HEADER TRANSFERASE 19-JAN-12 4DE4 TITLE CRYSTAL STRUCTURE OF AMINOGLYCOSIDE PHOSPHOTRANSFERASE APH(2")- TITLE 2 ID/APH(2")-IVA IN COMPLEX WITH HEPES COMPND MOL_ID: 1; COMPND 2 MOLECULE: APH(2")-ID; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: APH(2")-IVA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS CASSELIFLAVUS; SOURCE 3 ORGANISM_TAXID: 37734; SOURCE 4 GENE: APH(2")-ID; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P15TV LIC KEYWDS STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 2 DISEASES, CSGID, NIAID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS KEYWDS 3 DISEASES, EUKARYOTIC PROTEIN KINASE-LIKE FOLD, AMINOGLYCOSIDE KEYWDS 4 PHOSPHOTRANSFERASE, KINASE, TRANSFERASE, AMINOGLYCOSIDES, KEYWDS 5 INTRACELLULAR EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,G.MINASOV,K.TAN,B.NOCEK,E.EVDOKIMOVA,O.EGOROVA,R.DI LEO, AUTHOR 2 H.LI,A.SAVCHENKO,W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF AUTHOR 3 INFECTIOUS DISEASES (CSGID) REVDAT 3 16-OCT-24 4DE4 1 REMARK SEQADV LINK REVDAT 2 24-JAN-18 4DE4 1 AUTHOR REVDAT 1 08-FEB-12 4DE4 0 SPRSDE 08-FEB-12 4DE4 3R80 JRNL AUTH T.SHAKYA,P.J.STOGIOS,N.WAGLECHNER,E.EVDOKIMOVA,L.EJIM, JRNL AUTH 2 J.E.BLANCHARD,A.G.MCARTHUR,A.SAVCHENKO,G.D.WRIGHT JRNL TITL A SMALL MOLECULE DISCRIMINATION MAP OF THE ANTIBIOTIC JRNL TITL 2 RESISTANCE KINOME. JRNL REF CHEM.BIOL. V. 18 1591 2011 JRNL REFN ISSN 1074-5521 JRNL PMID 22195561 JRNL DOI 10.1016/J.CHEMBIOL.2011.10.018 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 38669 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 28.9911 - 4.3046 0.95 3677 200 0.1924 0.2338 REMARK 3 2 4.3046 - 3.4185 0.99 3817 208 0.1908 0.2541 REMARK 3 3 3.4185 - 2.9868 0.99 3767 206 0.2232 0.2815 REMARK 3 4 2.9868 - 2.7140 0.98 3741 203 0.2442 0.3037 REMARK 3 5 2.7140 - 2.5196 0.97 3703 202 0.2530 0.2780 REMARK 3 6 2.5196 - 2.3711 0.96 3635 198 0.2418 0.2883 REMARK 3 7 2.3711 - 2.2524 0.96 3653 199 0.2604 0.3095 REMARK 3 8 2.2524 - 2.1544 0.95 3615 198 0.2662 0.2954 REMARK 3 9 2.1544 - 2.0715 0.94 3584 195 0.2901 0.3391 REMARK 3 10 2.0715 - 2.0000 0.92 3478 190 0.3180 0.3603 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 : 0.35 REMARK 3 B_SOL : 48.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.550 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) : 11.99550 REMARK 3 B22 (A**2) : -4.21620 REMARK 3 B33 (A**2) : 1.49130 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.75160 REMARK 3 B23 (A**2) : 0.00000 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 : 0.002 5088 REMARK 3 ANGLE : 0.599 6860 REMARK 3 CHIRALITY : 0.043 720 REMARK 3 PLANARITY : 0.003 881 REMARK 3 DIHEDRAL : 11.448 1956 