HEADER HYDROLASE 19-MAY-20 6X1J TITLE THE HOMING ENDONUCLEASE I-WCAI BOUND TO ITS DNA RECOGNITION SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE INTRON-ENCODED ENDONUCLEASE 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (25-MER); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (25-MER); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: WICKERHAMOMYCES CANADENSIS; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 1156965; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: WICKERHAMOMYCES CANADENSIS; SOURCE 12 ORGANISM_TAXID: 1156965; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: WICKERHAMOMYCES CANADENSIS; SOURCE 16 ORGANISM_TAXID: 1156965 KEYWDS INTRON-ENCODED DNA HOMING ENDONUCLEASE, ENZYME, PROTEIN-DNA KEYWDS 2 INTERACTIONS, ISOSCHIZOMERS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.NAWIMANAGE,J.R.LOHMAN,F.S.GIMBLE REVDAT 3 18-OCT-23 6X1J 1 REMARK REVDAT 2 08-JUN-22 6X1J 1 JRNL REVDAT 1 26-MAY-21 6X1J 0 JRNL AUTH R.R.NAWIMANAGE,Z.YUAN,M.CASARES,R.JOSHI,J.R.LOHMAN, JRNL AUTH 2 F.S.GIMBLE JRNL TITL STRUCTURE-FUNCTION STUDIES OF TWO YEAST HOMING ENDONUCLEASES JRNL TITL 2 THAT EVOLVED TO CLEAVE IDENTICAL TARGETS WITH DISSIMILAR JRNL TITL 3 RATES AND SPECIFICITIES. JRNL REF J.MOL.BIOL. V. 434 67550 2022 JRNL REFN ESSN 1089-8638 JRNL PMID 35317996 JRNL DOI 10.1016/J.JMB.2022.167550 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 31986 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1627 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1650 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.4210 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.4400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1926 REMARK 3 NUCLEIC ACID ATOMS : 1004 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.212 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.699 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3202 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2483 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4468 ; 1.760 ; 1.458 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5818 ; 1.407 ; 1.912 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 483 ; 8.073 ; 5.498 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;33.759 ;24.257 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 398 ;17.935 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 8.072 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.136 ; 0.230 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2753 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 656 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6X1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000242853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33735 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.945 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.1 REMARK 200 STARTING MODEL: 1R7M REMARK 200 REMARK 200 REMARK: NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350, 0.1M TRIS-HCL, 0.2M REMARK 280 LITHIUM SULFATE, 2 MM DTT, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 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: 8420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 489 LIES ON A SPECIAL POSITION. 