HEADER TRANSFERASE 14-SEP-05 2B0Q TITLE CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE IIIA TITLE 2 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, APH3', 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: APHA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETSACG1 KEYWDS PROTEIN KINASE-LIKE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.H.FONG,A.M.BERGHUIS REVDAT 3 23-AUG-23 2B0Q 1 REMARK LINK REVDAT 2 24-FEB-09 2B0Q 1 VERSN REVDAT 1 27-SEP-05 2B0Q 0 SPRSDE 27-SEP-05 2B0Q 1L8U JRNL AUTH D.H.FONG,A.M.BERGHUIS JRNL TITL SUBSTRATE PROMISCUITY OF AN AMINOGLYCOSIDE ANTIBIOTIC JRNL TITL 2 RESISTANCE ENZYME VIA TARGET MIMICRY. JRNL REF EMBO J. V. 21 2323 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12006485 JRNL DOI 10.1093/EMBOJ/21.10.2323 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) : 46.36 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) (%) : 80.9 REMARK 3 NUMBER OF REFLECTIONS : 8027 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) : 0.225 REMARK 3 FREE R VALUE : 0.312 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 852 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) (%) : 50.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE : 0.4620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.050 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 : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.61100 REMARK 3 B22 (A**2) : 1.61100 REMARK 3 B33 (A**2) : -3.22100 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.42 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) : 0.57 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.76 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.396 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.93 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.838 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) : 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 : 54.01 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ATP.PAR REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : NMY.PAR REMARK 3 PARAMETER FILE 5 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2B0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034530. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 9.5 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) : 1.07 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR 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) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04800 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) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.16800 REMARK 200 R SYM FOR SHELL (I) : 0.16800 REMARK 200 FOR SHELL : 4.300 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: PDB ENTRY 1L8T 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): 2.60 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,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA A 2 REMARK 475 LYS A 3 REMARK 475 MET A 4 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 ILE A 6 CG1 CD1 REMARK 480 LYS A 11 CD CE NZ REMARK 480 LYS A 12 CB CG CD CE NZ REMARK 480 LEU A 13 CD1 CD2 REMARK 480 ILE A 14 CG1 CG2 CD1 REMARK 480 GLU A 15 CB CG CD OE1 OE2 REMARK 480 LYS A 16 CG CD CE REMARK 480 LYS A 21 CG CD CE NZ REMARK 480 LYS A 30 CD CE NZ REMARK 480 LYS A 51 CB CG CD CE NZ REMARK 480 ARG A 81 CG CD NE REMARK 480 GLU A 103 CB CG CD OE1 OE2 REMARK 480 ASP A 104 CB CG OD1 OD2 REMARK 480 GLU A 105 CB CG CD OE1 OE2 REMARK 480 GLN A 106 OE1 NE2 REMARK 480 ARG A 120 CD NE CZ NH1 NH2 REMARK 480 ILE A 125 CG1 CG2 CD1 REMARK 480 SER A 128 CB OG REMARK 480 LYS A 166 CG CD CE NZ REMARK 480 ARG A 229 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 235 CG CD OE1 OE2 REMARK 480 GLU A 239 CG CD OE1 OE2 REMARK 480 LYS A 255 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 SG CYS A 19 SG CYS A 156 7643 1.81 