PDB Short entry for 4AQX HEADER HYDROLASE 19-APR-12 4AQX TITLE CRYSTAL STRUCTURE OF I-CREI COMPLEXED WITH ITS TARGET TITLE 2 METHYLATED AT POSITION PLUS 2 (IN THE B STRAND) IN THE TITLE 3 PRESENCE OF MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA ENDONUCLEASE I-CREI; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 2-153; COMPND 5 SYNONYM: I-CREI, 23S RRNA INTRON PROTEIN; COMPND 6 EC: 3.1.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP)-3'; COMPND 10 CHAIN: C; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*GP*AP*CP*AP*GP*TP*TP*TP*GP*GP)-3'; COMPND 13 CHAIN: D; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CM)-3'; COMPND 16 CHAIN: E; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'; COMPND 19 CHAIN: F 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; 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; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 MOL_ID: 5; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 23 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, METHYLATION, GENE TARGETING, GENETICS, PROTEIN-DNA KEYWDS 2 INTERACTION, HOMING ENDONUCLEASES EXPDTA X-RAY DIFFRACTION AUTHOR J.VALTON,F.DABOUSSI,S.LEDUC,P.REDONDO,R.MACMASTER,R.MOLINA,G.MONTOYA, AUTHOR 2 P.DUCHATEAU REVDAT 2 12-SEP-12 4AQX 1 JRNL REVDAT 1 04-JUL-12 4AQX 0 JRNL AUTH J.VALTON,F.DABOUSSI,S.LEDUC,R.MOLINA,P.REDONDO,R.MACMASTER, JRNL AUTH 2 G.MONTOYA,P.DUCHATEAU JRNL TITL 5'-CYTOSINE-PHOSPHOGUANINE (CPG) METHYLATION IMPACTS THE JRNL TITL 2 ACTIVITY OF NATURAL AND ENGINEERED MEGANUCLEASES. JRNL REF J.BIOL.CHEM. V. 287 30139 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22740697 JRNL DOI 10.1074/JBC.M112.379966 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.200 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.793 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.34 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.79 REMARK 3 NUMBER OF REFLECTIONS : 30701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2041 REMARK 3 R VALUE (WORKING SET) : 0.2015 REMARK 3 FREE R VALUE : 0.2418 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.5 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 45.8029 - 5.2998 1.00 2225 155 0.1903 0.2267 REMARK 3 2 5.2998 - 4.2075 1.00 2101 147 0.1376 0.1667 REMARK 3 3 4.2075 - 3.6759 1.00 2098 145 0.1687 0.1831 REMARK 3 4 3.6759 - 3.3400 1.00 2043 143 0.1966 0.2471 REMARK 3 5 3.3400 - 3.1006 1.00 2046 141 0.1968 0.2331 REMARK 3 6 3.1006 - 2.9179 1.00 2045 143 0.2352 0.2912 REMARK 3 7 2.9179 - 2.7717 1.00 2034 142 0.2508 0.2763 REMARK 3 8 2.7717 - 2.6511 1.00 2018 140 0.2520 0.2992 REMARK 3 9 2.6511 - 2.5491 1.00 2010 140 0.2475 0.3282 REMARK 3 10 2.5491 - 2.4611 1.00 2041 143 0.2926 0.3569 REMARK 3 11 2.4611 - 2.3841 1.00 2003 139 0.3079 0.4017 REMARK 3 12 2.3841 - 2.3160 1.00 2022 141 0.3207 0.3784 REMARK 3 13 2.3160 - 2.2550 1.00 2015 140 0.2964 0.3361 REMARK 3 14 2.2550 - 2.2000 1.00 2002 139 0.3271 0.3968 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 : 0.357 REMARK 3 B_SOL : 49.936 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.80 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.08 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.1210 REMARK 3 B22 (A**2) : -8.6003 REMARK 3 B33 (A**2) : -3.5207 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 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 : 0.010 3656 REMARK 3 ANGLE : 1.279 5152 REMARK 3 CHIRALITY : 0.078 578 REMARK 3 PLANARITY : 0.005 476 REMARK 3 DIHEDRAL : 23.120 1423 