HEADER NUCLEOTIDYLTRANSFERASE 13-AUG-93 1KAN TITLE MOLECULAR STRUCTURE OF KANAMYCIN NUCLEOTIDYLTRANSFERASE DETERMINED TO TITLE 2 3.0-ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: KANAMYCIN NUCLEOTIDYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280 KEYWDS NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A, B AUTHOR H.M.HOLDEN,I.RAYMENT,J.SAKON REVDAT 4 07-FEB-24 1KAN 1 SEQADV REVDAT 3 24-FEB-09 1KAN 1 VERSN REVDAT 2 01-APR-03 1KAN 1 JRNL REVDAT 1 31-AUG-94 1KAN 0 JRNL AUTH J.SAKON,H.H.LIAO,A.M.KANIKULA,M.M.BENNING,I.RAYMENT, JRNL AUTH 2 H.M.HOLDEN JRNL TITL MOLECULAR STRUCTURE OF KANAMYCIN NUCLEOTIDYLTRANSFERASE JRNL TITL 2 DETERMINED TO 3.0-A RESOLUTION. JRNL REF BIOCHEMISTRY V. 32 11977 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8218273 JRNL DOI 10.1021/BI00096A006 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 3.000 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 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 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KAN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 109.60000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.45000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 164.40000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.45000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.45000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.80000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 164.40000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.80000 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 109.60000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 DBREF 1KAN A 1 253 UNP P05057 KANU_STAAU 1 253 DBREF 1KAN B 1 253 UNP P05057 KANU_STAAU 1 253 SEQADV 1KAN TYR A 80 UNP P05057 ASP 80 CONFLICT SEQADV 1KAN LYS A 130 UNP P05057 THR 130 CONFLICT SEQADV 1KAN TYR B 80 UNP P05057 ASP 80 CONFLICT SEQADV 1KAN LYS B 130 UNP P05057 THR 130 CONFLICT SEQRES 1 A 253 MET ASN GLY PRO ILE ILE MET THR ARG GLU GLU ARG MET SEQRES 2 A 253 LYS ILE VAL HIS GLU ILE LYS GLU ARG ILE LEU ASP LYS SEQRES 3 A 253 TYR GLY ASP ASP VAL LYS ALA ILE GLY VAL TYR GLY SER SEQRES 4 A 253 LEU GLY ARG GLN THR ASP GLY PRO TYR SER ASP ILE GLU SEQRES 5 A 253 MET MET CYS VAL MET SER THR GLU GLU ALA GLU PHE SER SEQRES 6 A 253 HIS GLU TRP THR THR GLY GLU TRP LYS VAL GLU VAL ASN SEQRES 7 A 253 PHE TYR SER GLU GLU ILE LEU LEU ASP TYR ALA SER GLN SEQRES 8 A 253 VAL GLU SER ASP TRP PRO LEU THR HIS GLY GLN PHE PHE SEQRES 9 A 253 SER ILE LEU PRO ILE TYR ASP SER GLY GLY TYR LEU GLU SEQRES 10 A 253 LYS VAL TYR GLN THR ALA LYS SER VAL GLU ALA GLN LYS SEQRES 11 A 253 PHE HIS ASP ALA ILE CYS ALA LEU ILE VAL GLU GLU LEU SEQRES 12 A 253 PHE GLU TYR ALA GLY LYS TRP ARG ASN ILE ARG VAL GLN SEQRES 13 A 253 GLY PRO THR THR PHE LEU PRO SER LEU THR VAL GLN VAL SEQRES 14 A 253 ALA MET ALA GLY ALA MET LEU ILE GLY LEU HIS HIS ARG SEQRES 15 A 253 ILE CYS TYR THR THR SER ALA SER VAL LEU THR GLU ALA SEQRES 16 A 253 VAL LYS GLN