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 MET A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 4 REMARK 465 GLN A 5 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DC C 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC C 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC C 1 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N3 DA C 22 O HOH C 201 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 DC C 15 O3' DA C 16 P -0.082 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 GLU A 80 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 DC C 5 O5' - P - OP1 ANGL. DEV. = -10.3 DEGREES REMARK 500 DC C 5 O5' - P - OP2 ANGL. DEV. = 8.9 DEGREES REMARK 500 DC C 15 O5' - P - OP1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC C 15 O5' - C5' - C4' ANGL. DEV. = -10.9 DEGREES REMARK 500 DG C 18 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 16 O5' - P - OP2 ANGL. DEV. = -7.8 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 THR A 30 -52.35 -120.41 REMARK 500 TYR A 135 -43.07 -132.53 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 K A 302 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 45 O REMARK 620 2 GLY A 46 O 67.3 REMARK 620 3 ASP A 148 OD2 76.1 98.0 REMARK 620 4 HOH A 456 O 104.1 83.2 178.7 REMARK 620 5 HOH A 484 O 85.4 152.6 76.2 102.5 REMARK 620 6 DC C 15 OP2 129.8 73.4 79.8 100.9 130.1 REMARK 620 7 HOH D 203 O 131.6 138.9 62.5 116.8 62.2 67.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 47 OD1 REMARK 620 2 ASP A 47 OD2 43.2 REMARK 620 3 ASP A 147 O 93.2 73.6 REMARK 620 4 HOH A 465 O 104.3 61.1 64.1 REMARK 620 5 DA C 14 OP1 97.9 75.3 119.4 55.4 REMARK 620 6 HOH C 213 O 156.4 137.9 109.8 82.1 66.7 REMARK 620 7 DC D 17 OP1 66.9 109.8 110.8 170.2 128.4 107.7 REMARK 620 8 DC D 17 O5' 112.8 144.0 84.0 132.1 140.7 76.0 52.5 REMARK 620 9 HOH D 215 O 105.2 138.3 145.9 134.5 86.8 58.1 54.5 62.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT C 12 O2 REMARK 620 2 DA C 13 O4' 92.6 REMARK 620 3 HOH C 218 O 109.5 83.5 REMARK 620 4 DT D 16 O2 88.6 176.0 92.5 REMARK 620 5 HOH D 207 O 86.8 92.7 163.3 91.2 REMARK 620 6 HOH D 222 O 167.3 95.1 81.3 84.4 82.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 15 OP1 REMARK 620 2 HOH C 214 O 68.7 REMARK 620 3 HOH C 218 O 89.8 104.9 REMARK 620 4 DT D 16 OP1 74.2 102.2 140.7 REMARK 620 5 DT D 16 O4' 87.8 156.4 72.3 71.4 REMARK 620 6 HOH D 212 O 124.2 73.3 139.4 75.8 124.5 REMARK 620 7 HOH D 219 O 64.3 49.0 147.5 53.6 122.5 60.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K D 101 DBREF 6X1J A 1 231 UNP Q34807 IEND1_WICCA 1 231 DBREF 6X1J C 1 25 PDB 6X1J 6X1J 1 25 DBREF 6X1J D 1 25 PDB 6X1J 6X1J 1 25 SEQRES 1 A 231 MET MET LYS LYS GLN ILE ILE ASN LYS LYS ASP LEU LEU SEQRES 2 A 231 GLY LEU GLY PRO ASN SER LYS LEU ILE LYS ASP TYR LYS SEQRES 3 A 231 LYS GLN TRP THR THR LEU SER LYS ILE GLN GLU GLU THR SEQRES 4 A 231 LEU ILE GLY ASN ILE LEU GLY ASP VAL TYR ILE LYS LYS SEQRES 5 A 231 LEU LYS ARG ASN LYS HIS PHE LEU LEU GLN PHE GLU TRP SEQRES 6 A 231 LYS ASN LYS ALA TYR ILE GLU HIS ILE VAL ARG VAL PHE SEQRES 7 A 231 ASP GLU TYR VAL ILE SER PRO PRO THR LEU TYR GLU ARG SEQRES 8 A 231 LYS ASN HIS LEU GLY ASN LYS VAL ILE THR TRP ARG ALA SEQRES 9 A 231 GLN THR PHE GLU HIS LYS ALA PHE ASP LYS LEU GLY TYR SEQRES 10 A 231 TYR PHE MET GLU ASN HIS LYS LYS ILE ILE LYS PRO ASP SEQRES 11 A 231 LEU VAL LEU ASN TYR ILE THR GLU ARG SER LEU ALA TYR SEQRES 12 A 231 TRP PHE MET ASP ASP GLY GLY LYS TRP ASP TYR ASN LYS SEQRES 13 A 231 LYS THR LYS ASN LYS SER LEU VAL LEU HIS THR GLN GLY SEQRES 14 A 231 PHE LYS LYS GLU GLU VAL