HEADER OXIDOREDUCTASE 18-APR-19 6JW7 TITLE THE CRYSTAL STRUCTURE OF KAND2 IN COMPLEX WITH NADH AND 3"-DEAMINO-3"- TITLE 2 HYDROXYKANAMYCIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: KAND2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES KANAMYCETICUS; SOURCE 3 ORGANISM_TAXID: 1967; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS ROSSMANN FOLD, NAD BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.KUDO,Y.KITAYAMA,A.MIYANAGA,A.HIRAYAMA,T.EGUCHI REVDAT 3 22-NOV-23 6JW7 1 REMARK REVDAT 2 29-APR-20 6JW7 1 JRNL REVDAT 1 15-APR-20 6JW7 0 JRNL AUTH F.KUDO,Y.KITAYAMA,A.MIYANAGA,A.HIRAYAMA,T.EGUCHI JRNL TITL BIOCHEMICAL AND STRUCTURAL ANALYSIS OF A DEHYDROGENASE, JRNL TITL 2 KAND2, AND AN AMINOTRANSFERASE, KANS2, THAT ARE RESPONSIBLE JRNL TITL 3 FOR THE CONSTRUCTION OF THE KANOSAMINE MOIETY IN KANAMYCIN JRNL TITL 4 BIOSYNTHESIS. JRNL REF BIOCHEMISTRY V. 59 1470 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 32237736 JRNL DOI 10.1021/ACS.BIOCHEM.0C00204 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43605 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 + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2319 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3174 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 191 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5172 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 121 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.78000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : -2.54000 REMARK 3 B12 (A**2) : 0.78000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.241 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.195 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.911 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5449 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5136 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7443 ; 2.073 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11746 ; 1.214 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 683 ; 6.466 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 246 ;34.385 ;22.683 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 792 ;18.107 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;23.208 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 825 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6217 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1289 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 5 361 B 5 361 19756 0.10 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 362 REMARK 3 RESIDUE RANGE : A 401 A 402 REMARK 3 ORIGIN FOR THE GROUP (A): 42.5900 -6.4250 18.2040 REMARK 3 T TENSOR REMARK 3 T11: 0.3685 T22: 0.3714 REMARK 3 T33: 0.0172 T12: -0.0857 REMARK 3 T13: -0.0400 T23: 0.0403 REMARK 3 L TENSOR REMARK 3 L11: 0.3576 L22: 1.2815 REMARK 3 L33: 0.4814 L12: -0.4349 REMARK 