HEADER HYDROLASE/DNA 31-AUG-10 3OOR TITLE I-SCEI MUTANT (K86R/G100T)COMPLEXED WITH C/G+4 DNA SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTRON ENCODED ENDONUCLEASE I-SCEI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 21S RRNA INTRON MATURASE, HOMING ENDONUCLEASE OMEGA; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*CP*GP*GP COMPND 10 *GP*TP*AP*AP*TP*AP*C)-3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: TOP STRAND OF I-SCEI C/G+4 DNA TARGET; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*CP*CP COMPND 16 *CP*TP*AP*GP*CP*GP*T)-3'; COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: BOTTOM STRAND OF I-SCEI C/G+4 DNA TARGET SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SCEI,OMEGA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS HOMING ENDONUCLEASE, INTRON HOMING, LAGLIDADG, HYDROLASE-DNA COMPLEX, KEYWDS 2 I-SCEI MUTANT (K86R/G100T) EXPDTA X-RAY DIFFRACTION AUTHOR R.JOSHI,J.-H.CHEN,B.L.GOLDEN,F.S.GIMBLE REVDAT 5 06-SEP-23 3OOR 1 REMARK SEQADV LINK REVDAT 4 24-JAN-18 3OOR 1 AUTHOR REVDAT 3 08-NOV-17 3OOR 1 REMARK REVDAT 2 12-JAN-11 3OOR 1 JRNL REVDAT 1 17-NOV-10 3OOR 0 JRNL AUTH R.JOSHI,K.K.HO,K.TENNEY,J.H.CHEN,B.L.GOLDEN,F.S.GIMBLE JRNL TITL EVOLUTION OF I-SCEI HOMING ENDONUCLEASES WITH INCREASED DNA JRNL TITL 2 RECOGNITION SITE SPECIFICITY. JRNL REF J.MOL.BIOL. V. 405 185 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21029741 JRNL DOI 10.1016/J.JMB.2010.10.029 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 13630 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1033 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 898 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3960 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1859 REMARK 3 NUCLEIC ACID ATOMS : 984 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.02000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -1.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.349 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.319 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.849 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3008 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4273 ; 1.011 ; 2.368 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 222 ; 4.343 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;32.906 ;25.217 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;15.405 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;13.055 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 468 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1929 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1114 ; 0.181 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1811 ; 0.336 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1894 ; 0.355 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2462 ; 0.598 ; 4.500 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 : 3 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 : C 2 C 25 REMARK 3 ORIGIN FOR THE GROUP (A): -25.9656 17.3302 13.8379 REMARK 3 T TENSOR REMARK 3 T11: 0.0889 T22: 0.2205 REMARK 3 T33: 0.2367 T12: 0.1018 REMARK 3 T13: -0.0640 T23: -0.0627 REMARK 3 L TENSOR REMARK 3 L11: 4.9111 L22: 6.2345 REMARK 3 L33: 10.0469 L12: -2.2913 REMARK 3 L13: -3.8868 L23: 5.0744 REMARK 3 S TENSOR REMARK 3 S11: -0.0346 S12: -0.0073 S13: -0.1313 REMARK 3 S21: 0.3735 S22: -0.1509 S23: 0.0833 REMARK 3 S31: 0.0288 S32: -0.5151 S33: 0.1855 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2 D 25 REMARK 3 ORIGIN FOR THE GROUP (A): -25.5119 15.6966 13.9530 REMARK 3 T TENSOR REMARK 3 T11: 0.1953 T22: 0.2712 REMARK 3 T33: 0.3108 T12: 0.1142 REMARK 3 T13: -0.1291 T23: -0.0926 REMARK 3 