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 1:99 REMARK 3 ORIGIN FOR THE GROUP (A): 12.5006 15.4054 16.0045 REMARK 3 T TENSOR REMARK 3 T11: 0.4471 T22: 0.3653 REMARK 3 T33: 0.2249 T12: 0.2044 REMARK 3 T13: 0.0977 T23: 0.0415 REMARK 3 L TENSOR REMARK 3 L11: 1.8194 L22: 4.2788 REMARK 3 L33: 2.9905 L12: 0.3474 REMARK 3 L13: 0.7413 L23: 1.0713 REMARK 3 S TENSOR REMARK 3 S11: -0.0137 S12: -0.0198 S13: -0.0765 REMARK 3 S21: 0.1274 S22: 0.1233 S23: -0.5161 REMARK 3 S31: 0.7969 S32: 0.7744 S33: -0.1091 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B AND RESID 1:99 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4510 47.8205 23.2011 REMARK 3 T TENSOR REMARK 3 T11: 0.1935 T22: 0.2208 REMARK 3 T33: 0.2654 T12: 0.0305 REMARK 3 T13: -0.0564 T23: 0.1634 REMARK 3 L TENSOR REMARK 3 L11: 2.4941 L22: 3.3198 REMARK 3 L33: 2.0628 L12: 0.1565 REMARK 3 L13: -0.8615 L23: 0.3566 REMARK 3 S TENSOR REMARK 3 S11: 0.0852 S12: 0.2109 S13: 0.2569 REMARK 3 S21: -0.1321 S22: -0.1868 S23: -0.4905 REMARK 3 S31: -0.2646 S32: 0.1038 S33: 0.1158 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 100:296 REMARK 3 ORIGIN FOR THE GROUP (A): 1.7328 27.8089 -2.8448 REMARK 3 T TENSOR REMARK 3 T11: 0.4557 T22: 0.0415 REMARK 3 T33: 0.0914 T12: 0.1376 REMARK 3 T13: -0.0134 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 0.9358 L22: 4.9862 REMARK 3 L33: 2.0584 L12: -0.1233 REMARK 3 L13: 0.2437 L23: 0.6005 REMARK 3 S TENSOR REMARK 3 S11: 0.0084 S12: 0.0858 S13: 0.0832 REMARK 3 S21: -0.5644 S22: -0.1023 S23: 0.1680 REMARK 3 S31: -0.2576 S32: 0.0502 S33: 0.0063 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND RESID 100:298 REMARK 3 ORIGIN FOR THE GROUP (A): -4.0975 34.2226 39.0345 REMARK 3 T TENSOR REMARK 3 T11: 0.1734 T22: 0.2268 REMARK 3 T33: 0.1442 T12: -0.0279 REMARK 3 T13: 0.0138 T23: -0.0413 REMARK 3 L TENSOR REMARK 3 L11: 0.5797 L22: 7.4242 REMARK 3 L33: 0.8990 L12: -1.2383 REMARK 3 L13: 0.3163 L23: 0.0781 REMARK 3 S TENSOR REMARK 3 S11: -0.0961 S12: -0.1290 S13: -0.0217 REMARK 3 S21: 0.3645 S22: 0.1035 S23: 0.2991 REMARK 3 S31: 0.1116 S32: -0.1328 S33: -0.0046 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 4DE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070214. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39540 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 35.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38800 REMARK 200 FOR SHELL : 3.