3 L13: -0.1948 L23: -0.1128 REMARK 3 S TENSOR REMARK 3 S11: 0.0526 S12: 0.1219 S13: -0.0048 REMARK 3 S21: -0.4933 S22: 0.0200 S23: 0.0694 REMARK 3 S31: 0.1354 S32: -0.3219 S33: -0.0726 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 361 REMARK 3 RESIDUE RANGE : B 401 B 401 REMARK 3 ORIGIN FOR THE GROUP (A): 30.8310 -26.5140 48.1890 REMARK 3 T TENSOR REMARK 3 T11: 0.1916 T22: 0.4516 REMARK 3 T33: 0.0882 T12: -0.2035 REMARK 3 T13: -0.0637 T23: 0.1257 REMARK 3 L TENSOR REMARK 3 L11: 0.1944 L22: 1.9630 REMARK 3 L33: 0.5366 L12: -0.0262 REMARK 3 L13: -0.0184 L23: -0.1123 REMARK 3 S TENSOR REMARK 3 S11: 0.0264 S12: -0.0263 S13: 0.0093 REMARK 3 S21: -0.0695 S22: 0.1454 S23: 0.2802 REMARK 3 S31: 0.1596 S32: -0.2769 S33: -0.1718 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6JW7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.99600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4H3V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, IMIDAZOLE, CALCIUM ACETATE, REMARK 280 NADH, 3"-DEAMINO-3"-HYDROXYKANAMYCIN A, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.28667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.57333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 88.57333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.28667 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL 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 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 88.57333 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 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 210 REMARK 465 ASP A 211 REMARK 465 ALA A 212 REMARK 465 GLU A 213 REMARK 465 ALA A 214 REMARK 465 ASP A 215 REMARK 465 ARG A 216 REMARK 465 ALA A 217 REMARK 465 SER A 218 REMARK 465 GLY A 219 REMARK 465 THR A 220 REMARK 465 ALA A 221 REMARK 465 GLY A 222 REMARK 465 THR A 223 REMARK 465 ALA A 224 REMARK 465 ARG A 225 REMARK 465 VAL A 226 REMARK 465 PRO A 363 REMARK 465 GLY A 364 REMARK 465 ALA A 365 REMARK 465 SER A 366 REMARK 465 THR A 367 REMARK 465 THR A 368 REMARK 465 ALA A 369 REMARK 465 ALA A 370 REMARK 465 GLY A 371 REMARK 465 SER A 372 REMARK 465 GLU A 373 REMARK 465 LYS A 374 REMARK 465 LEU A 375 REMARK 465 ALA A 376 REMARK 465 ALA A 377 REMARK 465 ALA A 378 REMARK 465 LEU A 379 REMARK 465 GLU A 380 REMARK 465 HIS A 381 REMARK 465 HIS A 382 REMARK 465 HIS A 383 REMARK 465 HIS A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ALA B 3 REMARK 465 HIS B 210 REMARK 465 ASP B 211 REMARK 465 ALA B 212 REMARK 465 GLU B 213 REMARK 465 ALA B 214 REMARK 465 ASP B 215 REMARK 465 ARG B 216 REMARK 465 ALA B 217 REMARK 465 SER B 218 REMARK 465 GLY B 219 REMARK 465 THR B 220 REMARK 465 ALA B 221 REMARK 465 GLY B 222 REMARK 465 THR B 223 REMARK 465 ALA B 224 REMARK 465 ARG B 225 REMARK 465 VAL B 226 REMARK 465 GLY B 362 REMARK 465 PRO B 363 REMARK 465 GLY B 364 REMARK 465 ALA B 