PDB Short entry for 2VBJ HEADER HYDROLASE/DNA 14-SEP-07 2VBJ TITLE MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY TITLE 2 ENGINEERED HOMING ENDONUCLEASE HETERODIMERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA ENDONUCLEASE I-CREI; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-153; COMPND 5 SYNONYM: AMEL3-4-CA, 23S RRNA INTRON PROTEIN; COMPND 6 EC: 3.1.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA ENDONUCLEASE I-CREI; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 2-153; COMPND 12 SYNONYM: AMEL3-4-CA, 23S RRNA INTRON PROTEIN; COMPND 13 EC: 3.1.-.-; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP COMPND 17 *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3'; COMPND 18 CHAIN: C; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP COMPND 22 *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3'; COMPND 23 CHAIN: E; COMPND 24 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_STRAIN: ROSETTA; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: D3PLYSS; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: CDFDUET-1; SOURCE 9 OTHER_DETAILS: AMEL4 STREP-TAG C-TERM AMEL3 HIS-TAG C-TERM; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 12 ORGANISM_TAXID: 3055; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: D3PLYSS; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: CDFDUET-1; SOURCE 18 OTHER_DETAILS: AMEL4 STREP-TAG C-TERM AMEL3 HIS-TAG C-TERM; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630; SOURCE 23 MOL_ID: 4; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 26 ORGANISM_TAXID: 32630 KEYWDS DOUBLE STRAND BREAK (DSB), CUTTING DNA ENDONUCLEASES, AMEL3-4- KEYWDS 2 CALCIUM, UV-INDUCED DNA DAMAGE, HOMING ENDONUCLEASES (HES), KEYWDS 3 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.REDONDO,J.PRIETO,I.G.MUNOZ,A.ALIBES,F.STRICHER,L.SERRANO,S.ARNOULD, AUTHOR 2 C.PEREZ,J.P.CABANIOLS,P.DUCHATEAU,F.PAQUES,F.J.BLANCO,G.MONTOYA REVDAT 6 13-DEC-23 2VBJ 1 REMARK LINK REVDAT 5 29-MAY-19 2VBJ 1 SOURCE REMARK REVDAT 4 20-JUN-12 2VBJ 1 HEADER KEYWDS JRNL REMARK REVDAT 4 2 1 VERSN FORMUL REVDAT 3 24-FEB-09 2VBJ 1 VERSN REVDAT 2 11-NOV-08 2VBJ 1 JRNL REVDAT 1 28-OCT-08 2VBJ 0 JRNL AUTH P.REDONDO,J.PRIETO,I.G.MUNOZ,A.ALIBES,F.STRICHER,L.SERRANO, JRNL AUTH 2 J.P.CABANIOLS,F.DABOUSSI,S.ARNOULD,C.PEREZ,P.DUCHATEAU, JRNL AUTH 3 F.PAQUES,F.J.BLANCO,G.MONTOYA JRNL TITL MOLECULAR BASIS OF XERODERMA PIGMENTOSUM GROUP C DNA JRNL TITL 2 RECOGNITION BY ENGINEERED MEGANUCLEASES JRNL REF NATURE V. 456 107 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18987743 JRNL DOI 10.1038/NATURE07343 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 32.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 35736 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1949 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2087 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.1410 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2456 REMARK 3 NUCLEIC ACID ATOMS : 978 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.42000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : 0.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.407 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.010 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3596 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5065 ; 2.081 ; 2.313 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 302 ; 7.686 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;41.746 ;24.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 477 ;17.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;22.257 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 580 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2335 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1500 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2331 ; 0.322 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 317 ; 0.233 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.100 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 29 ; 0.238 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.325 ; 0.200 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): 1565 ; 3.994 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2466 ; 5.244 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2638 ; 7.198 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2599 ; 8.695 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 2VBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1290033736. 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 : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.983 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35740 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 32.