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NASCN, 20% PEG3350, 2 MM GTP, REMARK 280 2.5 MM GENTAMICIN, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 50.60700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 MSE A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 ARG A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 SER A 297 REMARK 465 ILE A 298 REMARK 465 LYS A 299 REMARK 465 ILE A 300 REMARK 465 LYS A 301 REMARK 465 MSE B -20 REMARK 465 GLY B -19 REMARK 465 SER B -18 REMARK 465 SER B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 ARG B -7 REMARK 465 GLU B -6 REMARK 465 ASN B -5 REMARK 465 LEU B -4 REMARK 465 TYR B -3 REMARK 465 PHE B -2 REMARK 465 GLN B -1 REMARK 465 GLY B 0 REMARK 465 LYS B 299 REMARK 465 ILE B 300 REMARK 465 LYS B 301 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 B 626 O HOH B 627 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 ILE A 27 91.64 -64.75 REMARK 500 GLU A 30 118.07 -161.50 REMARK 500 ASP A 42 5.06 -152.00 REMARK 500 LYS A 139 -163.33 -76.46 REMARK 500 LYS A 188 51.69 -94.30 REMARK 500 ASN A 196 -2.96 70.98 REMARK 500 ASP A 197 42.47 -143.95 REMARK 500 ASP A 217 80.73 59.47 REMARK 500 SER A 224 -146.46 -153.10 REMARK 500 GLU A 239 -154.90 -125.35 REMARK 500 TYR A 284 71.40 57.86 REMARK 500 GLU B 30 115.52 -164.22 REMARK 500 ASN B 40 18.40 57.50 REMARK 500 MSE B 90 117.25 -162.46 REMARK 500 LYS B 188 43.53 -93.83 REMARK 500 ASP B 197 40.06 -156.36 REMARK 500 ASP B 217 78.62 59.85 REMARK 500 SER B 224 -149.50 -154.89 REMARK 500 GLU B 239 -164.15 -121.36 REMARK 500 ASP B 256 64.14 -154.60 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 EPE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R7Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMINOGLYCOSIDE PHOSPHOTRANSFERASE APH(2")-ID/ REMARK 900 APH(2")-IVA REMARK 900 RELATED ID: 3R81 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMINOGLYCOSIDE PHOSPHOTRANSFERASE APH(2")-ID/ REMARK 900 APH(2")-IVA IN COMPLEX WITH KANAMYCIN REMARK 900 RELATED ID: 3R82 RELATED DB: PDB REMARK 900 INHIBITION OF AN ANTIBIOTIC RESISTANCE ENZYME: CRYSTAL STRUCTURE OF REMARK 900 AMINOGLYCOSIDE PHOSPHOTRANSFERASE APH(2")-ID/APH(2")-IVA IN COMPLEX REMARK 900 WITH KANAMYCIN INHIBITED WITH QUERCETIN REMARK 900 RELATED ID: CSGID-IDP91189 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: IDP91189 RELATED DB: TARGETTRACK DBREF 4DE4 A 1 301 UNP O68183 O68183_ENTCA 1 301 DBREF 4DE4 B 1 301 UNP O68183 O68183_ENTCA 1 301 SEQADV 4DE4 MSE A -20 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLY A -19 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER A -18 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER A -17 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS A -16 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS A -15 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS A -14 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS A -13 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS A -12 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS A -11 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER A -10 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER A -9 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLY A -8 UNP O68183 EXPRESSION TAG SEQADV 4DE4 ARG A -7 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLU A -6 UNP O68183 EXPRESSION TAG SEQADV 4DE4 ASN A -5 UNP O68183 EXPRESSION TAG SEQADV 4DE4 LEU A -4 UNP O68183 EXPRESSION TAG SEQADV 4DE4 TYR A -3 UNP O68183 EXPRESSION TAG SEQADV 4DE4 PHE A -2 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLN A -1 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLY A 0 UNP O68183 EXPRESSION TAG SEQADV 4DE4 MSE B -20 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLY B -19 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER B -18 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER B -17 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS B -16 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS B -15 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS B -14 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS B -13 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS B -12 UNP O68183 EXPRESSION TAG SEQADV 4DE4 HIS B -11 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER B -10 UNP O68183 EXPRESSION TAG SEQADV 4DE4 SER B -9 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLY B -8 UNP O68183 EXPRESSION TAG SEQADV 4DE4 ARG B -7 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLU B -6 UNP O68183 EXPRESSION TAG SEQADV 4DE4 ASN B -5 UNP O68183 EXPRESSION TAG SEQADV 4DE4 LEU B -4 UNP O68183 EXPRESSION TAG SEQADV 4DE4 TYR B -3 UNP O68183 EXPRESSION TAG SEQADV 4DE4 PHE B -2 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLN B -1 UNP O68183 EXPRESSION TAG SEQADV 4DE4 GLY B 0 UNP O68183 EXPRESSION TAG SEQRES 1 A 322 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 322 ARG GLU ASN LEU TYR PHE GLN GLY MSE ARG THR TYR THR SEQRES 3 A 322 PHE ASP GLN VAL GLU LYS ALA ILE GLU GLN LEU TYR PRO SEQRES 4 A 322 ASP PHE THR ILE ASN THR ILE GLU ILE SER GLY GLU GLY SEQRES 5 A 322 ASN ASP CYS ILE ALA TYR GLU ILE ASN ARG ASP PHE ILE SEQRES 6 A 322 PHE LYS PHE PRO LYS HIS SER ARG GLY SER THR ASN LEU SEQRES 7 A 322 PHE ASN GLU VAL ASN ILE LEU LYS ARG ILE HIS ASN LYS SEQRES 8 A 322 LEU PRO LEU PRO ILE PRO GLU VAL VAL PHE THR GLY MSE SEQRES 9 A 322 PRO SER GLU THR TYR GLN MSE SER PHE ALA GLY PHE THR SEQRES 10 A 322 LYS ILE LYS GLY VAL PRO LEU THR PRO LEU LEU LEU ASN SEQRES 11 A 322 ASN LEU PRO LYS GLN SER GLN ASN GLN ALA ALA LYS ASP SEQRES 12 A 322 LEU ALA ARG PHE LEU SER GLU LEU HIS SER ILE ASN ILE SEQRES 13 A 