365 REMARK 465 SER B 366 REMARK 465 THR B 367 REMARK 465 THR B 368 REMARK 465 ALA B 369 REMARK 465 ALA B 370 REMARK 465 GLY B 371 REMARK 465 SER B 372 REMARK 465 GLU B 373 REMARK 465 LYS B 374 REMARK 465 LEU B 375 REMARK 465 ALA B 376 REMARK 465 ALA B 377 REMARK 465 ALA B 378 REMARK 465 LEU B 379 REMARK 465 GLU B 380 REMARK 465 HIS B 381 REMARK 465 HIS B 382 REMARK 465 HIS B 383 REMARK 465 HIS B 384 REMARK 465 HIS B 385 REMARK 465 HIS B 386 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP B 230 CB ASP B 230 CG -0.140 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 81 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 PRO A 209 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG B 136 CG - CD - NE ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG B 136 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 136 NE - CZ - NH2 ANGL. DEV. = 5.4 DEGREES REMARK 500 PRO B 209 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG B 339 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES 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 ALA A 12 53.66 -93.99 REMARK 500 TRP A 291 -115.64 13.34 REMARK 500 ASP A 292 121.62 -174.45 REMARK 500 ALA B 12 53.42 -98.45 REMARK 500 ASP B 289 40.80 -104.71 REMARK 500 TRP B 291 -114.32 16.30 REMARK 500 ASP B 292 120.28 -174.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CJX A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI B 401 DBREF 6JW7 A 1 373 UNP Q6L737 Q6L737_STRKN 1 373 DBREF 6JW7 B 1 373 UNP Q6L737 Q6L737_STRKN 1 373 SEQADV 6JW7 LYS A 374 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 LEU A 375 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 ALA A 376 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 ALA A 377 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 ALA A 378 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 LEU A 379 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 GLU A 380 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS A 381 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS A 382 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS A 383 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS A 384 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS A 385 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS A 386 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 LYS B 374 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 LEU B 375 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 ALA B 376 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 ALA B 377 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 ALA B 378 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 LEU B 379 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 GLU B 380 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS B 381 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS B 382 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS B 383 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS B 384 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS B 385 UNP Q6L737 EXPRESSION TAG SEQADV 6JW7 HIS B 386 UNP Q6L737 EXPRESSION TAG SEQRES 1 A 386 MET SER ALA PRO VAL ARG VAL GLY VAL VAL GLY ALA GLY SEQRES 2 A 386 PHE MET GLY GLY VAL HIS ALA GLU VAL VAL ALA ALA HIS SEQRES 3 A 386 PRO GLY ALA ARG LEU GLU ALA VAL HIS ASP LEU ASP PRO SEQRES 4 A 386 ALA ALA ALA ARG ASP LEU ALA GLU ARG PHE ARG ALA GLU SEQRES 5 A 386 ARG ALA GLU PRO SER TRP ALA ASP LEU LEU ALA ASP PRO SEQRES 6 A 386 ALA ILE ASP LEU LEU ILE ILE THR THR PRO ASN GLY LEU SEQRES 7 A 386 HIS HIS ARG GLN ALA ALA GLU ALA LEU ARG ALA GLY LYS SEQRES 8 A 386 HIS VAL LEU VAL GLU LYS PRO LEU GLY VAL THR PRO GLU SEQRES 9 A 386 GLN VAL ALA GLU LEU VAL GLU LEU ALA GLY ARG HIS ASP SEQRES 10 A 386 ARG VAL LEU ALA HIS GLY SER ASN PHE VAL HIS SER PRO SEQRES 11 A 386 LYS PHE VAL ARG ALA ARG GLN LEU VAL ALA ASP THR GLU SEQRES 12 A 386 ALA PHE GLY ARG PRO HIS LEU VAL ARG VAL VAL PHE ARG SEQRES 13 A 386 ASN SER GLY PRO GLU ALA ALA TRP ALA ALA SER LYS ASP SEQRES 14 A 386 LEU ALA GLY GLY GLY ALA LEU LEU ASP LEU GLY CYS HIS SEQRES 15 A 386 ALA VAL GLU LEU CYS ARG TRP LEU LEU ASP GLY ALA ASP SEQRES 16 A 386 VAL GLU SER VAL SER ALA ARG LEU GLN ARG VAL ARG PRO SEQRES 17 A 386 PRO HIS ASP ALA GLU ALA ASP ARG ALA SER GLY THR ALA SEQRES 18 A 386 GLY THR ALA ARG VAL ALA LEU GLU ASP GLN ALA LEU LEU SEQRES 19 A 386 VAL MET GLU PHE ALA ASP GLY ALA VAL GLY GLN CYS ASP SEQRES 20 A 386 VAL SER TRP VAL THR GLN GLY GLY GLU GLN VAL THR ALA SEQRES 21 A 386 GLU ILE ILE GLY THR LYS GLY ARG VAL GLU VAL ASP LEU SEQRES 22 A 386 TRP THR GLY MET GLY LEU ARG ALA TYR SER ASP LYS GLY SEQRES 23 A 386 TYR GLN ASP VAL TRP ASP PRO GLU GLN GLY TRP VAL HIS SEQRES 24 A 386 PRO GLU TRP GLU TRP ILE ARG ALA SER GLY TYR TYR HIS SEQRES 25 A 386 GLN ASP GLY THR VAL ILE GLU ALA VAL GLY GLN GLY ILE SEQRES 26 A 386 PRO LEU THR HIS GLY PRO ALA GLU ALA LEU ALA SER ALA SEQRES 27 A 386 ARG VAL LEU ALA THR GLY TYR ARG SER HIS ALA GLU GLY SEQRES 28 A 386 ARG VAL LEU ARG LEU SER GLY ALA PRO VAL GLY PRO GLY SEQRES 29 A 386 ALA SER THR THR ALA ALA GLY SER GLU LYS LEU ALA ALA SEQRES 30 A 386 ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 386 MET SER ALA PRO VAL ARG VAL GLY VAL VAL GLY ALA GLY SEQRES 2 B 386 PHE MET GLY GLY VAL HIS ALA GLU VAL VAL ALA ALA HIS SEQRES 3 B 386 PRO GLY ALA ARG LEU GLU ALA VAL HIS ASP LEU ASP PRO SEQRES 4 B 386 ALA ALA ALA ARG ASP LEU ALA GLU ARG PHE ARG ALA GLU SEQRES 5 B 386 ARG ALA GLU PRO SER TRP ALA ASP LEU LEU ALA ASP PRO SEQRES 6 B 386 ALA ILE ASP LEU LEU ILE ILE THR THR PRO ASN GLY LEU SEQRES 7 B 386 HIS HIS ARG GLN ALA ALA GLU ALA LEU ARG ALA GLY LYS SEQRES 8 B 386 HIS VAL LEU VAL GLU LYS PRO LEU GLY VAL THR PRO GLU SEQRES 9 B 386 GLN VAL ALA GLU LEU