L TENSOR REMARK 3 L11: 3.9834 L22: 5.1053 REMARK 3 L33: 8.4605 L12: -1.0871 REMARK 3 L13: -2.1996 L23: 4.6931 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: 0.0961 S13: -0.0621 REMARK 3 S21: 0.4148 S22: -0.4363 S23: 0.3271 REMARK 3 S31: -0.1059 S32: -0.7876 S33: 0.4314 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 225 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6587 25.1535 8.0614 REMARK 3 T TENSOR REMARK 3 T11: 0.2752 T22: 0.2332 REMARK 3 T33: 0.3105 T12: 0.0973 REMARK 3 T13: -0.0773 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 3.7161 L22: 3.3922 REMARK 3 L33: 6.0281 L12: -0.3963 REMARK 3 L13: -1.0012 L23: 1.7421 REMARK 3 S TENSOR REMARK 3 S11: 0.2987 S12: 0.1407 S13: 0.2006 REMARK 3 S21: -0.2712 S22: -0.0479 S23: -0.2762 REMARK 3 S31: -1.0138 S32: -0.0740 S33: -0.2509 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3OOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .979 REMARK 200 MONOCHROMATOR : DIAMOND[111] REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13729 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1R7M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400,CACL2,NAOAC,DTT, PH 4.7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 65.85050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.26900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.85050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.26900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASN A 226 REMARK 465 THR A 227 REMARK 465 ILE A 228 REMARK 465 SER A 229 REMARK 465 SER A 230 REMARK 465 GLU A 231 REMARK 465 THR A 232 REMARK 465 PHE A 233 REMARK 465 LEU A 234 REMARK 465 LYS A 235 REMARK 465 DC C 1 REMARK 465 DG D 1 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 DT C 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 17 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC D 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 13 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA D 15 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA D 15 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DG D 22 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT D 25 O4' - C1' - N1 ANGL. DEV. = 1.9 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 ASN A 11 -7.51 -145.34 REMARK 500 LEU A 74 -72.23 -52.07 REMARK 500 GLU A 87 102.15 60.98 REMARK 500 PHE A 116 -59.29 -123.34 REMARK 500 ASN A 120 -56.80 74.01 REMARK 500 ASN A 127 58.45 -119.20 REMARK 500 ASN A 154 89.30 69.59 REMARK 500 PRO A 214 22.45 -75.34 REMARK 500 TYR A 215 -9.38 -147.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 237 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 43 O REMARK 620 2 ASP A 44 OD1 85.2 REMARK 620 3 ASP A 145 OD1 91.9 81.8 REMARK 620 4 DC C 15 OP2 90.7 78.5 159.8 REMARK 620 5 DC D 17 OP2 161.5 78.6 77.0 94.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 236 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 44 OD2 REMARK 620 2 ASP A 144 O 85.2 REMARK 620 3 DA C 14 OP1 84.5 169.0 REMARK 620 4 DC D 17 OP1 115.7 94.1 93.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 26 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 15 OP1 REMARK 620 2 HOH C 28 O 78.2 REMARK 620 3 DT D 16 OP1 103.1 168.0 REMARK 620 4 HOH D 27 O 154.9 79.1 97.