322 SER GLY PHE LYS SER ASN LEU VAL LEU ASP PHE ARG GLU SEQRES 14 A 322 LYS ILE ASN GLU ASP ASN LYS LYS ILE LYS LYS LEU LEU SEQRES 15 A 322 SER ARG GLU LEU LYS GLY PRO GLN MSE LYS LYS VAL ASP SEQRES 16 A 322 ASP PHE TYR ARG ASP ILE LEU GLU ASN GLU ILE TYR PHE SEQRES 17 A 322 LYS TYR TYR PRO CYS LEU ILE HIS ASN ASP PHE SER SER SEQRES 18 A 322 ASP HIS ILE LEU PHE ASP THR GLU LYS ASN THR ILE CYS SEQRES 19 A 322 GLY ILE ILE ASP PHE GLY ASP ALA ALA ILE SER ASP PRO SEQRES 20 A 322 ASP ASN ASP PHE ILE SER LEU MSE GLU ASP ASP GLU GLU SEQRES 21 A 322 TYR GLY MSE GLU PHE VAL SER LYS ILE LEU ASN HIS TYR SEQRES 22 A 322 LYS HIS LYS ASP ILE PRO THR VAL LEU GLU LYS TYR ARG SEQRES 23 A 322 MSE LYS GLU LYS TYR TRP SER PHE GLU LYS ILE ILE TYR SEQRES 24 A 322 GLY LYS GLU TYR GLY TYR MSE ASP TRP TYR GLU GLU GLY SEQRES 25 A 322 LEU ASN GLU ILE ARG SER ILE LYS ILE LYS SEQRES 1 B 322 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 322 ARG GLU ASN LEU TYR PHE GLN GLY MSE ARG THR TYR THR SEQRES 3 B 322 PHE ASP GLN VAL GLU LYS ALA ILE GLU GLN LEU TYR PRO SEQRES 4 B 322 ASP PHE THR ILE ASN THR ILE GLU ILE SER GLY GLU GLY SEQRES 5 B 322 ASN ASP CYS ILE ALA TYR GLU ILE ASN ARG ASP PHE ILE SEQRES 6 B 322 PHE LYS PHE PRO LYS HIS SER ARG GLY SER THR ASN LEU SEQRES 7 B 322 PHE ASN GLU VAL ASN ILE LEU LYS ARG ILE HIS ASN LYS SEQRES 8 B 322 LEU PRO LEU PRO ILE PRO GLU VAL VAL PHE THR GLY MSE SEQRES 9 B 322 PRO SER GLU THR TYR GLN MSE SER PHE ALA GLY PHE THR SEQRES 10 B 322 LYS ILE LYS GLY VAL PRO LEU THR PRO LEU LEU LEU ASN SEQRES 11 B 322 ASN LEU PRO LYS GLN SER GLN ASN GLN ALA ALA LYS ASP SEQRES 12 B 322 LEU ALA ARG PHE LEU SER GLU LEU HIS SER ILE ASN ILE SEQRES 13 B 322 SER GLY PHE LYS SER ASN LEU VAL LEU ASP PHE ARG GLU SEQRES 14 B 322 LYS ILE ASN GLU ASP ASN LYS LYS ILE LYS LYS LEU LEU SEQRES 15 B 322 SER ARG GLU LEU LYS GLY PRO GLN MSE LYS LYS VAL ASP SEQRES 16 B 322 ASP PHE TYR ARG ASP ILE LEU GLU ASN GLU ILE TYR PHE SEQRES 17 B 322 LYS TYR TYR PRO CYS LEU ILE HIS ASN ASP PHE SER SER SEQRES 18 B 322 ASP HIS ILE LEU PHE ASP THR GLU LYS ASN THR ILE CYS SEQRES 19 B 322 GLY ILE ILE ASP PHE GLY ASP ALA ALA ILE SER ASP PRO SEQRES 20 B 322 ASP ASN ASP PHE ILE SER LEU MSE GLU ASP ASP GLU GLU SEQRES 21 B 322 TYR GLY MSE GLU PHE VAL SER LYS ILE LEU ASN HIS TYR SEQRES 22 B 322 LYS HIS LYS ASP ILE PRO THR VAL LEU GLU LYS TYR ARG SEQRES 23 B 322 MSE LYS GLU LYS TYR TRP SER PHE GLU LYS ILE ILE TYR SEQRES 24 B 322 GLY LYS GLU TYR GLY TYR MSE ASP TRP TYR GLU GLU GLY SEQRES 25 B 322 LEU ASN GLU ILE ARG SER ILE LYS ILE LYS MODRES 4DE4 MSE A 1 MET SELENOMETHIONINE MODRES 4DE4 MSE A 83 MET SELENOMETHIONINE MODRES 4DE4 MSE A 90 MET SELENOMETHIONINE MODRES 4DE4 MSE A 170 MET