VAL GLU LEU ALA GLY ARG HIS ASP SEQRES 10 B 386 ARG VAL LEU ALA HIS GLY SER ASN PHE VAL HIS SER PRO SEQRES 11 B 386 LYS PHE VAL ARG ALA ARG GLN LEU VAL ALA ASP THR GLU SEQRES 12 B 386 ALA PHE GLY ARG PRO HIS LEU VAL ARG VAL VAL PHE ARG SEQRES 13 B 386 ASN SER GLY PRO GLU ALA ALA TRP ALA ALA SER LYS ASP SEQRES 14 B 386 LEU ALA GLY GLY GLY ALA LEU LEU ASP LEU GLY CYS HIS SEQRES 15 B 386 ALA VAL GLU LEU CYS ARG TRP LEU LEU ASP GLY ALA ASP SEQRES 16 B 386 VAL GLU SER VAL SER ALA ARG LEU GLN ARG VAL ARG PRO SEQRES 17 B 386 PRO HIS ASP ALA GLU ALA ASP ARG ALA SER GLY THR ALA SEQRES 18 B 386 GLY THR ALA ARG VAL ALA LEU GLU ASP GLN ALA LEU LEU SEQRES 19 B 386 VAL MET GLU PHE ALA ASP GLY ALA VAL GLY GLN CYS ASP SEQRES 20 B 386 VAL SER TRP VAL THR GLN GLY GLY GLU GLN VAL THR ALA SEQRES 21 B 386 GLU ILE ILE GLY THR LYS GLY ARG VAL GLU VAL ASP LEU SEQRES 22 B 386 TRP THR GLY MET GLY LEU ARG ALA TYR SER ASP LYS GLY SEQRES 23 B 386 TYR GLN ASP VAL TRP ASP PRO GLU GLN GLY TRP VAL HIS SEQRES 24 B 386 PRO GLU TRP GLU TRP ILE ARG ALA SER GLY TYR TYR HIS SEQRES 25 B 386 GLN ASP GLY THR VAL ILE GLU ALA VAL GLY GLN GLY ILE SEQRES 26 B 386 PRO LEU THR HIS GLY PRO ALA GLU ALA LEU ALA SER ALA SEQRES 27 B 386 ARG VAL LEU ALA THR GLY TYR ARG SER HIS ALA GLU GLY SEQRES 28 B 386 ARG VAL LEU ARG LEU SER GLY ALA PRO VAL GLY PRO GLY SEQRES 29 B 386 ALA SER THR THR ALA ALA GLY SER GLU LYS LEU ALA ALA SEQRES 30 B 386 ALA LEU GLU HIS HIS HIS HIS HIS HIS HET NAI A 401 44 HET CJX A 402 33 HET NAI B 401 44 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM CJX (2R,3S,4S,5R,6R)-2-(AMINOMETHYL)-6-[(1R,2S,3S,4R,6S)-4, HETNAM 2 CJX 6-BIS(AZANYL)-3-[(2S,3R,4S,5S,6R)-6-(HYDROXYMETHYL)-3, HETNAM 3 CJX 4,5-TRIS(OXIDANYL)OXAN-2-YL]OXY-2-OXIDANYL- HETNAM 4 CJX CYCLOHEXYL]OXY-OXANE-3,4,5-TRIOL HETSYN NAI NADH HETSYN CJX 3"-DEAMINO-3"-HYDROXYKANAMYCIN A FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 CJX C18 H35 N3 O12 FORMUL 6 HOH *60(H2 O) HELIX 1 AA1 GLY A 13 HIS A 26 1 14 HELIX 2 AA2 ASP A 38 PHE A 49 1 12 HELIX 3 AA3 SER A 57 ASP A 64 1 8 HELIX 4 AA4 PRO A 75 GLY A 77 5 3 HELIX 5 AA5 LEU A 78 ALA A 89 1 12 HELIX 6 AA6 THR A 102 HIS A 116 1 15 HELIX 7 AA7 SER A 124 HIS A 128 5 5 HELIX 8 AA8 SER A 129 ALA A 140 1 12 HELIX 9 AA9 ASP A 141 GLY A 146 1 6 HELIX 10 AB1 ALA A 162 ALA A 166 5 5 HELIX 11 AB2 SER A 167 GLY A 172 1 6 HELIX 12 AB3 GLY A 174 LEU A 179 1 6 HELIX 13 AB4 LEU A 179 LEU A 191 1 13 HELIX 14 AB5 GLU A 303 SER A 308 1 6 HELIX 15 AB6 GLY A 309 GLY A 324 1 16 HELIX 16 AB7 GLY A 330 GLY A 351 1 22 HELIX 17 AB8 GLY B 13 HIS B 26 1 14 HELIX 18 AB9 ASP B 38 PHE B 49 1 12 HELIX 19 AC1 SER B 57 ASP B 64 1 8 HELIX 20 AC2 PRO B 75 GLY B 77 5 3 HELIX 21 AC3 LEU B 78 ALA B 89 1 12 HELIX 22 AC4 THR B 102 HIS B 116 1 15 HELIX 23 AC5 SER B 124 HIS B 128 5 5 HELIX 24 AC6 SER B 129 ALA B 140 1 12 HELIX 25 AC7 ASP B 141 GLY B 146 1 6 HELIX 26 