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): -11.0581 25.5431 -25.5515 REMARK 3 T TENSOR REMARK 3 T11: 0.3051 T22: 0.3003 REMARK 3 T33: 0.3224 T12: -0.0330 REMARK 3 T13: -0.0816 T23: 0.0491 REMARK 3 L TENSOR REMARK 3 L11: 2.4134 L22: 2.1327 REMARK 3 L33: 4.2129 L12: -1.1993 REMARK 3 L13: 1.9738 L23: -2.3737 REMARK 3 S TENSOR REMARK 3 S11: -0.1945 S12: 0.0110 S13: 0.1487 REMARK 3 S21: 0.3802 S22: -0.2611 S23: -0.1669 REMARK 3 S31: -0.4079 S32: 0.1685 S33: 0.3596 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 4AQX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-12. REMARK 100 THE PDBE ID CODE IS EBI-52140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30701 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 45.79 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.4 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.10 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.4 REMARK 200 R MERGE FOR SHELL (I) : 0.38 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.90 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 1G9Z REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.70050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 89.52700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.70050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.52700 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: 13930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E, C, F 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 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 NH1 ARG A 141 O3 GOL A 1155 2.14 REMARK 500 N ASN B 6 O3 GOL B 1354 2.18 REMARK 500 OP2 DT C 509 O HOH C 2009 1.97 REMARK 500 OP3 DG F 615 O HOH E 2005 2.20 REMARK 500 O1 GOL B 1355 O HOH B 2031 2.00 REMARK 500 O HOH A 2008 O HOH A 2009 1.86 REMARK 500 O HOH C 2017 O HOH C 2019 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 DG D 515 OP3 DG D 515 P -0.111 REMARK 500 DG F 615 OP3 DG F 615 P -0.106 REMARK 500 DA F 624 C1' DA F 624 N9 1.478 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 DC C 502 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC C 507 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 513 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA C 514 N9 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 DA D 516 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT D 522 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG D 523 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG D 524 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT E 609 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DT E 609 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA E 613 O4' - C1' - N9 ANGL. DEV. = -6.0 DEGREES REMARK 500 DA F 616 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA F 624 N9 - C1' - C2' ANGL. DEV. = 23.1 DEGREES REMARK 500 DA F 624 O4' - C1' - N9 ANGL. DEV. = -60.1 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 LYS A 96 -58.21 -122.40 REMARK 500 LYS A 142 -61.31 -122.88 REMARK 500 LYS B 139 -56.62 -130.58 REMARK 500 LYS B 142 -58.95 -127.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA F 624 0.27 SIDE CHAIN 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 D1526 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 19 O REMARK 620 2 HOH A2004 O 91.5 REMARK 620 3 DG D 515 OP3 94.4 98.2 REMARK 620 4 DG D 515 OP2 83.1 163.0 66.3 REMARK 620 5 ASP B 20 OD2 88.0 92.9 168.5 102.9 REMARK 620 6 5CM E 614 OP2 176.5 85.4 87.7 100.3 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D1525 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG F 615 OP1 REMARK 620 2 ASP A 20 OD1 83.3 REMARK 620 3 ASP B 20 OD1 96.8 81.5 REMARK 620 4 DA C 514 O3' 93.7 81.2 158.5 REMARK 620 5 DG D 515 OP2 174.8 91.5 81.9 86.0 REMARK 620 6 5CM E 614 O3' 86.8 167.0 91.3 108.0 98.