HEADER DNA BINDING PROTEIN/DNA 21-JUL-04 1U3E TITLE DNA BINDING AND CLEAVAGE BY THE HNH HOMING ENDONUCLEASE I-HMUI COMPND MOL_ID: 1; COMPND 2 MOLECULE: 36-MER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP COMPND 7 *AP*GP*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3'; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: HNH HOMING ENDONUCLEASE; COMPND 16 CHAIN: M; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: BACILLUS PHAGE SPO1; SOURCE 9 ORGANISM_TAXID: 10685; SOURCE 10 GENE: BACTERIOPHAGE SP01; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON+; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PKYB1 KEYWDS HNH CATALYTIC MOTIF, HELIX-TURN-HELIX DNA BINDING DOMAIN, PROTEIN-DNA KEYWDS 2 COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.W.SHEN,M.LANDTHALER,D.A.SHUB,B.L.STODDARD REVDAT 7 03-APR-24 1U3E 1 REMARK REVDAT 6 14-FEB-24 1U3E 1 REMARK LINK REVDAT 5 16-NOV-11 1U3E 1 VERSN HETATM REVDAT 4 15-JUN-11 1U3E 1 REMARK REVDAT 3 24-FEB-09 1U3E 1 VERSN REVDAT 2 04-JAN-05 1U3E 1 SCALE1 SCALE2 SCALE3 CRYST1 REVDAT 1 31-AUG-04 1U3E 0 JRNL AUTH B.W.SHEN,M.LANDTHALER,D.A.SHUB,B.L.STODDARD JRNL TITL DNA BINDING AND CLEAVAGE BY THE HNH HOMING ENDONUCLEASE JRNL TITL 2 I-HMUI. JRNL REF J.MOL.BIOL. V. 342 43 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15313606 JRNL DOI 10.1016/J.JMB.2004.07.032 REMARK 2 REMARK 2 RESOLUTION. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 10.0 REMARK 3 NUMBER OF REFLECTIONS : 13360 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 SET) : 0.216 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2174 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : 2.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4280 REMARK 3 BIN FREE R VALUE : 0.4650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 159 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1393 REMARK 3 NUCLEIC ACID ATOMS : 1471 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.85500 REMARK 3 B22 (A**2) : -14.82900 REMARK 3 B33 (A**2) : 7.97400 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.51 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.68 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.267 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-03; 10-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.75 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ALS; ALS REMARK 200 BEAMLINE : 5.0.2; 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796; 1.00 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111), REMARK 200 CYLINDRICALLY BENT; DOUBLE REMARK 200 CRYSTAL SI(220) REMARK 200 OPTICS : TOROIDAL FOCUSING MIRROR; REMARK 200 MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13360 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : 0.43300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB FROM SAD PHASE AND DM WITH SOLVENT FLIPPING REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG600, PH 8.75, HANGING DROP VAPOR REMARK 280 DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.15000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 124.05000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.15000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 124.05000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.15000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 124.05000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.50000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.15000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 124.05000 