SELENOMETHIONINE MODRES 4DE4 MSE A 234 MET SELENOMETHIONINE MODRES 4DE4 MSE A 242 MET SELENOMETHIONINE MODRES 4DE4 MSE A 266 MET SELENOMETHIONINE MODRES 4DE4 MSE A 285 MET SELENOMETHIONINE MODRES 4DE4 MSE B 1 MET SELENOMETHIONINE MODRES 4DE4 MSE B 83 MET SELENOMETHIONINE MODRES 4DE4 MSE B 90 MET SELENOMETHIONINE MODRES 4DE4 MSE B 170 MET SELENOMETHIONINE MODRES 4DE4 MSE B 234 MET SELENOMETHIONINE MODRES 4DE4 MSE B 242 MET SELENOMETHIONINE MODRES 4DE4 MSE B 266 MET SELENOMETHIONINE MODRES 4DE4 MSE B 285 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 83 13 HET MSE A 90 8 HET MSE A 170 8 HET MSE A 234 8 HET MSE A 242 8 HET MSE A 266 8 HET MSE A 285 8 HET MSE B 1 8 HET MSE B 83 13 HET MSE B 90 8 HET MSE B 170 8 HET MSE B 234 8 HET MSE B 242 8 HET MSE B 266 8 HET MSE B 285 8 HET EPE A 401 15 HET EPE B 401 15 HETNAM MSE SELENOMETHIONINE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 1 MSE 16(C5 H11 N O2 SE) FORMUL 3 EPE 2(C8 H18 N2 O4 S) FORMUL 5 HOH *270(H2 O) HELIX 1 1 THR A 5 TYR A 17 1 13 HELIX 2 2 HIS A 50 HIS A 68 1 19 HELIX 3 3 THR A 104 LEU A 111 1 8 HELIX 4 4 PRO A 112 HIS A 131 1 20 HELIX 5 5 ASP A 145 SER A 162 1 18 HELIX 6 6 LYS A 166 GLU A 182 1 17 HELIX 7 7 ASN A 183 PHE A 187 5 5 HELIX 8 8 SER A 199 ASP A 201 5 3 HELIX 9 9 ASP A 227 SER A 232 1 6 HELIX 10 10 GLY A 241 TYR A 252 1 12 HELIX 11 11 ILE A 257 TYR A 282 1 26 HELIX 12 12 TYR A 284 ARG A 296 1 13 HELIX 13 13 THR B 5 TYR B 17 1 13 HELIX 14 14 HIS B 50 ILE B 67 1 18 HELIX 15 15 THR B 104 ASN B 110 1 7 HELIX 16 16 PRO B 112 HIS B 131 1 20 HELIX 17 17 ASP B 145 SER B 162 1 18 HELIX 18 18 LYS B 166 GLU B 182 1 17 HELIX 19 19 ASN B 183 PHE B 187 5 5 HELIX 20 20 SER B 199 ASP B 201 5 3 HELIX 21 21 ASP B 227 SER B 232 1 6 HELIX 22 22 GLY B 241 TYR B 252 1 12 HELIX 23 23 ASP B 256 GLY B 283 1 28 HELIX 24 24 TYR B 284 SER B 297 1 14 SHEET 1 A 5 ILE A 25 GLU A 30 0 SHEET 2 A 5 CYS A 34 ILE A 39 -1 O GLU A 38 N GLU A 26 SHEET 3 A 5 PHE A 43 PRO A 48 -1 O PHE A 45 N TYR A 37 SHEET 4 A 5 ALA A 93 THR A 96 -1 O PHE A 95 N ILE A 44 SHEET 5 A 5 VAL A 78 THR A 81 -1 N VAL A 79 O GLY A 94 SHEET 1 B 3 VAL A 101 PRO A 102 0 SHEET 2 B 3 ILE A 203 ASP A 206 -1 O PHE A 205 N VAL A 101 SHEET 3 B 3 THR A 211 ILE A 215 -1 O THR A 211 N ASP A 206 SHEET 1 C 2 CYS A 192 ILE A 194 0 SHEET 2 C 2 ALA A 222 SER A 224 -1 O ALA A 222 N ILE A 194 SHEET 1 D 5 ILE B 25 GLU B 30 0 SHEET 2 D 5 CYS B 34 ILE B 39 -1 O GLU B 38 N GLU B 26 SHEET 3 D 5 PHE B 43 PRO B 48 -1 O PHE B 45 N TYR B 37 SHEET 4 D 5 ALA B 93 THR B 96 -1 O ALA B 93 N LYS B 46 SHEET 5 D 5 VAL B 78 THR B 81 -1 N PHE B 80 O GLY B 94 SHEET 1 E 3 VAL B 101 PRO B 102 0 SHEET 2 E 3 ILE B 203 ASP B 206 -1 O PHE B 205 N VAL B 101 