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.05000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1G9Z REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING-DROP DNA-PROTEIN COMPLEX REMARK 280 SOLUTION WAS 4 MG/ML. 35% 2-ETHOXYETHANOL IN 0.1M NA-CACODYLATE REMARK 280 PH6.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.35000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, E 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 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 LYS A 116 CG CD CE NZ REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 GLU B 28 CG CD OE1 OE2 REMARK 470 ASP B 69 CB CG OD1 OD2 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 O HOH B 1008 O HOH B 1070 1.03 REMARK 500 O HOH C 1049 O HOH C 1053 1.95 REMARK 500 O HOH C 1045 O HOH E 1039 2.01 REMARK 500 NH1 ARG A 68 OP2 DT E 7 2.05 REMARK 500 OG1 THR B 143 O HOH B 1107 2.08 REMARK 500 O LEU A 152 O HOH A 1089 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS B 100 OP2 DA C 24 2655 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 38 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 DT C 3 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT C 3 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG C 4 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DC C 6 C5 - C4 - N4 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT C 8 N1 - C2 - N3 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT C 8 N3 - C4 - O4 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT C 8 C5 - C4 - O4 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT C 8 C6 - C5 - C7 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT C 9 O5' - C5' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT C 9 C4 - C5 - C7 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT C 9 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT C 10 O4' - C1' - N1 ANGL. DEV. = -8.4 DEGREES REMARK 500 DT C 12 O5' - P - OP2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DT C 12 N1 - C1' - C2' ANGL. DEV. = 10.4 DEGREES REMARK 500 DT C 12 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG C 13 O4' - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = -7.0 DEGREES REMARK 500 DG C 13 C4 - C5 - N7 ANGL. DEV. = -2.7 DEGREES REMARK 500 DG C 13 C6 - C5 - N7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG C 13 N1 - C6 - O6 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA C 14 N1 - C2 - N3 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA C 15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 16 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG C 16 C4 - C5 - N7 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG C 16 N3 - C2 - N2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG C 17 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC C 21 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT C 22 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT C 22 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DA C 23 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT E 1 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT E 2 C4 - C5 - C7 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT E 2 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA E 3 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DG E 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG E 5 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT E 7 C5 - C4 - O4 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT E 10 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT E 11 OP1 - P - OP2 ANGL. DEV. = 11.2 DEGREES REMARK 500 DC E 12 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DC E 12 N3 - C4 - C5 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC E 12 N3 - C4 - N4 ANGL. DEV. = -6.1 DEGREES REMARK 500 DA E 13 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA E 13 O4' - C4' - C3' ANGL. DEV. = -4.4 DEGREES REMARK 500 DA E 13 C1' - O4' - C4' ANGL. DEV. = 4.4 DEGREES REMARK 500 DA E 13 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA E 13 O4' - C1' - N9 ANGL. DEV. = -8.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 67 ANGLE DEVIATIONS. 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 30 118.36 -167.55 REMARK 500 LYS A 36 8.38 59.47 REMARK 500 LYS A 116 39.39 -85.57 REMARK 500 GLU A 117 -4.05 -152.60 REMARK 500 ASP A 120 -43.05 76.34 REMARK 500 ARG A 149 59.24 -62.32 REMARK 500 VAL A 151 3.87 -62.41 REMARK 500 ASN B 30 113.89 -165.96 REMARK 500 LYS B 142 -52.98 -123.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 149 ALA A 150 144.