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 300 REMARK: ONE BIOLOGICAL ASSEMBLY PER ASYMMETRIC UNIT 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, M 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 SR SR A 415 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 The nick between Chain B and C was created by the enzyme 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 C 23 P DG C 23 OP3 -0.097 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 DG B 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 24 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT C 25 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DG C 27 O4' - C4' - C3' ANGL. DEV. = -4.1 DEGREES REMARK 500 DT C 30 O4' - C1' - C2' ANGL. DEV. = 3.4 DEGREES REMARK 500 DT C 30 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 33 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA C 35 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR M 9 23.01 -144.95 REMARK 500 PRO M 35 -164.38 -54.40 REMARK 500 ASN M 173 106.68 66.34 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 SR A 415 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 418 O REMARK 620 2 HOH A 418 O 175.8 REMARK 620 3 HOH B 405 O 117.4 66.5 REMARK 620 4 HOH B 405 O 65.6 117.4 81.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN M 413 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC B 22 O3' REMARK 620 2 DG C 23 OP3 82.0 REMARK 620 3 ASP M 74 OD1 145.8 69.0 REMARK 620 4 ASN M 96 OD1 75.7 94.7 88.7 REMARK 620 5 HOH M 420 O 131.1 99.9 73.5 150.9 REMARK 620 6 HOH M 421 O 72.2 152.8 131.5 71.2 103.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR M 418 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 404 O REMARK 620 2 LYS M 118 O 154.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR M 417 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS M 118 O REMARK 620 2 GLN M 120 O 90.8 REMARK 620 3 SR M 418 SR 56.0 116.8 REMARK 620 4 HOH M 425 O 144.9 89.9 148.9 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 MN M 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR M 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR M 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO M 398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO M 399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO M 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS M 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I3J RELATED DB: PDB REMARK 900 DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH SUBSTRATE REMARK 900 RELATED ID: 1A73 RELATED DB: PDB REMARK 900 INTRON-ENCODED ENDONUCLEASE I-PPO1 COMPLEXED WITH DNA (HIS-CYS BOX) REMARK 900 RELATED ID: 1FSJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN (NON-SPECIFIC HNH NUCLEASE) REMARK 900 RELATED ID: 1PT3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEASE-COLE& COMPLEXED WITH OCTAMER DNA (NON- REMARK 900 SPECIFIC HNH NUCLEASE) DBREF 1U3E M 1 174 UNP P34081 YG31_BPSP1 1 174 DBREF 1U3E A 2 37 PDB 1U3E 1U3E 2 37 DBREF 1U3E B 2 22 PDB 1U3E 1U3E 2 22 DBREF 1U3E C 23 37 PDB 1U3E 1U3E 23 37 SEQRES 1 A 36 DG DT DA DA DT DG DA DG DC DC DT DA DA SEQRES 2 A 36 DC DG DC DT DC DA DG DC DA DA DT DT DC SEQRES 3 A 36 DC DC DA DC DG DT DA DA DG DA SEQRES 1 B 21 DC DT DT DA DC DG DT DG DG DG DA DA DT SEQRES 2 B 21 DT DG DC DT DG DA DG DC SEQRES 1 C 15 DG DT DT DA DG DG DC DT DC DA DT DT DA SEQRES 2 C 15 DC DT SEQRES 1 M 174 MET GLU TRP LYS ASP ILE LYS GLY TYR GLU GLY HIS TYR SEQRES 2 M 174 GLN VAL SER ASN THR GLY GLU VAL TYR SER ILE LYS SER SEQRES 3 