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F1625 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD2 REMARK 620 2 GLY B 19 O 82.0 REMARK 620 3 HOH A2006 O 92.2 89.1 REMARK 620 4 DA C 514 OP1 83.6 165.2 88.0 REMARK 620 5 DG F 615 OP1 95.1 84.2 169.4 100.5 REMARK 620 6 DG F 615 OP2 164.5 93.3 102.6 101.5 69.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C1515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D1525 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F1625 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AF5 RELATED DB: PDB REMARK 900 GROUP I MOBILE INTRON ENDONUCLEASE REMARK 900 RELATED ID: 1BP7 RELATED DB: PDB REMARK 900 GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED REMARK 900 WITH HOMING SITE DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 1G9Y RELATED DB: PDB REMARK 900 HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX REMARK 900 WITHCALCIUM REMARK 900 RELATED ID: 1G9Z RELATED DB: PDB REMARK 900 LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT REMARK 900 COMPLEXWITH MAGNESIUM REMARK 900 RELATED ID: 1MOW RELATED DB: PDB REMARK 900 E-DREI REMARK 900 RELATED ID: 1N3E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC REMARK 900 DNASEQUENCE I (PALINDROME OF LEFT SIDE OF WILDTYPE DNA REMARK 900 TARGETSEQUENCE) REMARK 900 RELATED ID: 1N3F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC REMARK 900 DNASEQUENCE II (PALINDROME OF RIGHT SIDE OF WILDTYPE REMARK 900 DNATARGET SEQUENCE) REMARK 900 RELATED ID: 1T9I RELATED DB: PDB REMARK 900 I-CREI(D20N)/DNA COMPLEX REMARK 900 RELATED ID: 1T9J RELATED DB: PDB REMARK 900 I-CREI(Q47E)/DNA COMPLEX REMARK 900 RELATED ID: 1U0C RELATED DB: PDB REMARK 900 Y33C MUTATANT OF HOMING ENDONUCLEASE I-CREI REMARK 900 RELATED ID: 1U0D RELATED DB: PDB REMARK 900 Y33H MUTATANT OF HOMING ENDONUCLEASE I-CREI REMARK 900 RELATED ID: 2VBJ RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND REMARK 900 CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 2VBL RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND REMARK 900 CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 2VBN RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND REMARK 900 CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 2VBO RELATED DB: PDB REMARK 900 MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND REMARK 900 CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS REMARK 900 RELATED ID: 4AAB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN REMARK 900 COMPLEX WITH ITS WILD-TYPE TARGET (THE FOUR CENTRAL REMARK 900 BASES, 2NN REGION, ARE COMPOSED BY GTAC FROM 5' TO REMARK 900 3') REMARK 900 RELATED ID: 4AAD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN REMARK 900 COMPLEX WITH ITS WILD-TYPE TARGET IN ABSENCE OF REMARK 900 METAL IONS AT THE ACTIVE SITE (THE FOUR CENTRAL REMARK 900 BASES, 2NN REGION, ARE COMPOSED BY GTAC FROM 5' TO REMARK 900 3') REMARK 900 RELATED ID: 4AAE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN REMARK 900 COMPLEX WITH AN ALTERED TARGET (THE FOUR CENTRAL BASES REMARK 900 , 2NN REGION, ARE COMPOSED BY AGCG FROM 5' TO 3') REMARK 900 RELATED ID: 4AAF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN REMARK 900 COMPLEX WITH AN ALTERED TARGET (THE FOUR CENTRAL BASES REMARK 900 , 2NN REGION, ARE