HEADER LIGASE 31-AUG-18 6AKD TITLE CRYSTAL STRUCTURE OF IDNL7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMP-DEPENDENT SYNTHETASE AND LIGASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. ML694-90F3; SOURCE 3 ORGANISM_TAXID: 1265536; SOURCE 4 STRAIN: ML694-90F; SOURCE 5 GENE: IDNL7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD I KEYWDS LIGASE, ATP-BINDING, FIVE LAYERED ALPHA-BETA-ALPHA-BETA-ALPHA KEYWDS 2 SANDWICH FOLD EXPDTA X-RAY DIFFRACTION AUTHOR J.CIESLAK,A.MIYANAGA,F.KUDO,T.EGUCHI REVDAT 3 22-NOV-23 6AKD 1 REMARK REVDAT 2 17-APR-19 6AKD 1 JRNL REVDAT 1 06-MAR-19 6AKD 0 JRNL AUTH J.CIESLAK,A.MIYANAGA,M.TAKAISHI,F.KUDO,T.EGUCHI JRNL TITL FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF IDNL7, AN JRNL TITL 2 ADENYLATION ENZYME INVOLVED IN INCEDNINE BIOSYNTHESIS. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 75 299 2019 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 30950831 JRNL DOI 10.1107/S2053230X19002863 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30667 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1642 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2209 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3682 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30000 REMARK 3 B22 (A**2) : 0.30000 REMARK 3 B33 (A**2) : -0.59000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.192 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.933 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3810 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3612 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5197 ; 1.844 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8254 ; 0.885 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 481 ; 6.248 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;31.974 ;21.566 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 532 ;14.939 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;18.577 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 580 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4331 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 890 ; 0.001 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 515 REMARK 3 ORIGIN FOR THE GROUP (A): 4.5140 20.6130 67.1720 REMARK 3 T TENSOR REMARK 3 T11: 0.0142 T22: 0.0855 REMARK 3 T33: 0.1144 T12: 0.0140 REMARK 3 T13: -0.0249 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.7972 L22: 0.8292 REMARK 3 L33: 1.4129 L12: -0.0757 REMARK 3 L13: 0.0128 L23: -0.3853 REMARK 3 S TENSOR REMARK 3 S11: 0.0295 S12: 0.0152 S13: 0.1278 REMARK 3 S21: -0.0771 S22: -0.0672 S23: 0.1388 REMARK 3 S31: -0.0226 S32: 0.1304 S33: 0.0377 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 6AKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300008928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32390 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : 0.95400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: 1AMU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 0.2M MAGNESIUM CHLORIDE, REMARK 280 30% PEG4000, 0.5MM [N-(L-ALANYL)SULFAMOYL] ADENOSINE, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 299K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 