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 236 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 237 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R7M RELATED DB: PDB REMARK 900 RELATED ID: 3C0W RELATED DB: PDB REMARK 900 RELATED ID: 3C0X RELATED DB: PDB REMARK 900 RELATED ID: 3OOL RELATED DB: PDB DBREF 3OOR A 1 235 UNP P03882 SCE1_YEAST 1 235 DBREF 3OOR C 1 25 PDB 3OOR 3OOR 1 25 DBREF 3OOR D 1 25 PDB 3OOR 3OOR 1 25 SEQADV 3OOR ARG A 86 UNP P03882 LYS 86 ENGINEERED MUTATION SEQADV 3OOR THR A 100 UNP P03882 GLY 100 ENGINEERED MUTATION SEQRES 1 A 237 MET HIS MET LYS ASN ILE LYS LYS ASN GLN VAL MET ASN SEQRES 2 A 237 LEU GLY PRO ASN SER LYS LEU LEU LYS GLU TYR LYS SER SEQRES 3 A 237 GLN LEU ILE GLU LEU ASN ILE GLU GLN PHE GLU ALA GLY SEQRES 4 A 237 ILE GLY LEU ILE LEU GLY ASP ALA TYR ILE ARG SER ARG SEQRES 5 A 237 ASP GLU GLY LYS THR TYR CYS MET GLN PHE GLU TRP LYS SEQRES 6 A 237 ASN LYS ALA TYR MET ASP HIS VAL CYS LEU LEU TYR ASP SEQRES 7 A 237 GLN TRP VAL LEU SER PRO PRO HIS LYS ARG GLU ARG VAL SEQRES 8 A 237 ASN HIS LEU GLY ASN LEU VAL ILE THR TRP THR ALA GLN SEQRES 9 A 237 THR PHE LYS HIS GLN ALA PHE ASN LYS LEU ALA ASN LEU SEQRES 10 A 237 PHE ILE VAL ASN ASN LYS LYS THR ILE PRO ASN ASN LEU SEQRES 11 A 237 VAL GLU ASN TYR LEU THR PRO MET SER LEU ALA TYR TRP SEQRES 12 A 237 PHE MET ASP ASP GLY GLY LYS TRP ASP TYR ASN LYS ASN SEQRES 13 A 237 SER THR ASN LYS SER ILE VAL LEU ASN THR GLN SER PHE SEQRES 14 A 237 THR PHE GLU GLU VAL GLU TYR LEU VAL LYS GLY LEU ARG SEQRES 15 A 237 ASN LYS PHE GLN LEU ASN CYS TYR VAL LYS ILE ASN LYS SEQRES 16 A 237 ASN LYS PRO ILE ILE TYR ILE ASP SER MET SER TYR LEU SEQRES 17 A 237 ILE PHE TYR ASN LEU ILE LYS PRO TYR LEU ILE PRO GLN SEQRES 18 A 237 MET MET TYR LYS LEU PRO ASN THR ILE SER SER GLU THR SEQRES 19 A 237 PHE LEU LYS SEQRES 1 C 25 DC DA DC DG DC DT DA DG DG DG DA DT DA SEQRES 2 C 25 DA DC DC DG DG DG DT DA DA DT DA DC SEQRES 1 D 25 DG DG DT DA DT DT DA DC DC DC DG DG DT SEQRES 2 D 25 DT DA DT DC DC DC DT DA DG DC DG DT HET CA A 236 1 HET CA A 237 1 HET CA D 26 1 HETNAM CA CALCIUM ION FORMUL 4 CA 3(CA 2+) FORMUL 7 HOH *11(H2 O) HELIX 1 1 LYS A 5 MET A 10 5 6 HELIX 2 2 SER A 16 LEU A 26 1 11 HELIX 3 3 ASN A 30 GLY A 43 1 14 HELIX 4 4 ASN A 64 TYR A 75 1 12 HELIX 5 5 ASP A 76 VAL A 79 5 4 HELIX 6 6 HIS A 106 ALA A 108 5 3 HELIX 7 7 PHE A 109 ASN A 114 1 6 HELIX 8 8 ASN A 127 TYR A 132 1 6 HELIX 9 9 THR A 134 ASP A 145 1 12 HELIX 10 10 THR A 168 PHE A 183 1 16 HELIX 11 11 SER A 204 LYS A 213 1 10 HELIX 12 12 PRO A 214 LEU A 216 5 3 HELIX 13 13 ILE A 217 LEU A 224 5 8 SHEET 1 A 4 TYR A 46 ARG A 48 0 SHEET 2 A 4 CYS A 57 TRP A 62 -1 O GLN A 59 N TYR A 46 SHEET 3 A 4 TRP A 99 GLN A 102 -1 O TRP A 99 N TRP A 62 SHEET 4 A 4 HIS A 84 LYS A 85 -1 N HIS A 84 O THR A 100 SHEET 1 B 2 ARG A 88 VAL A 89 0 SHEET 2 B 2 LEU A 95 VAL A 96 -1 O VAL A 96 N ARG A 88 SHEET 1 C 4 GLY A 146 LYS A 148 0 SHEET 2 C 4 ILE A 160 LEU A 162 -1 O VAL A 161 N GLY A 147 SHEET 3 C 4 LYS A 195 ILE A 200 -1 O ILE A 200 N ILE A 160 SHEET 4 C 4 CYS A 187 ASN A 192 -1 N ASN A 192 O LYS A 195 LINK O GLY A 43 CA CA A 237 1555 1555 2.27 LINK OD2 ASP A 44 CA CA A 236 1555 1555 2.45 LINK OD1 ASP A 44 CA CA A 237 1555 1555 2.35 LINK O ASP A 144 CA CA A 236 1555 1555 2.38 LINK OD1 ASP A 145 CA CA A 237 1555 1555 2.24 LINK CA CA A 236 OP1 DA C 14 1555 1555 2.12 LINK CA CA A 236 OP1 DC D 17 1555 1555 2.36 LINK CA CA A 237 OP2 DC C 15 1555 1555 2.16 LINK CA CA A 237 OP2 DC D 17 1555 1555 2.98 LINK OP1 DC C 15 CA CA D 26 1555 1555 2.19 LINK O HOH C 28 CA CA D 26 1555 1555 2.20 LINK OP1 DT D 16 CA CA D 26 1555 1555 2.23 LINK CA CA D 26 O HOH D 27 1555 1555 2.19 SITE 1 AC1 4 ASP A 44 ASP A 144 DA C 14 DC D 17 SITE 1 AC2 5 GLY A 43 ASP A 44 ASP A 145 DC C 15 SITE 2 AC2 5 DC D 17 SITE 1 AC3 5 DC C 15 HOH C 28 DA D 15 DT D 16 SITE 2 AC3 5 HOH D 27 CRYST1 131.701 50.538 62.931 90.00 108.46 90.00 C 1 2 1 4 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 0.007593 0.000000 0.002535 0.00000 SCALE2 0.000000 0.019787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016752 0.00000