HEADER TRANSFERASE 23-MAR-11 3R7Z OBSLTE 01-FEB-12 3R7Z 4DBX TITLE CRYSTAL STRUCTURE OF AMINOGLYCOSIDE PHOSPHOTRANSFERASE APH(2")- TITLE 2 ID/APH(2")-IVA COMPND MOL_ID: 1; COMPND 2 MOLECULE: APH(2'')-ID; COMPND 3 CHAIN: A; COMPND 4 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, ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS, OCSP, KEYWDS 3 EUKARYOTIC PROTEIN KINASE-LIKE FOLD, AMINOGLYCOSIDE KEYWDS 4 PHOSPHOTRANSFERASE, KINASE, AMINOGLYCOSIDES, INTRACELLULAR, KEYWDS 5 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,K.TAN,B.NOCEK,A.U.SINGER,E.EVDOKIMOVA,E.EGOROVA,R.DI LEO, AUTHOR 2 H.LI,T.SHAKYA,G.D.WRIGHT,W.F.ANDERSON,A.SAVCHENKO,ONTARIO CENTRE FOR AUTHOR 3 STRUCTURAL PROTEOMICS (OCSP),MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 4 (MCSG) REVDAT 6 01-FEB-12 3R7Z 1 OBSLTE REVDAT 5 18-JAN-12 3R7Z 1 JRNL REVDAT 4 24-AUG-11 3R7Z 1 AUTHOR JRNL VERSN REVDAT 3 25-MAY-11 3R7Z 1 SPRSDE REVDAT 2 20-APR-11 3R7Z 1 HEADER KEYWDS REVDAT 1 13-APR-11 3R7Z 0 SPRSDE 25-MAY-11 3R7Z 3LZH 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: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 25283 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1274 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 30.2729 - 4.1657 0.99 2853 149 0.1785 0.2276 REMARK 3 2 4.1657 - 3.3077 1.00 2735 144 0.1694 0.2151 REMARK 3 3 3.3077 - 2.8900 1.00 2687 158 0.1811 0.2427 REMARK 3 4 2.8900 - 2.6259 1.00 2681 139 0.1857 0.2413 REMARK 3 5 2.6259 - 2.4378 1.00 2655 145 0.1945 0.2716 REMARK 3 6 2.4378 - 2.2941 0.99 2664 144 0.1764 0.2476 REMARK 3 7 2.2941 - 2.1793 0.99 2630 118 0.1855 0.2251 REMARK 3 8 2.1793 - 2.0844 0.98 2604 155 0.2067 0.2803 REMARK 3 9 2.0844 - 2.0042 0.94 2500 122 0.2425 0.2783 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 : 0.32 REMARK 3 B_SOL : 46.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : -0.33210 REMARK 3 B22 (A**2) : 0.06390 REMARK 3 B33 (A**2) : 0.26820 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.011 2506 REMARK 3 ANGLE : 1.246 3385 REMARK 3 CHIRALITY : 0.081 359 REMARK 3 PLANARITY : 0.005 439 REMARK 3 DIHEDRAL : 14.120 946 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain A and resid 1:99 REMARK 3 ORIGIN FOR THE GROUP (A): 33.8870 36.2004 13.5953 REMARK 3 T TENSOR REMARK 3 T11: 0.2613 T22: 0.2186 REMARK 3 T33: 0.1870 T12: 0.0010 REMARK 3 T13: 0.0133 T23: 0.0126 REMARK 3 L TENSOR REMARK 3 L11: 0.5929 L22: 0.7572 REMARK 3 L33: 0.4470 L12: 0.2779 REMARK 3 L13: -0.4742 L23: -0.0175 REMARK 3 S TENSOR REMARK 3 S11: -0.0215 S12: 0.0940 S13: 0.0323 REMARK 3 S21: -0.2015 S22: 0.0416 S23: 0.0024 REMARK 3 S31: -0.0803 S32: -0.1154 S33: -0.0238 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain A and resid 100:298 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1017 36.3761 36.9428 REMARK 3 T TENSOR REMARK 3 T11: 0.1048 T22: 0.1196 REMARK 3 T33: 0.1649 T12: -0.0218 REMARK 3 T13: -0.0085 T23: -0.0339 REMARK 3 L TENSOR REMARK 3 L11: 1.0007 L22: 1.1770 REMARK 3 L33: 1.5310 L12: -0.8967 REMARK 3 L13: -0.3836 L23: 0.4091 REMARK 3 S TENSOR REMARK 3 S11: 0.0091 S12: 0.0639 S13: -0.1440 REMARK 3 S21: 0.0068 S22: -0.1113 S23: 0.2178 REMARK 3 S31: 0.0088 S32: -0.1871 S33: 0.1095 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 3R7Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-11. REMARK 100 THE RCSB ID CODE IS RCSB064603. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-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 : 25489 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 34.0400 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50800 REMARK 200 FOR SHELL : 5.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 10% PEG 6K, 5% REMARK 280 MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 28.29150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.72800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.58850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.72800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.29150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.58850 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MSE A 1 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 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 GLU A 86 CG CD OE1 OE2 REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 LYS A 155 CG CD CE NZ REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 ASP A 237 CG OD1 OD2 REMARK 470 GLU A 238 CG CD OE1 OE2 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 41 18.90 54.72 REMARK 500 ASN A 196 -1.61 73.06 REMARK 500 ASP A 197 45.35 -141.57 REMARK 500 ASP A 217 73.51 67.93 REMARK 500 SER A 224 -159.12 -165.11 REMARK 500 ASP A 237 -75.91 -64.58 REMARK 500 GLU A 239 -148.98 -117.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 384 DISTANCE = 8.49 ANGSTROMS REMARK 525 HOH A 387 DISTANCE = 7.97 ANGSTROMS REMARK 525 HOH A 392 DISTANCE = 9.05 ANGSTROMS REMARK 525 HOH A 393 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A 395 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 396 DISTANCE = 5.32 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PE3 A 342 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 NA A 320 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 77 OE1 REMARK 620 2 HOH A 554 O 91.3 REMARK 620 3 HOH A 574 O 102.9 93.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 324 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 206 OD2 REMARK 620 2 HOH A 576 O 101.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 475 O REMARK 620 2 HOH A 557 O 81.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 319 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 320 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 321 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 322 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 323 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 324 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 326 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 327 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 328 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 329 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 330 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 331 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 