HEADER TRANSFERASE/ANTIBIOTIC 29-APR-09 3H8P OBSLTE 19-OCT-11 3H8P 3TM0 TITLE CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE IIIA TITLE 2 AMPPNP BUTIROSIN A 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_TAXID: 1351; SOURCE 4 GENE: APH(3')-IIIA, APHA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS KINASE, ANTIBIOTIC RESISTANCE, AMINOGLYCOSIDES, ATP-BINDING, KEYWDS 2 NUCLEOTIDE-BINDING, TRANSFERASE, TRANSFERASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.H.FONG,A.M.BERGHUIS REVDAT 2 19-OCT-11 3H8P 1 OBSLTE VERSN REVDAT 1 30-JUN-09 3H8P 0 JRNL AUTH D.H.FONG,A.M.BERGHUIS JRNL TITL STRUCTURAL BASIS OF APH(3')-IIIA MEDIATED RESISTANCE TO JRNL TITL 2 SECOND GENERATION AMINOGLYCOSIDE ANTIBIOTICS. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 53 3049 2009 JRNL REFN ISSN 0066-4804 JRNL PMID 19433564 JRNL DOI 10.1128/AAC.00062-09 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 354177.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 14475 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) : 0.218 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1473 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2054 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 207 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 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 : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : 0.49000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.85 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.300 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.080 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.050 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 42.15 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3H8P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-09. REMARK 100 THE RCSB ID CODE IS RCSB052832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : SI (111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS 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 : 14576 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 39.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 14.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 44.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13700 REMARK 200 FOR SHELL : 16.970 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1L8T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 600, 0.1M SODIUM ACETATE, 0.2M REMARK 280 MAGNESIUM CHLORIDE, 3% D(+)-SUCROSE, PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 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,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.05500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.29950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.05500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.05500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.29950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.05500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.05500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.29950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.05500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.05500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.29950 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 0.00000 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 80.11000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 80.11000 REMARK 350 BIOMT3 2 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 24 CD OE1 OE2 REMARK 480 GLU A 105 CG CD OE1 OE2 REMARK 480 GLU A 161 OE2 REMARK 480 LYS A 166 CE NZ REMARK 480 GLU A 230 CD OE1 OE2 REMARK 480 GLU A 252 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 THR A 23 -62.10 -99.28 REMARK 500 GLU A 24 88.06 -63.39 REMARK 500 ASN A 134 59.31 -93.76 REMARK 500 ASP A 153 58.03 -95.92 REMARK 500 CYS A 156 -115.17 57.39 REMARK 500 GLU A 157 -5.55 -51.32 REMARK 500 ASP A 190 58.27 -153.38 REMARK 500 ASP A 208 67.91 60.43 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 195 OD1 REMARK 620 2 ASP A 208 OD2 90.2 REMARK 620 3 ANP A 300 O1G 175.2 91.6 REMARK 620 4 ANP A 300 O2A 97.4 81.4 87.3 REMARK 620 5 HOH A 566 O 86.3 172.3 92.4 92.2 REMARK 620 6 HOH A 559 O 93.0 95.7 82.5 169.3 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 208 OD1 REMARK 620 2 ASP A 208 OD2 59.6 REMARK 620 3 ANP A 300 O3G 154.2 95.7 REMARK 620 4 ANP A 300 O2B 77.5 85.1 94.3 REMARK 620 5 HOH A 511 O 98.2 85.5 86.1 170.6 REMARK 620 6 HOH A 565 O 92.8 150.2 112.9 100.4 88.1 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 