HEADER TRANSFERASE 21-MAR-02 1L8U OBSLTE 27-SEP-05 1L8U 2B0Q TITLE CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE TITLE 2 PHOSPHOTRANSFERASE TYPE IIIA ADP NEOMYCIN B COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KANAMYCIN KINASE TYPE III, NEOMYCIN-KANAMYCIN COMPND 5 PHOSPHOTRANSFERASE TYPE III, APH(3')III; COMPND 6 EC: 2.7.1.95; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPCRG6 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.H.FONG,A.M.BERGHUIS REVDAT 2 27-SEP-05 1L8U 1 OBSLTE REVDAT 1 19-JUN-02 1L8U 0 JRNL AUTH D.H.FONG,A.M.BERGHUIS JRNL TITL SUBSTRATE PROMISCUITY OF AN AMINOGLYCOSIDE JRNL TITL 2 ANTIBIOTIC RESISTANCE ENZYME VIA TARGET MIMICRY. JRNL REF EMBO J. V. 21 2323 2002 JRNL REFN ASTM EMJODG UK ISSN 0261-4189 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 851 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE : 0.4210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 86 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.045 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2170 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 44 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.54 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.39 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L8U COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-2002. REMARK 100 THE RCSB ID CODE IS RCSB015750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-2000 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 9.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8074 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 600, CHES, PH 9.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 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 3555 -Y,X,3/4+Z REMARK 290 4555 Y,-X,1/4+Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,1/2-Z REMARK 290 7555 Y,X,1/4-Z REMARK 290 8555 -Y,-X,3/4-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 150.80650 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 226.20975 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 75.40325 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 150.80650 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 75.40325 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 226.20975 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER A 107 N - CA - C ANGL. DEV. = -8.7 DEGREES REMARK 500 CYS A 156 N - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 GLU A 160 N - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 GLU A 181 N - CA - C ANGL. DEV. =-10.4 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ARG A 5 -105.10 -155.63 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J7I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE REMARK 900 PHOSPHOTRANSFERASE TYPE IIIA APOENZYME REMARK 900 RELATED ID: 1J7L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE REMARK 900 PHOSPHOTRANSFERASE TYPE IIIA ADP COMPLEX REMARK 900 RELATED ID: 1J7U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE REMARK 900 PHOSPHOTRANSFERASE TYPE IIIA AMPPNP COMPLEX DBREF 1L8U A 2 264 UNP P00554 KKA3_ENTFA 2 264 SEQRES 1 A 263 ALA LYS MET ARG ILE SER PRO GLU LEU LYS LYS LEU ILE SEQRES 2 A 263 GLU LYS TYR ARG CYS VAL LYS ASP THR GLU GLY MET SER SEQRES 3 A 263 PRO ALA LYS VAL TYR LYS LEU VAL GLY GLU ASN GLU ASN SEQRES 4 A 263 LEU TYR LEU LYS MET THR ASP SER ARG TYR LYS GLY THR SEQRES 5 A 263 THR TYR ASP VAL GLU ARG GLU LYS ASP MET MET LEU TRP SEQRES 6 A 263 LEU GLU GLY LYS LEU PRO VAL PRO LYS VAL LEU HIS PHE SEQRES 7 A 263 GLU ARG HIS ASP GLY TRP SER ASN LEU LEU MET SER GLU SEQRES 8 A 263 ALA ASP GLY VAL LEU CYS SER GLU GLU TYR GLU ASP GLU SEQRES 9 A 263 GLN SER PRO GLU LYS ILE ILE GLU LEU TYR ALA GLU CYS SEQRES 10 A 263 ILE ARG LEU PHE HIS SER ILE ASP ILE SER ASP CYS PRO SEQRES 11 A 263 TYR THR ASN SER LEU ASP SER ARG LEU ALA GLU LEU ASP SEQRES 12 A 263 TYR LEU LEU ASN ASN ASP LEU ALA ASP VAL ASP CYS GLU SEQRES 13 A 263 ASN TRP GLU GLU ASP THR PRO PHE LYS ASP PRO ARG GLU SEQRES 14 A 263 LEU TYR ASP PHE LEU LYS THR GLU LYS PRO GLU GLU GLU SEQRES 15 A 263 LEU VAL PHE SER HIS GLY ASP LEU GLY ASP SER ASN ILE SEQRES 16 A 263 PHE VAL LYS ASP GLY LYS VAL SER GLY PHE ILE ASP LEU SEQRES 17 A 263 GLY ARG SER GLY ARG ALA ASP LYS TRP TYR ASP ILE ALA SEQRES 18 A 263 PHE CYS VAL ARG SER ILE ARG GLU ASP ILE GLY GLU GLU SEQRES 19 A 263 GLN TYR VAL GLU LEU PHE PHE ASP LEU LEU GLY ILE LYS SEQRES 20 A 263 PRO ASP TRP GLU LYS ILE LYS TYR TYR ILE LEU LEU ASP SEQRES 21 A 263 GLU LEU PHE HET MG A 301 1 HET MG A 302 1 HET ADP 300 27 HET NMY 305 42 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM NMY NEOMYCIN HETSYN NMY MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN FORMUL 2 MG 2(MG 2+) FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 NMY C23 H46 N6 O13 FORMUL 6 HOH *44(H2 O1) HELIX 1 1 SER A 7 TYR A 17 1 11 HELIX 2 2 ARG A 49 LYS A 51 5 3 HELIX 3 3 ASP A 56 LEU A 67 1 12 HELIX 4 4 CYS A 98 TYR A 102 1 5 HELIX 5 5 SER A 107 ILE A 125 1 19 HELIX 6 6 SER A 135 ASN A 149 1 15 HELIX 7 7 ASP A 167 LYS A 179 1 13 HELIX 8 8 LYS A 217 ILE A 232 1 16 HELIX 9 9 GLU A 234 GLY A 246 1 13 HELIX 10 10 ASP A 250 GLU A 262 1 13 SHEET 1 A 5 ARG A 18 LYS A 21 0 SHEET 2 A 5 LYS A 30 VAL A 35 -1 O LYS A 33 N VAL A 20 SHEET 3 A 5 ASN A 40 ASP A 47 -1 O LEU A 41 N LEU A 34 SHEET 4 A 5 TRP A 85 SER A 91 -1 O MET A 90 N TYR A 42 SHEET 5 A 5 VAL A 76 ARG A 81 -1 N GLU A 80 O ASN A 87 SHEET 1 B 3 VAL A 96 LEU A 97 0 SHEET 2 B 3 ILE A 196 LYS A 199 -1 O VAL A 198 N VAL A 96 SHEET 3 B 3 LYS A 202 PHE A 206 -1 O SER A 204 N PHE A 197 SHEET 1 C 2 LEU A 184 SER A 187 0 SHEET 2 C 2 GLY A 213 ASP A 216 -1 O ALA A 215 N VAL A 185 CRYST1 46.357 46.357 301.613 90.00 90.00 90.00 P 43 2 2 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 0.021572 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003316 0.00000