HEADER HYDROLASE/DNA 01-DEC-11 4AAB TITLE CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH ITS WILD- TITLE 2 TYPE TARGET (THE FOUR CENTRAL BASES, 2NN REGION, ARE COMPOSED BY GTAC TITLE 3 FROM 5' TO 3') COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA ENDONUCLEASE I-CREI; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 23S RRNA INTRON PROTEIN, I-CREI; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)- COMPND 10 3'; COMPND 11 CHAIN: D, F; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 10MER DNA 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'; COMPND 15 CHAIN: E, G; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_TAXID: 3055; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: CDFDUET1, PET24D; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-DNA COMPLEX, GENE TARGETING, PROTEIN-DNA INTERACTION, KEYWDS 2 HOMING ENDONUCLEASES EXPDTA X-RAY DIFFRACTION AUTHOR R.MOLINA,P.REDONDO,S.STELLA,M.MARENCHINO,M.D'ABRAMO,F.L.GERVASIO, AUTHOR 2 J.C.EPINAT,J.VALTON,S.GRIZOT,P.DUCHATEAU,J.PRIETO,G.MONTOYA REVDAT 3 20-DEC-23 4AAB 1 JRNL REMARK LINK REVDAT 2 22-AUG-12 4AAB 1 JRNL REVDAT 1 02-MAY-12 4AAB 0 JRNL AUTH R.MOLINA,P.REDONDO,S.STELLA,M.MARENCHINO,M.D'ABRAMO, JRNL AUTH 2 F.L.GERVASIO,J.CHARLES EPINAT,J.VALTON,S.GRIZOT,P.DUCHATEAU, JRNL AUTH 3 J.PRIETO,G.MONTOYA JRNL TITL NON-SPECIFIC PROTEIN-DNA INTERACTIONS CONTROL I-CREI TARGET JRNL TITL 2 BINDING AND CLEAVAGE. JRNL REF NUCLEIC ACIDS RES. V. 40 6936 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22495931 JRNL DOI 10.1093/NAR/GKS320 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20609 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1079 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.8173 - 4.9958 0.99 2596 136 0.1788 0.2303 REMARK 3 2 4.9958 - 3.9671 1.00 2469 134 0.1435 0.1837 REMARK 3 3 3.9671 - 3.4662 1.00 2442 150 0.1552 0.2145 REMARK 3 4 3.4662 - 3.1495 1.00 2412 122 0.1467 0.1716 REMARK 3 5 3.1495 - 2.9239 1.00 2400 149 0.1802 0.2761 REMARK 3 6 2.9239 - 2.7516 1.00 2406 114 0.1920 0.3007 REMARK 3 7 2.7516 - 2.6138 1.00 2390 148 0.2252 0.2571 REMARK 3 8 2.6138 - 2.5001 1.00 2415 126 0.2733 0.3664 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 47.86 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.840 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30220 REMARK 3 B22 (A**2) : 1.83210 REMARK 3 B33 (A**2) : -1.52980 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 3654 REMARK 3 ANGLE : 1.272 5152 REMARK 3 CHIRALITY : 0.065 585 REMARK 3 PLANARITY : 0.004 476 REMARK 3 DIHEDRAL : 22.130 1418 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 23.9366 26.9491 11.3878 REMARK 3 T TENSOR REMARK 3 T11: 0.2082 T22: 0.2849 REMARK 3 T33: 0.1974 T12: -0.0271 REMARK 3 T13: 0.0140 T23: -0.0819 REMARK 3 L TENSOR REMARK 3 L11: 2.1595 L22: 4.2962 REMARK 3 L33: 2.2844 L12: 1.8733 REMARK 3 L13: -1.1308 L23: -2.0052 REMARK 3 S TENSOR REMARK 3 S11: 0.1627 S12: -0.0889 S13: 0.0268 REMARK 3 S21: 0.0627 S22: -0.1690 S23: 0.0777 REMARK 3 S31: 0.0651 S32: -0.0192 S33: -0.0004 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4AAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1290050549. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : SLS REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 44.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 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) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2XE0 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PROPANEDIOL, 0.1M HEPES PH 7.5, REMARK 280 20% PEG400 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 85.98500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 85.