ANP A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B31 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 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 REMARK 900 RELATED ID: 1L8T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE REMARK 900 PHOSPHOTRANSFERASE TYPE IIIA ADP KANAMYCIN A COMPLEX REMARK 900 RELATED ID: 2B0Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE REMARK 900 PHOSPHOTRANSFERASE TYPE IIIA ADP NEOMYCIN B COMPLEX DBREF 3H8P A 1 264 UNP P0A3Y5 KKA3_ENTFA 1 264 SEQRES 1 A 264 MET ALA LYS MET ARG ILE SER PRO GLU LEU LYS LYS LEU SEQRES 2 A 264 ILE GLU LYS TYR ARG CYS VAL LYS ASP THR GLU GLY MET SEQRES 3 A 264 SER PRO ALA LYS VAL TYR LYS LEU VAL GLY GLU ASN GLU SEQRES 4 A 264 ASN LEU TYR LEU LYS MET THR ASP SER ARG TYR LYS GLY SEQRES 5 A 264 THR THR TYR ASP VAL GLU ARG GLU LYS ASP MET MET LEU SEQRES 6 A 264 TRP LEU GLU GLY LYS LEU PRO VAL PRO LYS VAL LEU HIS SEQRES 7 A 264 PHE GLU ARG HIS ASP GLY TRP SER ASN LEU LEU MET SER SEQRES 8 A 264 GLU ALA ASP GLY VAL LEU CYS SER GLU GLU TYR GLU ASP SEQRES 9 A 264 GLU GLN SER PRO GLU LYS ILE ILE GLU LEU TYR ALA GLU SEQRES 10 A 264 CYS ILE ARG LEU PHE HIS SER ILE ASP ILE SER ASP CYS SEQRES 11 A 264 PRO TYR THR ASN SER LEU ASP SER ARG LEU ALA GLU LEU SEQRES 12 A 264 ASP TYR LEU LEU ASN ASN ASP LEU ALA ASP VAL ASP CYS SEQRES 13 A 264 GLU ASN TRP GLU GLU ASP THR PRO PHE LYS ASP PRO ARG SEQRES 14 A 264 GLU LEU TYR ASP PHE LEU LYS THR GLU LYS PRO GLU GLU SEQRES 15 A 264 GLU LEU VAL PHE SER HIS GLY ASP LEU GLY ASP SER ASN SEQRES 16 A 264 ILE PHE VAL LYS ASP GLY LYS VAL SER GLY PHE ILE ASP SEQRES 17 A 264 LEU GLY ARG SER GLY ARG ALA ASP LYS TRP TYR ASP ILE SEQRES 18 A 264 ALA PHE CYS VAL ARG SER ILE ARG GLU ASP ILE GLY GLU SEQRES 19 A 264 GLU GLN TYR VAL GLU LEU PHE PHE ASP LEU LEU GLY ILE SEQRES 20 A 264 LYS PRO ASP TRP GLU LYS ILE LYS TYR TYR ILE LEU LEU SEQRES 21 A 264 ASP GLU LEU PHE HET ANP A 300 31 HET B31 A 305 38 HET MG A 301 1 HET MG A 302 1 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM B31 (2S)-4-AMINO-N-[(1R,2S,3R,4R,5S)-5-AMINO-4-[(2,6- HETNAM 2 B31 DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2- HETNAM 3 B31 HYDROXY-3-(BETA-D-XYLOFURANOSYLOXY)CYCLOHEXYL]-2- HETNAM 4 B31 HYDROXYBUTANAMIDE HETNAM MG MAGNESIUM ION HETSYN B31 BUTIROSIN A FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 B31 C21 H41 N5 O12 FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *85(H2 O) HELIX 1 1 SER A 7 GLU A 15 1 9 HELIX 2 2 ASP A 47 LYS A 51 5 5 HELIX 3 3 ASP A 56 GLU A 68 1 13 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 155 TRP A 159 5 5 HELIX 8 8 ASP A 167 GLU A 178 1 12 HELIX 9 9 LYS A 217 ILE A 232 1 16 HELIX 10 10 GLU A 234 GLY A 246 1 13 HELIX 11 11 ASP A 250 ASP A 261 1 12 SHEET 1 A 5 ARG A 18 LYS A 21 0 SHEET 2 A 5 LYS A 30 VAL A 35 -1 O VAL A 35 N ARG A 18 SHEET 3 A 5 ASN A 40 THR A 46 -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 HIS A 82 -1 N HIS A 78 O LEU A 89 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 GLY A 213 N SER A 187 SSBOND 1 CYS A 19 CYS A 156 1555 2665 2.02 LINK OD1 ASN A 195 MG MG A 301 1555 1555 1.95 LINK OD1 ASP A 208 MG MG A 302 1555 1555 2.24 LINK OD2 ASP A 208 MG MG A 301 1555 1555 2.36 LINK OD2 ASP A 208 MG MG A 302 1555 1555 2.18 LINK O1G ANP A 300 MG MG A 301 1555 1555 1.97 LINK O3G ANP A 300 MG MG A 302 1555 1555 1.98 LINK O2B ANP A 300 MG MG A 302 1555 1555 2.01 LINK O2A ANP A 300 MG MG A 301 1555 1555 2.09 LINK MG MG A 301 O HOH A 566 1555 1555 2.25 LINK MG MG A 301 O HOH A 559 1555 1555 2.05 LINK MG MG A 302 O HOH A 511 1555 1555 2.05 LINK MG MG A 302 O HOH A 565 1555 1555 2.11 SITE 1 AC1 30 ASP A 22 GLY A 25 MET A 26 SER A 27 SITE 2 AC1 30 ALA A 29 VAL A 31 TYR A 42 LYS A 44 SITE 3 AC1 30 PRO A 74 MET A 90 SER A 91 GLU A 92 SITE 4 AC1 30 ALA A 93 LEU A 97 SER A 194 ASN A 195 SITE 5 AC1 30 PHE A 197 ILE A 207 ASP A 208 MG A 301 SITE 6 AC1 30 MG A 302 B31 A 305 HOH A 502 HOH A 511 SITE 7 AC1 30 HOH A 523 HOH A 549 HOH A 559 HOH A 566 SITE 8 AC1 30 HOH A 571 HOH A 582 SITE 1 AC2 15 MET A 26 ASP A 153 GLU A 157 ASP A 190 SITE 2 AC2 15 ARG A 226 ASP A 261 GLU A 262 PHE A 264 SITE 3 AC2 15 ANP A 300 HOH A 504 HOH A 522 HOH A 531 SITE 4 AC2 15 HOH A 532 HOH A 554 HOH A 559 SITE 1 AC3 5 ASN A 195 ASP A 208 ANP A 300 HOH A 559 SITE 2 AC3 5 HOH A 566 SITE 1 AC4 4 ASP A 208 ANP A 300 HOH A 511 HOH A 565 CRYST1 80.110 80.110 110.599 90.00 90.00 90.00 P 42 21 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 0.012483 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009042 0.00000