SHEET 3 E 3 THR B 211 ILE B 215 -1 O THR B 211 N ASP B 206 SHEET 1 F 2 CYS B 192 ILE B 194 0 SHEET 2 F 2 ALA B 222 SER B 224 -1 O ALA B 222 N ILE B 194 LINK C MSE A 1 N ARG A 2 1555 1555 1.33 LINK C GLY A 82 N MSE A 83 1555 1555 1.33 LINK C MSE A 83 N PRO A 84 1555 1555 1.34 LINK C GLN A 89 N MSE A 90 1555 1555 1.33 LINK C MSE A 90 N SER A 91 1555 1555 1.33 LINK C GLN A 169 N MSE A 170 1555 1555 1.33 LINK C MSE A 170 N LYS A 171 1555 1555 1.33 LINK C LEU A 233 N MSE A 234 1555 1555 1.33 LINK C MSE A 234 N GLU A 235 1555 1555 1.33 LINK C GLY A 241 N MSE A 242 1555 1555 1.33 LINK C MSE A 242 N GLU A 243 1555 1555 1.33 LINK C ARG A 265 N MSE A 266 1555 1555 1.33 LINK C MSE A 266 N LYS A 267 1555 1555 1.33 LINK C TYR A 284 N MSE A 285 1555 1555 1.33 LINK C MSE A 285 N ASP A 286 1555 1555 1.33 LINK C MSE B 1 N ARG B 2 1555 1555 1.33 LINK C GLY B 82 N MSE B 83 1555 1555 1.33 LINK C MSE B 83 N PRO B 84 1555 1555 1.34 LINK C GLN B 89 N MSE B 90 1555 1555 1.33 LINK C MSE B 90 N SER B 91 1555 1555 1.33 LINK C GLN B 169 N MSE B 170 1555 1555 1.33 LINK C MSE B 170 N LYS B 171 1555 1555 1.33 LINK C LEU B 233 N MSE B 234 1555 1555 1.33 LINK C MSE B 234 N GLU B 235 1555 1555 1.33 LINK C GLY B 241 N MSE B 242 1555 1555 1.33 LINK C MSE B 242 N GLU B 243 1555 1555 1.33 LINK C ARG B 265 N MSE B 266 1555 1555 1.33 LINK C MSE B 266 N LYS B 267 1555 1555 1.33 LINK C TYR B 284 N MSE B 285 1555 1555 1.33 LINK C MSE B 285 N ASP B 286 1555 1555 1.33 SITE 1 AC1 5 ASN A 32 GLU A 235 GLU A 268 TRP A 271 SITE 2 AC1 5 TRP A 287 SITE 1 AC2 5 GLU B 235 GLU B 238 TRP B 271 HOH B 591 SITE 2 AC2 5 HOH B 651 CRYST1 42.541 101.214 71.166 90.00 97.51 90.00 P 1 21 1 4 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 0.023507 0.000000 0.003098 0.00000 SCALE2 0.000000 0.009880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014173 0.00000 HETATM 1 N MSE A 1 20.904 31.071 14.363 1.00 90.70 N ANISOU 1 N MSE A 1 9147 13301 12015 -249 1228 192 N HETATM 2 CA MSE A 1 20.698 29.657 14.069 1.00 90.83 C ANISOU 2 CA MSE A 1 9283 13344 11883 29 1307 187 C HETATM 3 C MSE A 1 21.619 28.758 14.887 1.00 94.06 C ANISOU 3 C MSE A 1 9453 13928 12358 304 1210 59 C HETATM 4 O MSE A 1 22.810 29.035 15.028 1.00 97.51 O ANISOU 4 O MSE A 1 9531 14555 12963 268 1220 -30 O HETATM 5 CB MSE A 1 20.905 29.378 12.579 1.00 91.19 C ANISOU 5 CB MSE A 1 9372 13436 11841 -42 1599 249 C HETATM 6 CG MSE A 1 19.881 30.026 11.670 1.00 89.54 C ANISOU 6 CG MSE A 1 9480 13025 11517 -260 1667 390 C HETATM 7 SE MSE A 1 19.976 29.296 9.864 0.60122.17 SE ANISOU 7 SE MSE A 1 13780 17196 15443 -269 2007 458 SE HETATM 8 CE MSE A 1 18.596 30.383 9.027 1.00 79.55 C ANISOU 8 CE MSE A 1 8801 11499 9928 -557 1955 642 C