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.55000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E, F, G 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 75 TO ASN REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASP 75 TO ASN 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 OP1 DG E 515 O2 PGO E 1526 1.90 REMARK 500 NH2 ARG A 70 O HOH A 2026 2.19 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 DG E 515 P DG E 515 OP3 -0.124 REMARK 500 DG G 615 P DG G 615 OP3 -0.130 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 DA D 504 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC D 507 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA D 513 O4' - C1' - N9 ANGL. DEV. = -8.0 DEGREES REMARK 500 DC D 514 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT E 522 N3 - C4 - O4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT E 522 C5 - C4 - O4 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG E 523 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC F 607 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA F 613 O4' - C1' - N9 ANGL. DEV. = -6.4 DEGREES REMARK 500 DC F 614 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DA G 616 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG G 623 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA G 624 O4' - C1' - N9 ANGL. DEV. = 3.2 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 LYS A 139 -30.36 -134.75 REMARK 500 LEU A 152 5.60 -67.09 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 MG E1527 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 19 O REMARK 620 2 HOH A2005 O 88.9 REMARK 620 3 ASP B 20 OD2 95.3 89.0 REMARK 620 4 DG E 515 OP3 89.6 99.1 170.7 REMARK 620 5 DG E 515 OP2 86.6 167.4 103.2 69.1 REMARK 620 6 DC F 614 OP1 167.3 79.2 89.1 87.8 104.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP B 20 OD1 90.6 REMARK 620 3 DC D 514 O3' 75.1 150.7 REMARK 620 4 DG E 515 OP2 78.3 85.2 67.2 REMARK 620 5 DC F 614 O3' 170.3 98.8 95.3 99.9 REMARK 620 6 DG G 615 OP1 90.7 108.8 97.0 162.5 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1157 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD2 REMARK 620 2 HOH A2007 O 105.1 REMARK 620 3 GLY B 19 O 83.3 97.9 REMARK 620 4 DC D 514 OP1 78.7 93.3 160.9 REMARK 620 5 DG G 615 OP2 144.1 110.6 94.8 95.7 REMARK 620 6 DG G 615 OP1 80.0 174.9 82.4 87.9 64.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA G1625 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D2012 O REMARK 620 2 DC F 614 O2 79.2 REMARK 620 3 DG G 615 O4' 161.2 88.9 REMARK 620 4 DG G 615 OP3 91.7 110.0 78.5 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 PGO B 1154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO E 1525 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO E 1526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO B 1155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO D 1515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 1527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA G 1625 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G9Z RELATED DB: PDB REMARK 900 LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEXWITH REMARK 900 MAGNESIUM REMARK 900 RELATED ID: 1BP7 RELATED DB: PDB REMARK 900 GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING REMARK 900 SITE DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 1AF5 RELATED DB: PDB REMARK 900 GROUP I MOBILE INTRON ENDONUCLEASE REMARK 900 RELATED ID: 2VBL RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY REMARK 900 ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 2VBJ RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY REMARK 900 ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 2VBO RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY REMARK 900 ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 1MOW RELATED DB: PDB REMARK 900 E-DREI REMARK 900 RELATED ID: 1G9Y RELATED DB: PDB REMARK 900 HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITHCALCIUM REMARK 900 RELATED ID: 2VBN RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY REMARK 900 ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 1N3F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNASEQUENCE II REMARK 900 (PALINDROME OF RIGHT SIDE OF WILDTYPE DNATARGET SEQUENCE) REMARK 900 RELATED ID: 1T9I RELATED DB: PDB REMARK 900 I-CREI(D20N)/DNA COMPLEX REMARK 900 RELATED ID: 1U0D RELATED DB: PDB REMARK 900 Y33H MUTATANT OF HOMING ENDONUCLEASE I-CREI REMARK 900 RELATED ID: 1T9J RELATED DB: PDB REMARK 900 I-CREI(Q47E)/DNA COMPLEX REMARK 900 RELATED ID: 1N3E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNASEQUENCE I REMARK 900 (PALINDROME OF LEFT SIDE OF WILDTYPE DNA TARGETSEQUENCE) REMARK 900 RELATED ID: 1U0C RELATED DB: PDB REMARK 900 Y33C MUTATANT OF HOMING ENDONUCLEASE I-CREI REMARK 900 RELATED ID: 4AAF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH AN REMARK 900 ALTERED TARGET (THE FOUR CENTRAL BASES, 2NN REGION, ARE COMPOSED BY REMARK 900 TGCA FROM 5' TO 3') REMARK 900 RELATED ID: 4AAD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH ITS REMARK 900 WILD-TYPE TARGET IN ABSENCE OF METAL IONS AT THE ACTIVE SITE (THE REMARK 900 FOUR CENTRAL BASES, 2NN REGION, ARE COMPOSED BY GTAC FROM 5' TO 3') REMARK 900 RELATED ID: 4AAE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH AN REMARK 900 ALTERED TARGET (THE FOUR CENTRAL BASES, 2NN REGION, ARE COMPOSED BY REMARK 900 AGCG FROM 5' TO 3') REMARK 900 RELATED ID: 4AAG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH ITS REMARK 900 WILD-TYPE TARGET IN PRESENCE OF CA AT THE ACTIVE SITE (THE FOUR REMARK 900 CENTRAL BASES, 2NN REGION, ARE COMPOSED BY GTAC FROM 5' TO 3') DBREF 4AAB A 2 153 UNP P05725 DNE1_CHLRE 2 153 DBREF 4AAB B 2 153 UNP P05725 DNE1_CHLRE 2 153 DBREF 4AAB D 501 514 PDB 4AAB 4AAB 501 514 DBREF 4AAB E 515 524 PDB 4AAB 4AAB 515 524 DBREF 4AAB F 601 614 PDB 4AAB 4AAB 601 614 DBREF 4AAB G 615 624 PDB 4AAB 4AAB 615 624 SEQADV 4AAB ASN A 75 UNP P05725 ASP 75 ENGINEERED MUTATION SEQADV 4AAB ASN B 75 UNP P05725 ASP 75 ENGINEERED MUTATION SEQRES 1 A 152 ASN THR LYS TYR ASN LYS GLU PHE LEU LEU TYR LEU ALA SEQRES 2 A 152 GLY PHE VAL ASP GLY ASP GLY SER ILE ILE ALA GLN ILE SEQRES 3 A 152 LYS PRO ASN GLN SER TYR LYS PHE LYS HIS GLN LEU SER SEQRES 4 A 152 LEU THR PHE GLN VAL THR GLN LYS THR GLN ARG ARG TRP SEQRES 5 A 152 PHE LEU ASP LYS LEU VAL ASP GLU ILE GLY VAL GLY TYR SEQRES 6 A 152 VAL ARG ASP ARG GLY SER VAL SER ASN TYR ILE LEU SER SEQRES 7 A 152 GLU ILE LYS PRO LEU HIS ASN PHE LEU THR GLN LEU GLN SEQRES 8 A 152 PRO PHE LEU LYS LEU LYS GLN LYS GLN ALA ASN LEU VAL SEQRES 9 A 152 LEU LYS ILE ILE GLU GLN LEU PRO SER ALA LYS GLU SER SEQRES 10 A 152 PRO ASP LYS PHE LEU GLU VAL CYS THR TRP VAL ASP GLN SEQRES 11 A 152 ILE ALA ALA LEU ASN ASP SER LYS THR ARG LYS THR THR SEQRES 12 A 152 SER GLU THR VAL ARG ALA VAL LEU ASP SEQRES 1 B 152 ASN THR LYS TYR ASN LYS GLU PHE LEU LEU TYR LEU ALA SEQRES 2 B 152 GLY PHE VAL ASP GLY ASP GLY SER ILE ILE ALA GLN ILE SEQRES 3 B 152 LYS PRO ASN GLN SER TYR LYS PHE LYS HIS GLN LEU SER SEQRES 4 B 152 LEU THR PHE GLN VAL THR GLN LYS THR GLN ARG ARG TRP SEQRES 5 B 152 PHE LEU ASP LYS LEU VAL ASP GLU ILE GLY VAL GLY TYR SEQRES 6 B 152 VAL ARG ASP ARG GLY SER VAL SER ASN TYR ILE LEU SER SEQRES 7 B 152 GLU ILE LYS PRO LEU HIS ASN PHE LEU THR