333 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 335 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 342 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R80 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMINOGLYCOSIDE PHOSPHOTRANSFERASE REMARK 900 APH(2")-ID/APH(2")-IVA IN COMPLEX WITH GENTAMICIN REMARK 900 RELATED ID: 3R81 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMINOGLYCOSIDE PHOSPHOTRANSFERASE REMARK 900 APH(2")-ID/APH(2")-IVA IN COMPLEX WITH KANAMYCIN REMARK 900 RELATED ID: APC40088 RELATED DB: TARGETDB DBREF 3R7Z A 1 301 UNP O68183 O68183_ENTCA 1 301 SEQADV 3R7Z MSE A -20 UNP O68183 EXPRESSION TAG SEQADV 3R7Z GLY A -19 UNP O68183 EXPRESSION TAG SEQADV 3R7Z SER A -18 UNP O68183 EXPRESSION TAG SEQADV 3R7Z SER A -17 UNP O68183 EXPRESSION TAG SEQADV 3R7Z HIS A -16 UNP O68183 EXPRESSION TAG SEQADV 3R7Z HIS A -15 UNP O68183 EXPRESSION TAG SEQADV 3R7Z HIS A -14 UNP O68183 EXPRESSION TAG SEQADV 3R7Z HIS A -13 UNP O68183 EXPRESSION TAG SEQADV 3R7Z HIS A -12 UNP O68183 EXPRESSION TAG SEQADV 3R7Z HIS A -11 UNP O68183 EXPRESSION TAG SEQADV 3R7Z SER A -10 UNP O68183 EXPRESSION TAG SEQADV 3R7Z SER A -9 UNP O68183 EXPRESSION TAG SEQADV 3R7Z GLY A -8 UNP O68183 EXPRESSION TAG SEQADV 3R7Z ARG A -7 UNP O68183 EXPRESSION TAG SEQADV 3R7Z GLU A -6 UNP O68183 EXPRESSION TAG SEQADV 3R7Z ASN A -5 UNP O68183 EXPRESSION TAG SEQADV 3R7Z LEU A -4 UNP O68183 EXPRESSION TAG SEQADV 3R7Z TYR A -3 UNP O68183 EXPRESSION TAG SEQADV 3R7Z PHE A -2 UNP O68183 EXPRESSION TAG SEQADV 3R7Z GLN A -1 UNP O68183 EXPRESSION TAG SEQADV 3R7Z GLY A 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 MODRES 3R7Z MSE A 83 MET SELENOMETHIONINE MODRES 3R7Z MSE A 90 MET SELENOMETHIONINE MODRES 3R7Z MSE A 170 MET SELENOMETHIONINE MODRES 3R7Z MSE A 234 MET SELENOMETHIONINE MODRES 3R7Z MSE A 242 MET SELENOMETHIONINE MODRES 3R7Z MSE A 266 MET SELENOMETHIONINE MODRES 3R7Z MSE A 285 MET SELENOMETHIONINE HET MSE A 83 8 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 NA A 302 1 HET NA A 303 1 HET NA A 304 1 HET NA A 305 1 HET NA A 306 1 HET NA A 307 1 HET NA A 308 1 HET NA A 309 1 HET NA A 310 1 HET NA A 311 1 HET NA A 312 1 HET NA A 313 1 HET NA A 314 1 HET NA A 315 1 HET NA A 316 1 HET NA A 317 1 HET NA A 318 1 HET NA A 319 1 HET NA A 320 1 HET NA A 321 1 HET NA A 322 1 HET NA A 323 1 HET NA A 324 1 HET NA A 325 1 HET NA A 326 1 HET NA A 327 1 HET NA A 328 1 HET NA A 329 1 HET NA A 330 1 HET NA A 331 1 HET NA A 332 1 HET NA A 333 1 HET NA A 334 1 HET CL A 335 1 HET CL A 336 1 HET CL A 337 1 HET CL A 338 1 HET CL A 339 1 HET CL A 340 1 HET CL A 341 1 HET PE3 A 342 6 HETNAM MSE SELENOMETHIONINE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PE3 3,6,9,12,15,18,21,24,27,30,33,36,39- HETNAM 2 PE3 TRIDECAOXAHENTETRACONTANE-1,41-DIOL HETSYN PE3 POLYETHYLENE GLYCOL FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 NA 33(NA 1+) FORMUL 35 CL 7(CL 1-) FORMUL 42 PE3 C28 H58 O15 FORMUL 43 HOH *254(H2 O) HELIX 1 1 THR A 5 TYR A 17 1 13 HELIX 2 2 HIS A 50 ILE A 67 1 18 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 LYS A 139 VAL A 143 5 5 HELIX 6 6 ASP A 145 LEU A 161 1 17 HELIX 