AC8 ALA B 162 ALA B 166 5 5 HELIX 27 AC9 SER B 167 GLY B 172 1 6 HELIX 28 AD1 GLY B 174 LEU B 179 1 6 HELIX 29 AD2 LEU B 179 LEU B 191 1 13 HELIX 30 AD3 GLU B 303 SER B 308 1 6 HELIX 31 AD4 GLY B 309 GLY B 324 1 16 HELIX 32 AD5 PRO B 331 GLY B 351 1 21 SHEET 1 AA1 6 ARG A 53 ALA A 54 0 SHEET 2 AA1 6 ALA A 29 HIS A 35 1 N GLU A 32 O ARG A 53 SHEET 3 AA1 6 VAL A 5 VAL A 10 1 N VAL A 7 O ARG A 30 SHEET 4 AA1 6 LEU A 69 ILE A 72 1 O LEU A 69 N GLY A 8 SHEET 5 AA1 6 HIS A 92 VAL A 95 1 O HIS A 92 N LEU A 70 SHEET 6 AA1 6 LEU A 120 HIS A 122 1 O ALA A 121 N VAL A 93 SHEET 1 AA2 8 VAL A 196 GLN A 204 0 SHEET 2 AA2 8 GLN A 231 PHE A 238 -1 O VAL A 235 N SER A 200 SHEET 3 AA2 8 VAL A 243 SER A 249 -1 O GLY A 244 N MET A 236 SHEET 4 AA2 8 PRO A 148 ARG A 156 1 N VAL A 153 O GLN A 245 SHEET 5 AA2 8 GLN A 257 GLY A 264 -1 O GLN A 257 N ARG A 156 SHEET 6 AA2 8 ARG A 268 ASP A 272 -1 O VAL A 269 N ILE A 262 SHEET 7 AA2 8 LEU B 279 SER B 283 -1 O ARG B 280 N GLU A 270 SHEET 8 AA2 8 GLY B 296 VAL B 298 -1 O VAL B 298 N ALA B 281 SHEET 1 AA3 8 GLY A 296 VAL A 298 0 SHEET 2 AA3 8 LEU A 279 SER A 283 -1 N ALA A 281 O VAL A 298 SHEET 3 AA3 8 ARG B 268 ASP B 272 -1 O GLU B 270 N ARG A 280 SHEET 4 AA3 8 GLN B 257 GLY B 264 -1 N ILE B 262 O VAL B 269 SHEET 5 AA3 8 PRO B 148 ARG B 156 -1 N ARG B 156 O GLN B 257 SHEET 6 AA3 8 VAL B 243 SER B 249 1 O GLN B 245 N VAL B 151 SHEET 7 AA3 8 GLN B 231 PHE B 238 -1 N MET B 236 O GLY B 244 SHEET 8 AA3 8 VAL B 196 GLN B 204 -1 N GLU B 197 O GLU B 237 SHEET 1 AA4 6 ARG B 53 ALA B 54 0 SHEET 2 AA4 6 ALA B 29 HIS B 35 1 N VAL B 34 O ARG B 53 SHEET 3 AA4 6 VAL B 5 VAL B 10 1 N VAL B 7 O ARG B 30 SHEET 4 AA4 6 LEU B 69 ILE B 72 1 O ILE B 71 N VAL B 10 SHEET 5 AA4 6 HIS B 92 VAL B 95 1 O HIS B 92 N LEU B 70 SHEET 6 AA4 6 LEU B 120 HIS B 122 1 O ALA B 121 N VAL B 93 CISPEP 1 LYS A 97 PRO A 98 0 -2.10 CISPEP 2 ASP A 292 PRO A 293 0 1.38 CISPEP 3 LYS B 97 PRO B 98 0 -0.55 CISPEP 4 ASP B 292 PRO B 293 0 5.54 SITE 1 AC1 23 GLY A 11 GLY A 13 PHE A 14 MET A 15 SITE 2 AC1 23 ASP A 36 LEU A 37 THR A 73 THR A 74 SITE 3 AC1 23 PRO A 75 ASN A 76 LEU A 78 HIS A 79 SITE 4 AC1 23 GLN A 82 GLU A 96 LYS A 97 ASN A 125 SITE 5 AC1 23 TRP A 164 HIS A 182 TYR A 310 CJX A 402 SITE 6 AC1 23 HOH A 507 HOH A 519 GLU B 111 SITE 1 AC2 10 PHE A 14 ASN A 157 ASP A 178 HIS A 182 SITE 2 AC2 10 GLU A 256 TRP A 274 TRP A 291 ASP A 292 SITE 3 AC2 10 TYR A 310 NAI A 401 SITE 1 AC3 17 GLY B 13 PHE B 14 MET B 15 ASP B 36 SITE 2 AC3 17 LEU B 37 THR B 73 THR B 74 PRO B 75 SITE 3 AC3 17 ASN B 76 LEU B 78 HIS B 79 GLN B 82 SITE 4 AC3 17 GLU B 96 LYS B 97 ASN B 125 TRP B 164 SITE 5 AC3 17 TYR B 310 CRYST1 120.010 120.010 132.860 90.00 90.00 120.00 P 31 2 1 12 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 0.008333 0.004811 0.000000 0.00000 SCALE2 0.000000 0.009622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007527 0.00000