HEADER OXIDOREDUCTASE 18-APR-19 6JW8 TITLE THE CRYSTAL STRUCTURE OF KAND2 IN COMPLEX WITH NADH AND 3"-DEAMINO-3"- TITLE 2 HYDROXYKANAMYCIN B 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 6JW8 1 REMARK REVDAT 2 29-APR-20 6JW8 1 JRNL REVDAT 1 15-APR-20 6JW8 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 41453 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2124 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3048 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3770 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 : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.97000 REMARK 3 B22 (A**2) : 0.97000 REMARK 3 B33 (A**2) : -3.16000 REMARK 3 B12 (A**2) : 0.97000 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): 0.277 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.218 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.592 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5437 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5126 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7426 ; 1.995 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11723 ; 1.173 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 681 ; 6.692 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 245 ;33.434 ;22.735 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 789 ;18.654 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 53 ;20.308 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 824 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6198 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1283 ; 0.006 ; 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 19693 0.11 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): 42.4070 6.4310 3.9090 REMARK 3 T TENSOR REMARK 3 T11: 0.5908 T22: 0.6534 REMARK 3 T33: 0.1048 T12: 0.2233 REMARK 3 T13: 0.1124 T23: 0.0913 REMARK 3 L TENSOR REMARK 3 L11: 0.8521 L22: 2.7630 REMARK 3 L33: 0.8790 L12: 0.6038 REMARK 3 L13: 0.5701 L23: -0.3335 REMARK 3 S TENSOR REMARK 3 S11: 0.0178 S12: -0.2509 S13: 0.0503 REMARK 3 S21: 0.9557 S22: 0.1390 S23: 0.2071 REMARK 3 S31: -0.2871 S32: -0.5054 S33: -0.1567 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): 30.7770 26.5560 -26.0240 REMARK 3 T TENSOR REMARK 3 T11: 0.2621 T22: 0.7075 REMARK 3 T33: 0.2570 T12: 0.2799 REMARK 3 T13: 0.0956 T23: 0.2225 REMARK 3 L TENSOR REMARK 3 L11: 0.5919 L22: 3.2915 REMARK 3 L33: 0.7417 L12: -0.7283 REMARK 3 L13: -0.1506 L23: -0.1249 REMARK 3 S TENSOR REMARK 3 S11: -0.0442 S12: 0.0169 S13: -0.0283 REMARK 3 S21: 0.2133 S22: 0.3317 S23: 0.7077 REMARK 3 S31: -0.2064 S32: -0.4257 S33: -0.2874 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 6JW8 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_1300011899. 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 : 9.900 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.5000 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) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.71300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 62.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, IMIDAZOLE, CALCIUM ACETATE, REMARK 280 NADH, 3"-DEAMINO-3"-HYDROXYKANAMYCIN B, 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 44.30133 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 88.60267 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 88.60267 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 44.30133 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: 18050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 -44.30133 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 -0.263 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 280 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 48 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 136 CG - CD - NE ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG B 136 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 136 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP B 230 CB - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 ASP B 230 CB - CG - OD1 ANGL. DEV. = -11.0 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 59.10 -100.07 REMARK 500 ASP A 240 6.90 -65.47 REMARK 500 PRO A 293 164.15 -45.96 REMARK 500 GLN A 323 58.94 -145.58 REMARK 500 ALA B 12 59.17 -102.46 REMARK 500 ASP B 240 3.77 -64.26 REMARK 500 LYS B 285 -77.85 -64.76 REMARK 500 TRP B 291 -115.89 -65.88 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 CK0 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 6JW8 A 1 373 UNP Q6L737 Q6L737_STRKN 1 373 DBREF 6JW8 B 1 373 UNP Q6L737 Q6L737_STRKN 1 373 SEQADV 6JW8 LYS A 374 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 LEU A 375 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 ALA A 376 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 ALA A 377 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 ALA A 378 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 LEU A 379 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 GLU A 380 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS A 381 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS A 382 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS A 383 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS A 384 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS A 385 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS A 386 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 LYS B 374 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 LEU B 375 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 ALA B 376 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 ALA B 377 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 ALA B 378 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 LEU B 379 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 GLU B 380 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS B 381 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS B 382 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS B 383 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS B 384 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 HIS B 385 UNP Q6L737 EXPRESSION TAG SEQADV 6JW8 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 CK0 A 402 33 HET NAI B 401 44 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM CK0 (2S,3R,4S,5S,6R)-2-[(1S,2S,3R,4S,6R)-3-[(2R,3R,4R,5S, HETNAM 2 CK0 6R)-6-(AMINOMETHYL)-3-AZANYL-4,5-BIS(OXIDANYL)OXAN-2- HETNAM 3 CK0 YL]OXY-4,6-BIS(AZANYL)-2-OXIDANYL-CYCLOHEXYL]OXY-6- HETNAM 4 CK0 (HYDROXYMETHYL)OXANE-3,4,5-TRIOL HETSYN NAI NADH HETSYN CK0 3"-DEAMINO-3"-HYDROXYKANAMYCIN B FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 CK0 C18 H36 N4 O11 FORMUL 6 HOH *30(H2 O) HELIX 1 AA1 GLY A 13 ALA A 25 1 13 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 PRO A 331 GLY A 351 1 21 HELIX 17 AB8 GLY B 13 ALA B 25 1 13 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 VAL A 34 O ARG A 53 SHEET 3 AA1 6 VAL A 5 VAL A 10 1 N VAL A 9 O HIS A 35 SHEET 4 AA1 6 LEU A 69 ILE A 72 1 O ILE A 71 N VAL A 10 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 THR A 259 N VAL A 154 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 VAL B 154 O THR B 259 SHEET 6 AA3 8 VAL B 243 SER B 249 1 O GLN B 245 N VAL B 153 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 9 O HIS B 35 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 LEU B 94 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 -4.18 CISPEP 2 ASP A 292 PRO A 293 0 -28.07 CISPEP 3 LYS B 97 PRO B 98 0 2.73 CISPEP 4 ASP B 292 PRO B 293 0 -6.64 SITE 1 AC1 22 GLY A 11 ALA A 12 GLY A 13 PHE A 14 SITE 2 AC1 22 MET A 15 ASP A 36 LEU A 37 THR A 73 SITE 3 AC1 22 THR A 74 PRO A 75 ASN A 76 LEU A 78 SITE 4 AC1 22 HIS A 79 GLN A 82 GLU A 96 LYS A 97 SITE 5 AC1 22 ASN A 125 TRP A 164 HIS A 182 TYR A 310 SITE 6 AC1 22 CK0 A 402 HOH A 501 SITE 1 AC2 11 PHE A 14 PHE A 155 ASN A 157 ASP A 178 SITE 2 AC2 11 HIS A 182 GLU A 256 TRP A 274 TRP A 291 SITE 3 AC2 11 ASP A 292 NAI A 401 HOH A 511 SITE 1 AC3 16 GLY B 13 PHE B 14 MET B 15 ASP B 36 SITE 2 AC3 16 LEU B 37 THR B 73 THR B 74 ASN B 76 SITE 3 AC3 16 LEU B 78 HIS B 79 GLN B 82 GLU B 96 SITE 4 AC3 16 LYS B 97 ASN B 125 TRP B 164 TYR B 310 CRYST1 119.761 119.761 132.904 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 0.008350 0.004821 0.000000 0.00000 SCALE2 0.000000 0.009642 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007524 0.00000