7 7 LYS A 166 GLU A 182 1 17 HELIX 8 8 ASN A 183 PHE A 187 5 5 HELIX 9 9 SER A 199 ASP A 201 5 3 HELIX 10 10 ASP A 227 SER A 232 1 6 HELIX 11 11 GLY A 241 TYR A 252 1 12 HELIX 12 12 ASP A 256 GLU A 281 1 26 HELIX 13 13 TYR A 284 ARG A 296 1 13 SHEET 1 A 5 ILE A 25 GLU A 30 0 SHEET 2 A 5 CYS A 34 ILE A 39 -1 O ALA A 36 N GLY A 29 SHEET 3 A 5 PHE A 43 PRO A 48 -1 O PHE A 43 N ILE A 39 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 PHE A 80 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 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 1.34 LINK C LEU A 233 N MSE A 234 1555 1555 1.34 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 1.32 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 OE2 GLU A 26 NA NA A 307 1555 1555 2.89 LINK OE1 GLN A 116 NA NA A 311 1555 1555 2.92 LINK O HIS A 254 NA NA A 321 1555 1555 2.96 LINK NA NA A 304 O HOH A 529 1555 1555 2.99 LINK NA NA A 329 O HOH A 358 1555 1555 2.99 LINK OE1 GLU A 77 NA NA A 320 1555 1555 3.04 LINK NA NA A 322 O HOH A 450 1555 1555 3.04 LINK OD2 ASP A 206 NA NA A 324 1555 1555 3.04 LINK NA NA A 303 O HOH A 475 1555 1555 3.05 LINK NA NA A 320 O HOH A 554 1555 1555 3.07 LINK OE2 GLU A 30 NA NA A 306 1555 1555 3.10 LINK NA NA A 303 O HOH A 557 1555 1555 3.11 LINK NA NA A 309 O HOH A 469 1555 1555 3.14 LINK NA NA A 325 O HOH A 473 1555 1555 3.14 LINK OE1 GLU A 14 NA NA A 312 1555 1555 3.14 LINK NA NA A 320 O HOH A 574 1555 1555 3.16 LINK NA NA A 305 O HOH A 454 1555 1555 3.16 LINK NA NA A 324 O HOH A 576 1555 1555 3.19 LINK O LYS A 99 NA NA A 327 1555 1555 3.19 LINK NA NA A 323 O HOH A 428 1555 1555 3.20 SITE 1 AC1 4 PHE A 146 MSE A 266 LYS A 267 HOH A 475 SITE 1 AC2 3 GLU A 184 CL A 340 HOH A 529 SITE 1 AC3 2 GLN A 114 SER A 115 SITE 1 AC4 3 ILE A 27 GLU A 30 ILE A 135 SITE 1 AC5 5 GLU A 26 ASP A 145 PHE A 146 ARG A 147 SITE 2 AC5 5 HOH A 579 SITE 1 AC6 2 ASN A 109 GLN A 116 SITE 1 AC7 1 PHE A 43 SITE 1 AC8 3 LYS A 113 GLN A 116 LYS A 247 SITE 1 AC9 1 GLU A 14 SITE 1 BC1 1 LEU A 165 SITE 1 BC2 2 LYS A 166 GLN A 169 SITE 1 BC3 1 ILE A 22 SITE 1 BC4 1 LYS A 269 SITE 1 BC5 2 GLU A 77 HOH A 554 SITE 1 BC6 3 ASN A 250 LYS A 253 HIS A 254 SITE 1 BC7 2 PHE A 43 HOH A 450 SITE 1 BC8 1 PHE A 20 SITE 1 BC9 2 ASP A 206 LYS A 209 SITE 1 CC1 2 MSE A 234 ASP A 236 SITE 1 CC2 1 LYS A 99 SITE 1 CC3 3 ASP A 7 LYS A 171 LYS A 188 SITE 1 CC4 2 ARG A 2 HOH A 358 SITE 1 CC5 2 ASN A 62 LYS A 65 SITE 1 CC6 2 LYS A 255 PRO A 258 SITE 1 CC7 1 ASP A 145 SITE 1 CC8 4 ILE A 231 GLU A 235 LYS A 267 GLU A 268 SITE 1 CC9 2 LYS A 139 HOH A 480 SITE 1 DC1 4 ASP A 7 LYS A 11 LYS A 172 HOH A 369 SITE 1 DC2 4 GLY A 31 ASN A 32 ASP A 33 CYS A 34 SITE 1 DC3 2 ASN A 109 GLN A 116 SITE 1 DC4 3 HOH A 382 HOH A 422 HOH A 439 SITE 1 DC5 6 THR A 5 PHE A 6 ASP A 7 TYR A 190 SITE 2 DC5 6 HOH A 347 HOH A 596 SITE 1 DC6 3 NA A 304 HOH A 553 HOH A 560 SITE 1 DC7 3 ASN A 154 HOH A 451 HOH A 593 SITE 1 DC8 5 ARG A 125 SER A 128 GLU A 129 SER A 132 SITE 2 DC8 5 HOH A 477 CRYST1 56.583 63.177 103.456 90.00 90.00 90.00 P 21 21 21 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 0.017673 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009666 0.00000