GLN LEU GLN SEQRES 8 B 152 PRO PHE LEU LYS LEU LYS GLN LYS GLN ALA ASN LEU VAL SEQRES 9 B 152 LEU LYS ILE ILE GLU GLN LEU PRO SER ALA LYS GLU SER SEQRES 10 B 152 PRO ASP LYS PHE LEU GLU VAL CYS THR TRP VAL ASP GLN SEQRES 11 B 152 ILE ALA ALA LEU ASN ASP SER LYS THR ARG LYS THR THR SEQRES 12 B 152 SER GLU THR VAL ARG ALA VAL LEU ASP SEQRES 1 D 14 DT DC DA DA DA DA DC DG DT DC DG DT DA SEQRES 2 D 14 DC SEQRES 1 E 10 DG DA DC DG DT DT DT DT DG DA SEQRES 1 F 14 DT DC DA DA DA DA DC DG DT DC DG DT DA SEQRES 2 F 14 DC SEQRES 1 G 10 DG DA DC DG DT DT DT DT DG DA HET PGO B1154 5 HET PGO B1155 5 HET MG B1156 1 HET MG B1157 1 HET PGO D1515 5 HET PGO E1525 5 HET PGO E1526 5 HET MG E1527 1 HET NA G1625 1 HETNAM PGO S-1,2-PROPANEDIOL HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 7 PGO 5(C3 H8 O2) FORMUL 9 MG 3(MG 2+) FORMUL 15 NA NA 1+ FORMUL 16 HOH *122(H2 O) HELIX 1 1 ASN A 6 ASP A 20 1 15 HELIX 2 2 ARG A 51 GLY A 63 1 13 HELIX 3 3 GLU A 80 GLN A 92 1 13 HELIX 4 4 PRO A 93 LEU A 95 5 3 HELIX 5 5 LYS A 98 LYS A 116 1 19 HELIX 6 6 SER A 118 ASN A 136 1 19 HELIX 7 7 THR A 144 ALA A 150 1 7 HELIX 8 8 ASN B 6 ASP B 20 1 15 HELIX 9 9 ARG B 51 GLY B 63 1 13 HELIX 10 10 GLU B 80 GLN B 92 1 13 HELIX 11 11 PRO B 93 LEU B 95 5 3 HELIX 12 12 LYS B 98 LYS B 116 1 19 HELIX 13 13 SER B 118 ASN B 136 1 19 HELIX 14 14 THR B 144 LEU B 152 1 9 SHEET 1 AA 4 GLY A 21 PRO A 29 0 SHEET 2 AA 4 HIS A 37 LYS A 48 -1 O GLN A 38 N LYS A 28 SHEET 3 AA 4 VAL A 73 LEU A 78 -1 O SER A 74 N GLN A 47 SHEET 4 AA 4 TYR A 66 ASP A 69 -1 O TYR A 66 N ILE A 77 SHEET 1 BA 4 GLY B 21 PRO B 29 0 SHEET 2 BA 4 HIS B 37 LYS B 48 -1 O GLN B 38 N LYS B 28 SHEET 3 BA 4 VAL B 73 LEU B 78 -1 O SER B 74 N GLN B 47 SHEET 4 BA 4 TYR B 66 ASP B 69 -1 O TYR B 66 N ILE B 77 LINK O GLY A 19 MG MG E1527 1555 1555 2.16 LINK OD1 ASP A 20 MG MG B1156 1555 1555 2.15 LINK OD2 ASP A 20 MG MG B1157 1555 1555 2.14 LINK O HOH A2005 MG MG E1527 1555 1555 2.11 LINK O HOH A2007 MG MG B1157 1555 1555 2.08 LINK O GLY B 19 MG MG B1157 1555 1555 2.36 LINK OD1 ASP B 20 MG MG B1156 1555 1555 2.05 LINK OD2 ASP B 20 MG MG E1527 1555 1555 2.02 LINK MG MG B1156 O3' DC D 514 1555 1555 2.53 LINK MG MG B1156 OP2 DG E 515 1555 1555 2.06 LINK MG MG B1156 O3' DC F 614 1555 1555 2.25 LINK MG MG B1156 OP1 DG G 615 1555 1555 1.89 LINK MG MG B1157 OP1 DC D 514 1555 1555 2.00 LINK MG MG B1157 OP2 DG G 615 1555 1555 2.38 LINK MG MG B1157 OP1 DG G 615 1555 1555 2.28 LINK O HOH D2012 NA NA G1625 1555 1555 2.40 LINK OP3 DG E 515 MG MG E1527 1555 1555 1.93 LINK OP2 DG E 515 MG MG E1527 1555 1555 2.21 LINK MG MG E1527 OP1 DC F 614 1555 1555 2.07 LINK O2 DC F 614 NA NA G1625 1555 1555 2.91 LINK O4' DG G 615 NA NA G1625 1555 1555 2.95 LINK OP3 DG G 615 NA NA G1625 1555 1555 2.51 SITE 1 AC1 8 ARG A 51 GLY B 19 LYS B 98 ASP B 137 SITE 2 AC1 8 MG B1157 HOH B2044 DG G 615 DA G 616 SITE 1 AC2 7 LYS A 98 ASP A 137 HOH A2037 HOH A2041 SITE 2 AC2 7 ARG B 51 DG E 515 DA E 516 SITE 1 AC3 8 HOH A2040 HOH A2041 DC D 514 HOH D2014 SITE 2 AC3 8 DG E 515 DG F 611 DT F 612 DA F 613 SITE 1 AC4 8 GLN B 38 SER B 40 LEU B 41 SER B 79 SITE 2 AC4 8 ILE B 81 HOH B2016 DA D 503 DA D 504 SITE 1 AC5 5 LYS B 28 ILE B 77 DA D 505 DA D 506 SITE 2 AC5 5 DC D 507 SITE 1 AC6 5 GLY A 19 HOH A2005 ASP B 20 DG E 515 SITE 2 AC6 5 DC F 614 SITE 1 AC7 6 ASP A 20 ASP B 20 DC D 514 DG E 515 SITE 2 AC7 6 DC F 614 DG G 615 SITE 1 AC8 6 ASP A 20 HOH A2007 GLY B 19 PGO B1154 SITE 2 AC8 6 DC D 514 DG G 615 SITE 1 AC9 4 DG D 511 HOH D2012 DC F 614 DG G 615 CRYST1 171.970 71.100 46.920 90.00 90.00 90.00 P 21 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 0.005815 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021313 0.00000