GLU ILE LEU ILE ASN ASP LEU SEQRES 15 A 231 ASN ILE LYS PHE ASN LEU ASN CYS SER ILE LYS PHE ASN SEQRES 16 A 231 LYS ASN LYS PRO ILE ILE TYR ILE PRO ASN LYS ASP TYR SEQRES 17 A 231 GLU LEU PHE TYR ASN LEU VAL ASN PRO TYR ILE ILE PRO SEQRES 18 A 231 GLU MET LYS TYR LYS LEU LEU PHE ASN VAL SEQRES 1 C 25 DC DA DC DG DC DT DA DG DG DG DA DT DA SEQRES 2 C 25 DA DC DA DG DG DG DT DA DA DT DA DC SEQRES 1 D 25 DG DG DT DA DT DT DA DC DC DC DT DG DT SEQRES 2 D 25 DT DA DT DC DC DC DT DA DG DC DG DT HET K A 301 1 HET K A 302 1 HET K C 101 1 HET K D 101 1 HETNAM K POTASSIUM ION FORMUL 4 K 4(K 1+) FORMUL 8 HOH *140(H2 O) HELIX 1 AA1 ASN A 8 LEU A 13 5 6 HELIX 2 AA2 SER A 19 LYS A 27 1 9 HELIX 3 AA3 SER A 33 GLY A 46 1 14 HELIX 4 AA4 ASN A 67 PHE A 78 1 12 HELIX 5 AA5 ASP A 79 VAL A 82 5 4 HELIX 6 AA6 HIS A 109 ALA A 111 5 3 HELIX 7 AA7 PHE A 112 PHE A 119 1 8 HELIX 8 AA8 ASP A 130 TYR A 135 1 6 HELIX 9 AA9 THR A 137 ASP A 148 1 12 HELIX 10 AB1 LYS A 171 ASN A 187 1 17 HELIX 11 AB2 PRO A 204 LYS A 206 5 3 HELIX 12 AB3 ASP A 207 ASN A 216 1 10 HELIX 13 AB4 PRO A 217 ILE A 219 5 3 HELIX 14 AB5 ILE A 220 LEU A 227 5 8 SHEET 1 AA1 4 TYR A 49 LYS A 51 0 SHEET 2 AA1 4 LEU A 60 TRP A 65 -1 O LEU A 60 N LYS A 51 SHEET 3 AA1 4 LYS A 98 GLN A 105 -1 O TRP A 102 N TRP A 65 SHEET 4 AA1 4 THR A 87 LYS A 92 -1 N ARG A 91 O VAL A 99 SHEET 1 AA2 2 MET A 120 GLU A 121 0 SHEET 2 AA2 2 LYS A 124 LYS A 125 -1 O LYS A 124 N GLU A 121 SHEET 1 AA3 4 GLY A 149 LYS A 151 0 SHEET 2 AA3 4 LEU A 163 LEU A 165 -1 O VAL A 164 N GLY A 150 SHEET 3 AA3 4 LYS A 198 ILE A 203 -1 O ILE A 203 N LEU A 163 SHEET 4 AA3 4 SER A 191 ASN A 195 -1 N LYS A 193 O ILE A 200 LINK O LEU A 45 K K A 302 1555 1555 3.19 LINK O GLY A 46 K K A 302 1555 1555 2.66 LINK OD1 ASP A 47 K K A 301 1555 1555 2.95 LINK OD2 ASP A 47 K K A 301 1555 1555 2.97 LINK O ASP A 147 K K A 301 1555 1555 2.33 LINK OD2 ASP A 148 K K A 302 1555 1555 2.79 LINK K K A 301 O HOH A 465 1555 1555 3.45 LINK K K A 301 OP1 DA C 14 1555 1555 2.63 LINK K K A 301 O HOH C 213 1555 1555 2.61 LINK K K A 301 OP1 DC D 17 1555 1555 2.72 LINK K K A 301 O5' DC D 17 1555 1555 2.86 LINK K K A 301 O HOH D 215 1555 1555 3.31 LINK K K A 302 O HOH A 456 1555 1555 2.87 LINK K K A 302 O HOH A 484 1555 1555 3.18 LINK K K A 302 OP2 DC C 15 1555 1555 2.95 LINK K K A 302 O HOH D 203 1555 1555 2.95 LINK O2 DT C 12 K K C 101 1555 1555 2.57 LINK O4' DA C 13 K K C 101 1555 1555 3.08 LINK OP1 DC C 15 K K D 101 1555 1555 2.73 LINK K K C 101 O HOH C 218 1555 1555 2.85 LINK K K C 101 O2 DT D 16 1555 1555 2.60 LINK K K C 101 O BHOH D 207 1555 1555 2.96 LINK K K C 101 O HOH D 222 1555 1555 2.64 LINK O HOH C 214 K K D 101 1555 1555 2.72 LINK O HOH C 218 K K D 101 1555 1555 3.14 LINK OP1 DT D 16 K K D 101 1555 1555 2.89 LINK O4' DT D 16 K K D 101 1555 1555 3.12 LINK K K D 101 O HOH D 212 1555 1555 2.61 LINK K K D 101 O HOH D 219 1555 1555 3.34 SITE 1 AC1 5 ASP A 47 ASP A 147 DA C 14 HOH C 213 SITE 2 AC1 5 DC D 17 SITE 1 AC2 6 LEU A 45 GLY A 46 ASP A 148 HOH A 456 SITE 2 AC2 6 DC C 15 HOH D 203 SITE 1 AC3 6 DT C 12 DA C 13 HOH C 218 DT D 16 SITE 2 AC3 6 HOH D 207 HOH D 222 SITE 1 AC4 5 DC C 15 HOH C 214 DA D 15 DT D 16 SITE 2 AC4 5 HOH D 212 CRYST1 67.601 37.281 94.064 90.00 100.44 90.00 P 1 2 1 2 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 0.014793 0.000000 0.002727 0.00000 SCALE2 0.000000 0.026823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010810 0.00000