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 LYS A 3 -152.51 -164.28 REMARK 500 MET A 4 -127.13 -142.09 REMARK 500 ARG A 5 -100.10 -160.03 REMARK 500 THR A 23 21.38 -154.10 REMARK 500 MET A 26 -2.93 -54.98 REMARK 500 LEU A 34 77.56 -106.70 REMARK 500 GLU A 39 -161.31 -179.87 REMARK 500 ARG A 49 -34.04 -39.52 REMARK 500 LYS A 51 147.73 -39.87 REMARK 500 LYS A 70 -58.04 -120.71 REMARK 500 TYR A 102 31.37 -145.05 REMARK 500 GLU A 105 -131.12 73.78 REMARK 500 SER A 107 41.73 -153.39 REMARK 500 HIS A 123 44.07 -71.30 REMARK 500 SER A 124 -33.21 -142.50 REMARK 500 ASN A 134 65.01 -118.00 REMARK 500 CYS A 156 39.05 -97.67 REMARK 500 ASN A 158 59.74 -96.78 REMARK 500 TRP A 159 159.40 -43.94 REMARK 500 GLU A 161 -15.96 67.88 REMARK 500 ASP A 162 -71.17 -94.05 REMARK 500 THR A 163 96.84 -9.21 REMARK 500 LYS A 179 112.95 -37.00 REMARK 500 VAL A 185 -162.61 -123.38 REMARK 500 ASP A 190 50.61 -174.22 REMARK 500 ASP A 193 -16.51 -49.60 REMARK 500 ASP A 200 11.57 53.01 REMARK 500 GLU A 235 -30.82 -37.82 REMARK 500 ASP A 250 76.67 -101.51 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 SER A 194 OG REMARK 620 2 ASN A 195 OD1 99.7 REMARK 620 3 ADP A 300 O3B 139.6 106.9 REMARK 620 4 ADP A 300 O2A 149.8 76.9 67.6 REMARK 620 5 HOH A 519 O 99.8 65.7 66.0 105.7 REMARK 620 N 1 2 3 4 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 OD2 REMARK 620 2 ASP A 208 OD1 50.4 REMARK 620 3 ADP A 300 O1B 65.7 74.9 REMARK 620 4 HOH A 520 O 83.5 131.6 72.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMY A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J7I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE REMARK 900 IIIA APOENZYME REMARK 900 RELATED ID: 1J7L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE REMARK 900 IIIA ADP COMPLEX REMARK 900 RELATED ID: 1J7U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE REMARK 900 IIIA AMPPNP COMPLEX REMARK 900 RELATED ID: 1L8T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE REMARK 900 IIIA ADP KANAMYCIN A COMPLEX DBREF 2B0Q A 2 264 UNP P0A3Y5 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 NMY A 305 42 HET MG A 301 1 HET MG A 302 1 HET ADP A 300 27 HETNAM NMY NEOMYCIN HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETSYN NMY MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN FORMUL 2 NMY C23 H46 N6 O13 FORMUL 3 MG 2(MG 2+) FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 HOH *45(H2 O) 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 SER A 99 GLU A 101 5 3 HELIX 5 5 SER A 107 HIS A 123 1 17 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 GLY A 233 1 17 HELIX 9 9 GLU A 234 GLY A 246 1 13 HELIX 10 10 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 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 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 LINK OG SER A 194 MG MG A 301 1555 1555 2.78 LINK OD1 ASN A 195 MG MG A 301 1555 1555 2.32 LINK OD2 ASP A 208 MG MG A 302 1555 1555 2.81 LINK OD1 ASP A 208 MG MG A 302 1555 1555 2.19 LINK O3B ADP A 300 MG MG A 301 1555 1555 2.51 LINK O2A ADP A 300 MG MG A 301 1555 1555 2.19 LINK O1B ADP A 300 MG MG A 302 1555 1555 2.27 LINK MG MG A 301 O HOH A 519 1555 1555 2.26 LINK MG MG A 302 O HOH A 520 1555 1555 2.12 SITE 1 AC1 15 GLU A 24 GLU A 157 ASN A 158 GLU A 160 SITE 2 AC1 15 ASP A 190 ASP A 193 SER A 194 ARG A 226 SITE 3 AC1 15 GLU A 230 ASP A 231 ASP A 261 GLU A 262 SITE 4 AC1 15 PHE A 264 HOH A 519 HOH A 520 SITE 1 AC2 5 SER A 194 ASN A 195 ASP A 208 ADP A 300 SITE 2 AC2 5 HOH A 519 SITE 1 AC3 4 ASP A 190 ASP A 208 ADP A 300 HOH A 520 SITE 1 AC4 23 ASP A 22 GLU A 24 GLY A 25 SER A 27 SITE 2 AC4 23 VAL A 31 TYR A 42 LYS A 44 PRO A 74 SITE 3 AC4 23 MET A 90 SER A 91 GLU A 92 ALA A 93 SITE 4 AC4 23 LEU A 97 SER A 194 ASN A 195 PHE A 197 SITE 5 AC4 23 ILE A 207 ASP A 208 MG A 301 MG A 302 SITE 6 AC4 23 HOH A 519 HOH A 520 HOH A 544 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