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B1031 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH C1005 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH C1011 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH E1005 DISTANCE = 6.25 ANGSTROMS 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 A1155 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 19 O REMARK 620 2 HOH A1013 O 88.7 REMARK 620 3 ASP B 20 OD1 86.9 126.9 REMARK 620 4 ASP B 20 OD2 93.8 78.7 48.9 REMARK 620 5 DA C 15 OP2 84.6 154.5 77.4 126.2 REMARK 620 6 HOH C1051 O 95.6 78.7 154.4 155.2 77.5 REMARK 620 7 DA E 14 OP1 177.1 88.9 93.1 84.1 98.2 85.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1154 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP A 20 OD2 49.6 REMARK 620 3 ALA B 19 O 86.9 95.1 REMARK 620 4 HOH B1016 O 126.2 77.6 88.7 REMARK 620 5 DA C 14 OP1 93.8 84.4 178.6 89.9 REMARK 620 6 DA E 15 OP2 76.1 125.6 81.9 155.4 99.5 REMARK 620 7 HOH E1035 O 154.7 154.9 93.2 79.0 86.7 78.9 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 CA A 1154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1155 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: 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: 1AF5 RELATED DB: PDB REMARK 900 GROUP I MOBILE INTRON ENDONUCLEASE 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 DBREF 2VBJ A 2 153 UNP P05725 DNE1_CHLRE 2 153 DBREF 2VBJ B 2 153 UNP P05725 DNE1_CHLRE 2 153 DBREF 2VBJ C 1 24 PDB 2VBJ 2VBJ 1 24 DBREF 2VBJ E 1 24 PDB 2VBJ 2VBJ 1 24 SEQADV 2VBJ GLU A 28 UNP P05725 LYS 28 CONFLICT SEQADV 2VBJ ARG A 38 UNP P05725 GLN 38 CONFLICT SEQADV 2VBJ LYS A 40 UNP P05725 SER 40 CONFLICT SEQADV 2VBJ THR A 42 UNP P05725 ALA 42 CONFLICT SEQADV 2VBJ LYS A 44 UNP P05725 GLN 44 CONFLICT SEQADV 2VBJ GLU A 70 UNP P05725 ARG 70 CONFLICT SEQADV 2VBJ ASN A 75 UNP P05725 ASP 75 CONFLICT SEQADV 2VBJ ARG A 85 UNP P05725 HIS 85 CONFLICT SEQADV 2VBJ THR A 109 UNP P05725 ILE 109 CONFLICT SEQADV 2VBJ GLU A 110 UNP P05725 TRP 110 CONFLICT SEQADV 2VBJ GLN A 111 UNP P05725 ARG 111 CONFLICT SEQADV 2VBJ ALA B 19 UNP P05725 GLY 19 CONFLICT SEQADV 2VBJ GLU B 28 UNP P05725 LYS 28 CONFLICT SEQADV 2VBJ SER B 33 UNP P05725 TYR 33 CONFLICT SEQADV 2VBJ ARG B 38 UNP P05725 GLN 38 CONFLICT SEQADV 2VBJ LYS B 40 UNP P05725 SER 40 CONFLICT SEQADV 2VBJ THR B 42 UNP P05725 ALA 42 CONFLICT SEQADV 2VBJ SER B 70 UNP P05725 ARG 70 CONFLICT SEQADV 2VBJ ASN B 75 UNP P05725 ASP 75 CONFLICT SEQADV 2VBJ GLU B 110 UNP P05725 TRP 110 CONFLICT SEQADV 2VBJ GLN B 111 UNP P05725 ARG 111 CONFLICT 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 GLU PRO ASN GLN SER TYR LYS PHE LYS HIS ARG LEU LYS SEQRES 4 A 152 LEU THR PHE LYS 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 GLU GLY SER VAL SER ASN TYR ILE LEU SER SEQRES 7 A 152 GLU ILE LYS PRO LEU ARG 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 THR 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 ALA ASP GLY SER ILE ILE ALA GLN ILE SEQRES 3 B 152 GLU PRO ASN GLN SER SER LYS PHE LYS HIS ARG LEU LYS 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 SER 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 C 24 DT DC DT DG DC DC DT DT DT DT DT DT DG SEQRES 2 C 24 DA DA DG DG DA DT DC DC DT DA DA SEQRES 1 E 24 DT DT DA DG DG DA DT DC DC DT DT DC DA SEQRES 2 E 24 DA DA DA DA DA DG DG DC DA DG DA HET CA A1154 1 HET CA A1155 1 HETNAM CA CALCIUM ION FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *330(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 ASP A 120 ASN A 136 1 17 HELIX 7 7 THR A 144 ARG A 149 1 6 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 ARG A 38 N GLU 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 ARG B 38 N GLU 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 SER B 70 -1 O TYR B 66 N ILE B 77 LINK O GLY A 19 CA CA A1155 1555 1555 2.35 LINK OD1 ASP A 20 CA CA A1154 1555 1555 2.75 LINK OD2 ASP A 20 CA CA A1154 1555 1555 2.49 LINK O HOH A1013 CA CA A1155 1555 1555 2.45 LINK CA CA A1154 O ALA B 19 1555 1555 2.40 LINK CA CA A1154 O HOH B1016 1555 1555 2.35 LINK CA CA A1154 OP1 DA C 14 1555 1555 2.25 LINK CA CA A1154 OP2 DA E 15 1555 1555 2.36 LINK CA CA A1154 O HOH E1035 1555 1555 2.47 LINK CA CA A1155 OD1 ASP B 20 1555 1555 2.72 LINK CA CA A1155 OD2 ASP B 20 1555 1555 2.49 LINK CA CA A1155 OP2 DA C 15 1555 1555 2.30 LINK CA CA A1155 O HOH C1051 1555 1555 2.39 LINK CA CA A1155 OP1 DA E 14 1555 1555 2.27 SITE 1 AC1 6 ASP A 20 ALA B 19 HOH B1016 DA C 14 SITE 2 AC1 6 DA E 15 HOH E1035 SITE 1 AC2 6 GLY A 19 HOH A1013 ASP B 20 DA C 15 SITE 2 AC2 6 HOH C1051 DA E 14 CRYST1 44.552 68.700 88.731 90.00 95.36 90.00 P 1 21 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 0.022446 0.000000 0.002106 0.00000 SCALE2 0.000000 0.014556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011320 0.00000