112.58450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.26300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.26300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.29225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.26300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.26300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 168.87675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.26300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.26300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 56.29225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.26300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.26300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 168.87675 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 112.58450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 -15 REMARK 465 ASN A -14 REMARK 465 HIS A -13 REMARK 465 LYS A -12 REMARK 465 VAL A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 ILE A -4 REMARK 465 GLU A -3 REMARK 465 GLY A -2 REMARK 465 ARG A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 GLY A 3 REMARK 465 ILE A 4 REMARK 465 ASP A 122 REMARK 465 GLY A 123 REMARK 465 ALA A 124 REMARK 465 ALA A 125 REMARK 465 GLY A 173 REMARK 465 SER A 174 REMARK 465 THR A 175 REMARK 465 GLY A 176 REMARK 465 ARG A 177 REMARK 465 PRO A 354 REMARK 465 ASP A 355 REMARK 465 HIS A 422 REMARK 465 GLY A 423 REMARK 465 TRP A 424 REMARK 465 ARG A 425 REMARK 465 ASP A 449 REMARK 465 THR A 450 REMARK 465 PRO A 451 REMARK 465 GLY A 452 REMARK 465 GLY A 453 REMARK 465 ASP A 480 REMARK 465 GLY A 481 REMARK 465 VAL A 482 REMARK 465 PRO A 516 REMARK 465 ARG A 517 REMARK 465 SER A 518 REMARK 465 GLY A 519 REMARK 465 PRO A 520 REMARK 465 ALA A 521 REMARK 465 LEU A 522 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 GLU A 196 CD GLU A 196 OE2 0.098 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 12 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 12 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 280 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 280 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 442 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 442 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 468 NE - CZ - NH1 ANGL. DEV. = 3.1 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 120 35.87 -97.13 REMARK 500 ASP A 242 79.13 -162.56 REMARK 500 MET A 276 59.89 -117.77 REMARK 500 THR A 316 80.83 54.31 REMARK 500 ILE A 317 -78.85 80.11 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 A5A A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 DBREF1 6AKD A 1 522 UNP A0A077KUW8_9ACTN DBREF2 6AKD A A0A077KUW8 1 522 SEQADV 6AKD MET A -15 UNP A0A077KUW INITIATING METHIONINE SEQADV 6AKD ASN A -14 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A -13 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD LYS A -12 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD VAL A -11 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A -10 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A -9 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A -8 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A -7 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A -6 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A -5 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD ILE A -4 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD GLU A -3 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD GLY A -2 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD ARG A -1 UNP A0A077KUW EXPRESSION TAG SEQADV 6AKD HIS A 0 UNP A0A077KUW EXPRESSION TAG SEQRES 1 A 538 MET ASN HIS LYS VAL HIS HIS HIS HIS HIS HIS ILE GLU SEQRES 2 A 538 GLY ARG HIS MET ASP GLY ILE LEU ASP HIS GLY LEU HIS SEQRES 3 A 538 ALA ARG PHE LEU ARG GLY LEU SER ALA ALA PRO ASP GLY SEQRES 4 A 538 ALA ALA VAL ARG ILE GLY THR THR SER VAL SER TYR ARG SEQRES 5 A 538 HIS LEU HIS ARG THR ALA LEU LEU TRP ALA GLY ALA LEU SEQRES 6 A 538 THR ALA ALA GLY ALA ARG SER VAL GLY VAL LEU ALA GLY SEQRES 7 A 538 LYS SER ALA THR GLY TYR ALA GLY ILE LEU ALA ALA LEU SEQRES 8 A 538 TYR ALA GLY ALA ALA VAL VAL PRO LEU ARG PRO ASP PHE SEQRES 9 A 538 PRO ALA ALA ARG THR ARG GLU VAL LEU ARG ALA SER ASP SEQRES 10 A 538 ALA ASP VAL LEU ILE ALA ASP ARG ALA GLY LEU PRO VAL SEQRES 11 A 538 LEU ALA GLY ALA LEU ALA GLY ASP GLY ALA ALA ASP VAL SEQRES 12 A 538 PRO VAL LEU ALA PRO ASP ALA LEU ASP GLY GLU LEU PRO SEQRES 13 A 538 GLU GLY VAL ALA ARG LEU VAL PRO ARG PRO GLU LEU SER SEQRES 14 A 538 LEU SER GLU PRO ALA ARG CYS LYS PRO ALA ASP PRO ALA SEQRES 15 A 538 TYR LEU LEU PHE THR SER GLY SER THR GLY ARG PRO LYS SEQRES 16 A 538 GLY VAL VAL ILE THR HIS GLY ALA THR GLY HIS TYR PHE SEQRES 17 A 538 ASP VAL MET GLU ARG ARG TYR ASP PHE GLY ALA SER ASP SEQRES 18 A 538 VAL PHE SER GLN ALA PHE ASP LEU ASN PHE ASP CYS ALA SEQRES 19 A 538 VAL PHE ASP LEU PHE CYS ALA TRP GLY ALA GLY ALA THR SEQRES 20 A 538 VAL VAL PRO VAL PRO PRO PRO ALA TYR ARG ASP LEU PRO SEQRES 21 A 538 GLY PHE ILE THR ALA GLN GLY ILE THR VAL TRP PHE SER SEQRES 22 A 538 THR PRO SER VAL ILE ASP LEU THR ARG ARG LEU GLY ALA SEQRES 23 A 538 LEU ASP GLY PRO ARG MET PRO GLY LEU ARG TRP SER LEU SEQRES 24 A 538 PHE ALA GLY GLU ALA LEU LYS CYS ARG ASP ALA ALA ASP SEQRES 25 A 538 TRP ARG ALA ALA ALA PRO GLY ALA THR LEU GLU ASN LEU SEQRES 26 A 538 TYR GLY PRO THR GLU LEU THR ILE THR VAL ALA ALA HIS SEQRES 27 A 538 ARG TRP ASP ASP GLU GLU SER PRO ARG ALA ALA VAL ASN SEQRES 28 A 538 GLY LEU ALA PRO ILE GLY ALA VAL ASN ASP GLY HIS ASP SEQRES 29 A 538 HIS LEU LEU LEU GLY PRO ASP GLY ASP PRO SER PRO ASP SEQRES 30 A 538 GLU GLY GLU LEU TRP VAL THR GLY PRO GLN LEU ALA ALA SEQRES 31 A 538 GLY TYR LEU ASP PRO ALA ASP GLU ARG GLY ARG PHE ALA SEQRES 32 A 538 GLU ARG ASP GLY ARG ARG TRP TYR ARG THR GLY ASP ARG SEQRES 33 A 538 VAL ARG ARG ALA PRO GLY GLY ASP LEU VAL TYR VAL GLY SEQRES 34 A 538 ARG LEU ASP SER GLN LEU GLN VAL HIS GLY TRP ARG VAL SEQRES 35 A 538 GLU PRO ALA GLU VAL GLU HIS ALA VAL ARG ALA CYS GLY SEQRES 36 A 538 ALA ASP ASP ALA VAL VAL VAL GLY VAL ASP THR PRO GLY SEQRES 37 A 538 GLY THR GLU LEU VAL ALA PHE TYR THR GLY ILE PRO VAL SEQRES 38 A 538 GLU PRO ARG GLU LEU VAL ARG ARG LEU ARG GLU VAL VAL SEQRES 39 A 538 PRO ASP GLY VAL LEU PRO ARG HIS PHE ARG HIS LEU ASP SEQRES 40 A 538 ALA PHE PRO LEU ASN ALA ASN ARG LYS THR ASP ARG LEU