HEADER TRANSFERASE 26-SEP-19 6SXJ TITLE CRYSTAL STRUCTURE OF SPECTINOMYCIN ADENYLTRANSFERASE AAD(9) FROM TITLE 2 ENTEROCOCCUS FAECIALIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTOMYCIN 3''-ADENYLYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AAD(9); COMPND 5 EC: 2.7.7.47; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 GENE: SPC, AAD9; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NUCLEOTIDYLTRANSFERASE, ANTIBIOTIC RESISTANCE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KANCHUGAL P,M.SELMER REVDAT 3 24-JAN-24 6SXJ 1 REMARK REVDAT 2 10-JUN-20 6SXJ 1 JRNL REVDAT 1 15-APR-20 6SXJ 0 JRNL AUTH S.KANCHUGAL P,M.SELMER JRNL TITL STRUCTURAL RECOGNITION OF SPECTINOMYCIN BY RESISTANCE ENZYME JRNL TITL 2 ANT(9) FROM ENTEROCOCCUS FAECALIS. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 64 2020 JRNL REFN ESSN 1098-6596 JRNL PMID 32253216 JRNL DOI 10.1128/AAC.00371-20 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 18983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 958 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 0.0000 - 4.0200 1.00 2645 148 0.1815 0.2175 REMARK 3 2 4.0200 - 3.1900 1.00 2598 133 0.0000 0.2736 REMARK 3 3 3.1900 - 2.7900 1.00 2594 146 0.0000 0.3564 REMARK 3 4 2.7900 - 2.5300 1.00 2577 135 0.0000 0.3548 REMARK 3 5 2.5300 - 2.3500 0.99 2568 111 0.0000 0.3326 REMARK 3 6 2.3500 - 2.2100 0.98 2542 133 0.0000 0.3969 REMARK 3 7 2.2100 - 2.1000 0.98 2501 152 0.0000 0.3766 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) : 0.296 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.332 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.97 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 2087 REMARK 3 ANGLE : 0.730 2819 REMARK 3 CHIRALITY : 0.044 318 REMARK 3 PLANARITY : 0.005 361 REMARK 3 DIHEDRAL : 2.683 1296 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 6SXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18995 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 1.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : 1.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MORDA REMARK 200 STARTING MODEL: 5G4A REMARK 200 REMARK 200 REMARK: HEXAGONAL PRISM SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 4000, 20% V/V GLYCEROL, REMARK 280 0.02 M OF EACH AMINOACID, 0.1 M BICINE/TRIZMA BASE PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.98550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.98550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.50950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.98550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.98550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.50950 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 51.98550 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 51.98550 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 30.50950 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 51.98550 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 51.98550 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 30.50950 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: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 ILE A 4 REMARK 465 TYR A 5 REMARK 465 LYS A 256 REMARK 465 GLY A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 465 HIS A 263 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 LYS A 24 -127.66 47.43 REMARK 500 SER A 80 -174.41 -69.28 REMARK 500 PHE A 106 147.42 -170.32 REMARK 500 ASN A 176 42.75 -142.14 REMARK 500 GLN A 178 103.31 -51.08 REMARK 500 ASP A 179 -11.54 97.30 REMARK 500 ASP A 196 -84.39 -94.07 REMARK 500 GLU A 232 132.30 -33.42 REMARK 500 GLU A 235 84.83 60.39 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 GOL A 401 DBREF 6SXJ A 1 255 UNP Q07448 S3AD_ENTFL 1 255 SEQADV 6SXJ LYS A 256 UNP Q07448 EXPRESSION TAG SEQADV 6SXJ GLY A 257 UNP Q07448 EXPRESSION TAG SEQADV 6SXJ HIS A 258 UNP Q07448 EXPRESSION TAG SEQADV 6SXJ HIS A 259 UNP Q07448 EXPRESSION TAG SEQADV 6SXJ HIS A 260 UNP Q07448 EXPRESSION TAG SEQADV 6SXJ HIS A 261 UNP Q07448 EXPRESSION TAG SEQADV 6SXJ HIS A 262 UNP Q07448 EXPRESSION TAG SEQADV 6SXJ HIS A 263 UNP Q07448 EXPRESSION TAG SEQRES 1 A 263 MET ARG ARG ILE TYR LEU ASN THR TYR GLU GLN ILE ASN SEQRES 2 A 263 LYS VAL LYS LYS ILE LEU ARG LYS HIS LEU LYS ASN ASN SEQRES 3 A 263 LEU ILE GLY THR TYR MET PHE GLY SER GLY VAL GLU SER SEQRES 4 A 263 GLY LEU LYS PRO ASN SER ASP LEU ASP PHE LEU VAL VAL SEQRES 5 A 263 VAL SER GLU PRO LEU THR ASP GLN SER LYS GLU ILE LEU SEQRES 6 A 263 ILE GLN LYS ILE ARG PRO ILE SER LYS LYS ILE GLY ASP SEQRES 7 A 263 LYS SER ASN LEU ARG TYR ILE GLU LEU THR ILE ILE ILE SEQRES 8 A 263 GLN GLN GLU MET VAL PRO TRP ASN HIS PRO PRO LYS GLN SEQRES 9 A 263 GLU PHE ILE TYR GLY GLU TRP LEU GLN GLU LEU TYR GLU SEQRES 10 A 263 GLN GLY TYR ILE PRO GLN LYS GLU LEU ASN SER ASP LEU SEQRES 11 A 263 THR ILE MET LEU TYR GLN ALA LYS ARG LYS ASN LYS ARG SEQRES 12 A 263 ILE TYR GLY ASN TYR ASP LEU GLU GLU LEU LEU PRO ASP SEQRES 13 A 263 ILE PRO PHE SER ASP VAL ARG ARG ALA ILE MET ASP SER SEQRES 14 A 263 SER GLU GLU LEU ILE ASP ASN TYR GLN ASP ASP GLU THR SEQRES 15 A 263 ASN SER ILE LEU THR LEU CYS ARG MET ILE LEU THR MET SEQRES 16 A 263 ASP THR GLY LYS ILE ILE PRO LYS ASP ILE ALA GLY ASN SEQRES 17 A 263 ALA VAL ALA GLU SER SER PRO LEU GLU HIS ARG GLU ARG SEQRES 18 A 263 ILE LEU LEU ALA VAL ARG SER TYR LEU GLY GLU ASN ILE SEQRES 19 A 263 GLU TRP THR ASN GLU ASN VAL ASN LEU THR ILE ASN TYR SEQRES 20 A 263 LEU ASN ASN ARG LEU LYS LYS LEU LYS GLY HIS HIS HIS SEQRES 21 A 263 HIS HIS HIS HET GOL A 401 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *16(H2 O) HELIX 1 AA1 ASN A 7 LYS A 24 1 18 HELIX 2 AA2 GLY A 34 SER A 39 1 6 HELIX 3 AA3 THR A 58 ARG A 70 1 13 HELIX 4 AA4 PRO A 71 SER A 73 5 3 HELIX 5 AA5 GLN A 93 VAL A 96 5 4 HELIX 6 AA6 GLY A 109 TRP A 111 5 3 HELIX 7 AA7 LEU A 112 GLN A 118 1 7 HELIX 8 AA8 ASP A 129 LYS A 140 1 12 HELIX 9 AA9 ASP A 149 LEU A 154 5 6 HELIX 10 AB1 PRO A 158 ILE A 174 1 17 HELIX 11 AB2 ASP A 180 THR A 197 1 18 HELIX 12 AB3 PRO A 202 SER A 213 1 12 HELIX 13 AB4 PRO A 215 LEU A 230 1 16 HELIX 14 AB5 GLU A 235 GLU A 239 5 5 HELIX 15 AB6 ASN A 240 LYS A 254 1 15 SHEET 1 AA1 5 PHE A 106 TYR A 108 0 SHEET 2 AA1 5 ILE A 85 ILE A 91 -1 N LEU A 87 O TYR A 108 SHEET 3 AA1 5 LEU A 47 VAL A 53 1 N PHE A 49 O GLU A 86 SHEET 4 AA1 5 LEU A 27 PHE A 33 -1 N TYR A 31 O LEU A 50 SHEET 5 AA1 5 LYS A 142 GLY A 146 -1 O ILE A 144 N THR A 30 SHEET 1 AA2 2 LYS A 103 GLN A 104 0 SHEET 2 AA2 2 GLU A 125 LEU A 126 -1 O GLU A 125 N GLN A 104 CISPEP 1 VAL A 96 PRO A 97 0 -8.21 CISPEP 2 HIS A 100 PRO A 101 0 1.44 SITE 1 AC1 2 GLN A 92 TYR A 148 CRYST1 103.971 103.971 61.019 90.00 90.00 90.00 I 4 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 0.009618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016388 0.00000