COMPOSED BY TGCA FROM 5' TO 3') REMARK 900 RELATED ID: 4AAG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN REMARK 900 COMPLEX WITH ITS WILD-TYPE TARGET IN PRESENCE OF CA REMARK 900 AT THE ACTIVE SITE (THE FOUR CENTRAL BASES, 2NN REMARK 900 REGION, ARE COMPOSED BY GTAC FROM 5' TO 3') REMARK 900 RELATED ID: 4AQU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF I-CREI COMPLEXED WITH ITS TARGET REMARK 900 METHYLATED AT POSITION PLUS 2 (IN THE B STRAND) IN REMARK 900 THE PRESENCE OF CALCIUM DBREF 4AQX A 2 153 UNP P05725 DNE1_CHLRE 2 153 DBREF 4AQX B 2 153 UNP P05725 DNE1_CHLRE 2 153 DBREF 4AQX C 501 514 PDB 4AQX 4AQX 501 514 DBREF 4AQX D 515 524 PDB 4AQX 4AQX 515 524 DBREF 4AQX E 601 614 PDB 4AQX 4AQX 601 614 DBREF 4AQX F 615 624 PDB 4AQX 4AQX 615 624 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 ASP 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 ASP 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 C 14 DT DC DA DA DA DA DC DG DT DC DG DT DG SEQRES 2 C 14 DA SEQRES 1 D 10 DG DA DC DA DG DT DT DT DG DG SEQRES 1 E 14 DC DC DA DA DA DC DT DG DT DC DT DC DA SEQRES 2 E 14 5CM SEQRES 1 F 10 DG DA DC DG DT DT DT DT DG DA MODRES 4AQX 5CM E 614 DC HET 5CM E 614 20 HET GOL A1154 6 HET GOL A1155 6 HET GOL B1354 6 HET GOL B1355 6 HET GOL C1515 6 HET MG D1525 1 HET MG D1526 1 HET MG F1625 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 7 5CM C10 H16 N3 O7 P FORMUL 8 GOL 5(C3 H8 O3) FORMUL 9 MG 3(MG 2+) FORMUL 10 HOH *133(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 ASP A 153 1 10 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 ASN B 136 1 39 HELIX 13 13 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 ARG A 70 -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 ARG B 70 -1 O TYR B 66 N ILE B 77 LINK MG MG D1525 OP1 DG F 615 1555 1555 2.06 LINK MG MG D1525 OD1 ASP A 20 1555 1555 2.16 LINK MG MG D1525 OD1 ASP B 20 1555 1555 2.22 LINK MG MG D1525 O3' DA C 514 1555 1555 2.10 LINK MG MG D1525 OP2 DG D 515 1555 1555 2.15 LINK MG MG D1526 OP3 DG D 515 1555 1555 2.29 LINK MG MG D1526 OP2 DG D 515 1555 1555 2.08 LINK MG MG D1526 OD2 ASP B 20 1555 1555 2.00 LINK MG MG D1526 O HOH A2004 1555 1555 2.10 LINK MG MG D1526 O GLY A 19 1555 1555 2.07 LINK OP2 5CM E 614 MG MG D1526 1555 1555 2.08 LINK P 5CM E 614 O3' DA E 613 1555 1555 1.61 LINK O3' 5CM E 614 MG MG D1525 1555 1555 2.10 LINK MG MG F1625 O GLY B 19 1555 1555 2.26 LINK MG MG F1625 O HOH A2006 1555 1555 2.14 LINK MG MG F1625 OP1 DA C 514 1555 1555 2.08 LINK MG MG F1625 OP1 DG F 615 1555 1555 2.19 LINK MG MG F1625 OP2 DG F 615 1555 1555 2.21 LINK MG MG F1625 OD2 ASP A 20 1555 1555 2.07 SITE 1 AC1 5 PHE A 54 LYS A 57 LEU A 58 GLU A 61 SITE 2 AC1 5 LYS B 96 SITE 1 AC2 9 ALA A 25 GLN A 26 ILE A 27 VAL A 129 SITE 2 AC2 9 ARG A 141 THR A 143 HOH A2012 DC D 517 SITE 3 AC2 9 DA D 518 SITE 1 AC3 4 TYR B 5 ASN B 6 PHE B 9 GLU B 61 SITE 1 AC4 11 ARG A 51 LEU B 97 LYS B 98 GLN B 101 SITE 2 AC4 11 LEU B 135 ASN B 136 ASP B 137 HOH B2030 SITE 3 AC4 11 HOH B2031 HOH B2038 DA F 616 SITE 1 AC5 9 GLN B 38 SER B 40 SER B 79 ILE B 81 SITE 2 AC5 9 HOH B2011 HOH B2014 HOH B2016 DA C 503 SITE 3 AC5 9 DA C 504 SITE 1 AC6 6 ASP A 20 ASP B 20 DA C 514 DG D 515 SITE 2 AC6 6 5CM E 614 DG F 615 SITE 1 AC7 5 ASP A 20 HOH A2006 GLY B 19 DA C 514 SITE 2 AC7 5 DG F 615 CRYST1 45.839 71.401 179.054 90.00 90.00 90.00 P 2 21 21 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 0.021815 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014005 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005585 0.00000