SEQRES 41 A 538 ARG LEU THR THR MET ALA ALA ASP GLY TYR GLY PRO ARG SEQRES 42 A 538 SER GLY PRO ALA LEU HET A5A A 601 28 HET GOL A 602 6 HET GOL A 603 6 HETNAM A5A '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 A5A C13 H19 N7 O7 S FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *155(H2 O) HELIX 1 AA1 LEU A 9 ALA A 20 1 12 HELIX 2 AA2 TYR A 35 ALA A 52 1 18 HELIX 3 AA3 SER A 64 ALA A 77 1 14 HELIX 4 AA4 PRO A 89 ASP A 101 1 13 HELIX 5 AA5 GLY A 111 LEU A 119 1 9 HELIX 6 AA6 LEU A 135 LEU A 139 5 5 HELIX 7 AA7 ARG A 149 SER A 153 5 5 HELIX 8 AA8 HIS A 185 ARG A 197 1 13 HELIX 9 AA9 ASP A 216 ALA A 228 1 13 HELIX 10 AB1 PRO A 236 ARG A 241 5 6 HELIX 11 AB2 ASP A 242 GLY A 251 1 10 HELIX 12 AB3 PRO A 259 LEU A 268 1 10 HELIX 13 AB4 LYS A 290 ALA A 301 1 12 HELIX 14 AB5 PRO A 312 THR A 316 5 5 HELIX 15 AB6 GLU A 328 ALA A 333 1 6 HELIX 16 AB7 ASP A 378 ARG A 383 5 6 HELIX 17 AB8 ASP A 416 GLN A 418 5 3 HELIX 18 AB9 GLU A 427 CYS A 438 1 12 HELIX 19 AC1 GLU A 466 VAL A 478 1 13 HELIX 20 AC2 ASP A 502 GLY A 515 1 14 SHEET 1 AA1 2 ALA A 24 ILE A 28 0 SHEET 2 AA1 2 THR A 31 SER A 34 -1 O VAL A 33 N ALA A 25 SHEET 1 AA2 4 ALA A 80 LEU A 84 0 SHEET 2 AA2 4 SER A 56 LEU A 60 1 N VAL A 59 O VAL A 82 SHEET 3 AA2 4 VAL A 104 ALA A 107 1 O ILE A 106 N GLY A 58 SHEET 4 AA2 4 VAL A 129 LEU A 130 1 O LEU A 130 N LEU A 105 SHEET 1 AA3 3 PRO A 165 PHE A 170 0 SHEET 2 AA3 3 GLY A 180 THR A 184 -1 O ILE A 183 N ALA A 166 SHEET 3 AA3 3 GLY A 375 TYR A 376 -1 O GLY A 375 N VAL A 182 SHEET 1 AA4 2 VAL A 206 GLN A 209 0 SHEET 2 AA4 2 THR A 231 PRO A 234 1 O THR A 231 N PHE A 207 SHEET 1 AA5 5 VAL A 254 SER A 257 0 SHEET 2 AA5 5 TRP A 281 ALA A 285 1 O LEU A 283 N TRP A 255 SHEET 3 AA5 5 THR A 305 TYR A 310 1 O LEU A 309 N PHE A 284 SHEET 4 AA5 5 ALA A 320 ARG A 323 -1 O HIS A 322 N ASN A 308 SHEET 5 AA5 5 ALA A 342 VAL A 343 -1 O ALA A 342 N ALA A 321 SHEET 1 AA6 4 ASP A 348 LEU A 352 0 SHEET 2 AA6 4 GLU A 362 THR A 368 -1 O TRP A 366 N LEU A 350 SHEET 3 AA6 4 ARG A 392 ARG A 403 -1 O TYR A 395 N VAL A 367 SHEET 4 AA6 4 PHE A 386 ARG A 389 -1 N ALA A 387 O TRP A 394 SHEET 1 AA7 4 ASP A 348 LEU A 352 0 SHEET 2 AA7 4 GLU A 362 THR A 368 -1 O TRP A 366 N LEU A 350 SHEET 3 AA7 4 ARG A 392 ARG A 403 -1 O TYR A 395 N VAL A 367 SHEET 4 AA7 4 LEU A 409 ARG A 414 -1 O GLY A 413 N ARG A 400 SHEET 1 AA8 3 ASP A 442 GLY A 447 0 SHEET 2 AA8 3 LEU A 456 THR A 461 -1 O PHE A 459 N VAL A 444 SHEET 3 AA8 3 HIS A 486 HIS A 489 1 O ARG A 488 N ALA A 458 SITE 1 AC1 19 PHE A 215 ASP A 216 CYS A 217 GLY A 286 SITE 2 AC1 19 GLU A 287 ALA A 288 ASN A 308 LEU A 309 SITE 3 AC1 19 TYR A 310 GLY A 311 PRO A 312 THR A 313 SITE 4 AC1 19 ILE A 317 ASP A 399 TYR A 411 LYS A 500 SITE 5 AC1 19 HOH A 740 HOH A 763 HOH A 802 SITE 1 AC2 9 PRO A 83 LEU A 84 ARG A 85 PHE A 88 SITE 2 AC2 9 THR A 93 PHE A 170 ASN A 214 HOH A 720 SITE 3 AC2 9 HOH A 741 SITE 1 AC3 6 TYR A 411 VAL A 412 ALA A 429 GLU A 432 SITE 2 AC3 6 ARG A 503 HOH A 819 CRYST1 68.526 68.526 225.169 90.00 90.00 90.00 P 41 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 0.014593 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014593 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004441 0.00000