 1555 1.56 LINK P AMP A 305 O4 NMY A 307 1555 1555 1.56 LINK OD2 ASP A 50 MG MG A 303 1555 1555 2.00 LINK OD1 ASP A 50 MG MG A 304 1555 1555 2.16 LINK OD1 ASP A 52 MG MG A 303 1555 1555 2.52 LINK OD2 ASP A 52 MG MG A 304 1555 1555 2.63 LINK OE1 GLU A 145 MG MG A 308 1555 1555 2.54 LINK O31 PPV A 302 MG MG A 304 1555 1555 2.33 LINK MG MG A 303 O1P AMP A 306 1555 1555 2.47 LINK MG MG A 303 O HOH A 901 1555 1555 1.76 LINK MG MG A 303 O HOH A 911 1555 1555 2.49 LINK MG MG A 303 O HOH A 913 1555 1555 2.26 LINK MG MG A 303 OE2 GLU D 145 1555 1555 2.20 LINK MG MG A 304 O1P AMP A 306 1555 1555 2.50 LINK MG MG A 304 O HOH A 927 1555 1555 2.87 LINK O1P AMP A 305 MG MG A 308 1555 1555 2.49 LINK O1P AMP A 305 MG MG D 302 1555 1555 2.29 LINK O4 NMY A 307 MG MG A 308 1555 1555 2.83 LINK MG MG A 308 OD2 ASP D 50 1555 1555 2.21 LINK MG MG A 308 OD1 ASP D 52 1555 1555 2.19 LINK MG MG A 308 OD2 ASP D 52 1555 1555 2.99 LINK MG MG A 308 O HOH D 914 1555 1555 2.73 LINK MG MG A 308 O HOH D 923 1555 1555 2.17 LINK OD1 ASP D 50 MG MG D 302 1555 1555 2.20 LINK OD2 ASP D 52 MG MG D 302 1555 1555 2.61 LINK O31 PPV D 301 MG MG D 302 1555 1555 2.54 LINK MG MG D 302 O HOH D 901 1555 1555 2.01 LINK MG MG D 302 O HOH D 902 1555 1555 1.86 CISPEP 1 GLY A 157 PRO A 158 0 1.77 CISPEP 2 GLY D 157 PRO D 158 0 1.21 SITE 1 AC1 10 GLY A 38 SER A 39 ARG A 42 SER A 49 SITE 2 AC1 10 THR A 187 MG A 304 AMP A 306 HOH A 982 SITE 3 AC1 10 LYS D 149 HOH D 944 SITE 1 AC2 9 ASP A 50 ASP A 52 NMY A 301 MG A 304 SITE 2 AC2 9 AMP A 306 HOH A 901 HOH A 911 HOH A 913 SITE 3 AC2 9 GLU D 145 SITE 1 AC3 6 ASP A 50 ASP A 52 PPV A 302 MG A 303 SITE 2 AC3 6 AMP A 306 HOH A 927 SITE 1 AC4 8 GLU A 145 AMP A 305 NMY A 307 ASP D 50 SITE 2 AC4 8 ASP D 52 MG D 302 HOH D 914 HOH D 923 SITE 1 AC5 15 LYS A 149 AMP A 305 GLY D 38 SER D 39 SITE 2 AC5 15 ARG D 42 SER D 49 THR D 187 MG D 302 SITE 3 AC5 15 HOH D 901 HOH D 902 HOH D 904 HOH D 906 SITE 4 AC5 15 HOH D 909 HOH D 932 HOH D 972 SITE 1 AC6 7 AMP A 305 MG A 308 ASP D 50 ASP D 52 SITE 2 AC6 7 PPV D 301 HOH D 901 HOH D 902 SITE 1 AC7 29 TYR A 37 GLY A 38 ARG A 42 ASP A 50 SITE 2 AC7 29 ASP A 52 GLU A 63 GLU A 67 GLU A 76 SITE 3 AC7 29 ASP A 80 LEU A 85 TYR A 88 LEU A 98 SITE 4 AC7 29 THR A 99 GLN A 102 THR A 186 PPV A 302 SITE 5 AC7 29 MG A 303 MG A 304 HOH A 901 HOH A 906 SITE 6 AC7 29 HOH A 909 HOH A 912 HOH A 924 HOH A 950 SITE 7 AC7 29 HOH A 969 HOH A 982 GLU D 141 GLU D 145 SITE 8 AC7 29 LYS D 149 SITE 1 AC8 27 GLU A 141 GLU A 145 LYS A 149 MG A 308 SITE 2 AC8 27 HOH A 907 HOH A 930 HOH A 932 HOH A 949 SITE 3 AC8 27 HOH A 952 HOH A 975 HOH A 988 HOH A 993 SITE 4 AC8 27 TYR D 37 GLY D 38 ARG D 42 ASP D 50 SITE 5 AC8 27 ASP D 52 GLU D 63 GLU D 67 GLU D 76 SITE 6 AC8 27 ASP D 80 TYR D 88 THR D 99 GLN D 102 SITE 7 AC8 27 PPV D 301 MG D 302 HOH D 949 CRYST1 59.750 99.300 101.490 90.00 90.00 90.00 P 21 21 21 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 0.016736 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009853 0.00000