SER ASP LEU PRO SER GLY TYR ASP HIS LEU SEQRES 17 A 253 CYS GLN PHE VAL MET SER GLY GLN LEU SER ASP SER GLU SEQRES 18 A 253 LYS LEU LEU GLU SER LEU GLU ASN PHE TRP ASN GLY ILE SEQRES 19 A 253 GLN GLU TRP THR GLU ARG HIS GLY TYR ILE VAL ASP VAL SEQRES 20 A 253 SER LYS ARG ILE PRO PHE SEQRES 1 B 253 MET ASN GLY PRO ILE ILE MET THR ARG GLU GLU ARG MET SEQRES 2 B 253 LYS ILE VAL HIS GLU ILE LYS GLU ARG ILE LEU ASP LYS SEQRES 3 B 253 TYR GLY ASP ASP VAL LYS ALA ILE GLY VAL TYR GLY SER SEQRES 4 B 253 LEU GLY ARG GLN THR ASP GLY PRO TYR SER ASP ILE GLU SEQRES 5 B 253 MET MET CYS VAL MET SER THR GLU GLU ALA GLU PHE SER SEQRES 6 B 253 HIS GLU TRP THR THR GLY GLU TRP LYS VAL GLU VAL ASN SEQRES 7 B 253 PHE TYR SER GLU GLU ILE LEU LEU ASP TYR ALA SER GLN SEQRES 8 B 253 VAL GLU SER ASP TRP PRO LEU THR HIS GLY GLN PHE PHE SEQRES 9 B 253 SER ILE LEU PRO ILE TYR ASP SER GLY GLY TYR LEU GLU SEQRES 10 B 253 LYS VAL TYR GLN THR ALA LYS SER VAL GLU ALA GLN LYS SEQRES 11 B 253 PHE HIS ASP ALA ILE CYS ALA LEU ILE VAL GLU GLU LEU SEQRES 12 B 253 PHE GLU TYR ALA GLY LYS TRP ARG ASN ILE ARG VAL GLN SEQRES 13 B 253 GLY PRO THR THR PHE LEU PRO SER LEU THR VAL GLN VAL SEQRES 14 B 253 ALA MET ALA GLY ALA MET LEU ILE GLY LEU HIS HIS ARG SEQRES 15 B 253 ILE CYS TYR THR THR SER ALA SER VAL LEU THR GLU ALA SEQRES 16 B 253 VAL LYS GLN SER ASP LEU PRO SER GLY TYR ASP HIS LEU SEQRES 17 B 253 CYS GLN PHE VAL MET SER GLY GLN LEU SER ASP SER GLU SEQRES 18 B 253 LYS LEU LEU GLU SER LEU GLU ASN PHE TRP ASN GLY ILE SEQRES 19 B 253 GLN GLU TRP THR GLU ARG HIS GLY TYR ILE VAL ASP VAL SEQRES 20 B 253 SER LYS ARG ILE PRO PHE HELIX 1 A1 ARG A 9 ASP A 25 1 17 HELIX 2 A3 SER A 39 ARG A 42 1ALPHA-HELICAL TURN 4 HELIX 3 A7 GLU A 82 SER A 90 1 9 HELIX 4 A8 TRP A 96 PHE A 104 1 9 HELIX 5 A10 TYR A 115 LYS A 124 1 10 HELIX 6 A11 ALA A 128 ILE A 153 1 26 HELIX 7 A12 LEU A 162 HIS A 180 1 19 HELIX 8 A13 ALA A 189 ALA A 195 1 7 HELIX 9 A14 TYR A 205 SER A 214 1 10 HELIX 10 A15 SER A 220 HIS A 241 1 22 HELIX 11 B1 ARG B 9 ASP B 25 1 17 HELIX 12 B3 SER B 39 ARG B 42 1ALPHA-HELICAL TURN 4 HELIX 13 B7 GLU B 82 SER B 90 1 9 HELIX 14 B8 TRP B 96 PHE B 104 1 9 HELIX 15 B10 TYR B 115 LYS B 124 1 10 HELIX 16 B11 ALA B 128 ILE B 153 1 26 HELIX 17 B12 LEU B 162 HIS B 180 1 19 HELIX 18 B13 ALA B 189 ALA B 195 1 7 HELIX 19 B14 TYR B 205 SER B 214 1 10 HELIX 20 B15 SER B 220 HIS B 241 1 22 SHEET 1 SHA 5 ALA A 62 THR A 69 0 SHEET 2 SHA 5 LYS A 74 SER A 81 -1 SHEET 3 SHA 5 ILE A 51 MET A 57 -1 SHEET 4 SHA 5 VAL A 31 VAL A 36 -1 SHEET 5 SHA 5 LEU A 107 ASP A 111 -1 SHEET 1 SHB 5 ALA B 62 THR B 69 0 SHEET 2 SHB 5 LYS B 74 SER B 81 -1 SHEET 3 SHB 5 ILE B 51 MET B 57 -1 SHEET 4 SHB 5 VAL B 31 VAL B 36 -1 SHEET 5 SHB 5 LEU B 107 ASP B 111 -1 CRYST1 78.900 78.900 219.200 90.00 90.00 90.00 P 43 21 2 16 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 0.012674 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012674 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004562 0.00000