M 174 GLY LYS THR LEU LYS HIS GLN ILE PRO LYS ASP GLY TYR SEQRES 4 M 174 HIS ARG ILE GLY LEU PHE LYS GLY GLY LYS GLY LYS THR SEQRES 5 M 174 PHE GLN VAL HIS ARG LEU VAL ALA ILE HIS PHE CYS GLU SEQRES 6 M 174 GLY TYR GLU GLU GLY LEU VAL VAL ASP HIS LYS ASP GLY SEQRES 7 M 174 ASN LYS ASP ASN ASN LEU SER THR ASN LEU ARG TRP VAL SEQRES 8 M 174 THR GLN LYS ILE ASN VAL GLU ASN GLN MET SER ARG GLY SEQRES 9 M 174 THR LEU ASN VAL SER LYS ALA GLN GLN ILE ALA LYS ILE SEQRES 10 M 174 LYS ASN GLN LYS PRO ILE ILE VAL ILE SER PRO ASP GLY SEQRES 11 M 174 ILE GLU LYS GLU TYR PRO SER THR LYS CYS ALA CYS GLU SEQRES 12 M 174 GLU LEU GLY LEU THR ARG GLY LYS VAL THR ASP VAL LEU SEQRES 13 M 174 LYS GLY HIS ARG ILE HIS HIS LYS GLY TYR THR PHE ARG SEQRES 14 M 174 TYR LYS LEU ASN GLY HET SR A 414 1 HET SR A 415 1 HET EDO A 401 4 HET EDO A 402 4 HET EDO B 403 4 HET EDO C 397 4 HET MN M 413 1 HET SR M 417 1 HET SR M 418 1 HET EDO M 398 4 HET EDO M 399 4 HET EDO M 400 4 HET TRS M 404 8 HETNAM SR STRONTIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM MN MANGANESE (II) ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN EDO ETHYLENE GLYCOL HETSYN TRS TRIS BUFFER FORMUL 5 SR 4(SR 2+) FORMUL 7 EDO 7(C2 H6 O2) FORMUL 11 MN MN 2+ FORMUL 17 TRS C4 H12 N O3 1+ FORMUL 18 HOH *31(H2 O) HELIX 1 1 VAL M 55 CYS M 64 1 10 HELIX 2 2 LEU M 84 THR M 86 5 3 HELIX 3 3 THR M 92 GLY M 104 1 13 HELIX 4 4 VAL M 108 ASN M 119 1 12 HELIX 5 5 SER M 137 GLY M 146 1 10 HELIX 6 6 THR M 148 LYS M 157 1 10 SHEET 1 A 4 TRP M 3 ASP M 5 0 SHEET 2 A 4 TYR M 13 SER M 16 -1 O VAL M 15 N LYS M 4 SHEET 3 A 4 VAL M 21 SER M 23 -1 O TYR M 22 N GLN M 14 SHEET 4 A 4 THR M 29 LEU M 30 -1 O LEU M 30 N VAL M 21 SHEET 1 B 2 ARG M 41 LYS M 46 0 SHEET 2 B 2 LYS M 49 GLN M 54 -1 O PHE M 53 N ILE M 42 SHEET 1 C 2 VAL M 72 HIS M 75 0 SHEET 2 C 2 LEU M 88 VAL M 91 -1 O VAL M 91 N VAL M 72 SHEET 1 D 3 GLU M 132 TYR M 135 0 SHEET 2 D 3 ILE M 123 ILE M 126 -1 N VAL M 125 O LYS M 133 SHEET 3 D 3 THR M 167 TYR M 170 -1 O ARG M 169 N ILE M 124 LINK SR SR A 414 O HOH A 424 1555 1555 3.13 LINK SR SR A 415 O HOH A 418 1555 1555 3.38 LINK SR SR A 415 O HOH A 418 1555 3555 3.34 LINK SR SR A 415 O HOH B 405 1555 1555 3.09 LINK SR SR A 415 O HOH B 405 1555 3555 3.13 LINK O3' DC B 22 MN MN M 413 1555 1555 2.67 LINK O HOH B 404 SR SR M 418 1555 1555 3.09 LINK OP3 DG C 23 MN MN M 413 1555 1555 2.28 LINK OD1 ASP M 74 MN MN M 413 1555 1555 2.47 LINK OD1 ASN M 96 MN MN M 413 1555 1555 2.43 LINK O LYS M 118 SR SR M 417 1555 1555 2.81 LINK O LYS M 118 SR SR M 418 1555 1555 2.83 LINK O GLN M 120 SR SR M 417 1555 1555 3.02 LINK MN MN M 413 O HOH M 420 1555 1555 1.91 LINK MN MN M 413 O HOH M 421 1555 1555 1.86 LINK SR SR M 417 SR SR M 418 1555 1555 3.18 LINK SR SR M 417 O HOH M 425 1555 1555 3.17 SITE 1 AC1 6 DC B 22 DG C 23 ASP M 74 ASN M 96 SITE 2 AC1 6 HOH M 420 HOH M 421 SITE 1 AC2 1 EDO B 403 SITE 1 AC3 1 HOH B 405 SITE 1 AC4 3 LYS M 118 GLN M 120 SR M 418 SITE 1 AC5 3 HOH B 404 LYS M 118 SR M 417 SITE 1 AC6 4 DG C 27 DG C 28 GLY M 50 THR M 52 SITE 1 AC7 4 DT B 8 ARG M 160 ILE M 161 HIS M 162 SITE 1 AC8 2 PRO M 128 HOH M 427 SITE 1 AC9 5 LYS M 7 HIS M 62 CYS M 64 GLU M 65 SITE 2 AC9 5 GLU M 134 SITE 1 BC1 4 DA A 20 DG A 21 HOH A 416 DG B 16 SITE 1 BC2 5 DC A 27 DC A 28 SR A 414 DA B 12 SITE 2 BC2 5 DA B 13 SITE 1 BC3 5 TRP M 3 GLN M 14 ASP M 129 HOH M 430 SITE 2 BC3 5 HOH M 432 CRYST1 45.000 108.300 248.100 90.00 90.00 90.00 I 2 2 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 0.022222 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004031 0.00000