PDB Short entry for 1M0D HEADER HYDROLASE 12-JUN-02 1M0D TITLE CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I WITH A WILD-TYPE TITLE 2 ACTIVE SITE AND BOUND MANGANESE IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDODEOXYRIBONUCLEASE I; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 12-149; COMPND 5 SYNONYM: ENDONUCLEASE; COMPND 6 EC: 3.1.21.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T7; SOURCE 3 ORGANISM_TAXID: 10760; SOURCE 4 GENE: ENDONUCLEASE I; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET 19B KEYWDS HOLLIDAY JUNCTION RESOLVASE, HOMODIMER, DOMAIN SWAPPED, COMPOSITE KEYWDS 2 ACTIVE SITE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.HADDEN,A.C.DECLAIS,S.E.PHILLIPS,D.M.LILLEY REVDAT 3 14-FEB-24 1M0D 1 REMARK LINK REVDAT 2 24-FEB-09 1M0D 1 VERSN REVDAT 1 10-JUL-02 1M0D 0 JRNL AUTH J.M.HADDEN,A.C.DECLAIS,S.E.PHILLIPS,D.M.LILLEY JRNL TITL METAL IONS BOUND AT THE ACTIVE SITE OF THE JRNL TITL 2 JUNCTION-RESOLVING ENZYME T7 ENDONUCLEASE I. JRNL REF EMBO J. V. 21 3505 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12093751 JRNL DOI 10.1093/EMBOJ/CDF337 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1676632.530 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 81189 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) : 0.210 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4083 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7559 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 400 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4125 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 473 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.63000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : -4.14000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 59.33 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD TARGET USED AS REMARK 3 IMPLEMENTED IN CNS REMARK 4 REMARK 4 1M0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE (220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81257 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1FZR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM SULPHATE, SODIUM REMARK 280 CHLORIDE, TRIS HCL, PH 7.2, VAPOR DIFFUSION, HANGING DROP. SEEDS REMARK 280 OF E65K MUTANT USED, TEMPERATURE 291K 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 61.90500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 61.90500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.98000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: ENDONUCLEASE I IS ACTIVE AS A HOMODIMER. THERE ARE 2 REMARK 300 HOMODIMERS IN THE ASYMMETRIC UNIT. CHAINS A AND B FORM ONE REMARK 300 HOMODIMER. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 VAL A 12 REMARK 465 GLY A 13 REMARK 465 ALA A 14 REMARK 465 PHE A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 146 REMARK 465 GLY A 147 REMARK 465 LYS A 148 REMARK 465 LYS A 149 REMARK 465 VAL B 12 REMARK 465 GLY B 13 REMARK 465 ALA B 14 REMARK 465 PHE B 15 REMARK 465 ARG B 16 REMARK 465 GLY B 146 REMARK 465 GLY B 147 REMARK 465 LYS B 148 REMARK 465 LYS B 149 REMARK 465 VAL C 12 REMARK 465 GLY C 13 REMARK 465 ALA C 14 REMARK 465 PHE C 15 REMARK 465 ARG C 16 REMARK 465 GLY C 146 REMARK 465 GLY C 147 REMARK 465 LYS C 148 REMARK 465 LYS C 149 REMARK 465 VAL D 12 REMARK 465 GLY D 13 REMARK 465 ALA D 14 REMARK 465 PHE D 15 REMARK 465 ARG D 16 REMARK 465 GLY D 146 REMARK 465 GLY D 147 REMARK 465 LYS D 148 REMARK 465 LYS D 149 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 25 CG CD CE NZ REMARK 470 GLN A 26 CG CD OE1 NE2 REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 GLU A 136 CG CD OE1 OE2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 ARG A 144 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 LYS B 30 CG CD CE NZ REMARK 470 LYS B 143 CG CD CE NZ REMARK 470 LYS C 33 CG CD CE NZ REMARK 470 GLU C 71 CG CD OE1 OE2 REMARK 470 ARG C 82 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 87 CG CD OE1 OE2 REMARK 470 LYS C 103 CG CD CE NZ REMARK 470 LYS C 115 CG CD CE NZ REMARK 470 LYS C 131 CG CD CE NZ REMARK 470 LYS C 135 CG CD CE NZ REMARK 470 GLU C 136 CG CD OE1 OE2 REMARK 470 VAL C 137 CG1 CG2 REMARK 470 PRO C 138 CG CD REMARK 470 PHE C 139 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP C 140 CG OD1 OD2 REMARK 470 LEU C 142 CG CD1 CD2 REMARK 470 LYS C 143 CG CD CE NZ REMARK 470 ARG C 144 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 145 CG CD CE NZ REMARK 470 ASP D 21 CG OD1 OD2 REMARK 470 LYS D 25 CG CD CE NZ REMARK 470 GLU D 28 CG CD OE1 OE2 REMARK 470 LYS D 30 CG CD CE NZ REMARK 470 ILE D 32 CG1 CG2 CD1 REMARK 470 LYS D 33 CG CD CE NZ REMARK 470 GLU D 38 CG CD OE1 OE2 REMARK 470 TRP D 39 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP D 39 CZ3 CH2 REMARK 470 LYS D 40 CG CD CE NZ REMARK 470 ARG D 98 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 131 CG CD CE NZ REMARK 470 LYS D 145 CG CD CE NZ 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 C 1004 O HOH C 1008 2.17 REMARK 500 O HOH A 1078 O HOH D 1092 2.17 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 123 -50.32 63.50 REMARK 500 LYS B 123 -47.56 69.74 REMARK 500 LYS C 103 -54.62 -25.41 REMARK 500 LYS C 123 -54.07 61.99 REMARK 500 PRO C 138 70.65 -66.55 REMARK 500 SER D 29 -6.40 -59.26 REMARK 500 GLU D 37 37.38 82.41 REMARK 500 GLU D 38 33.33 -95.10 REMARK 500 TRP D 39 125.59 -174.23 REMARK 500 LYS D 123 -52.64 69.24 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 MN A 1 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 55 OD2 REMARK 620 2 GLU A 65 OE2 86.0 REMARK 620 3 THR A 66 O 92.5 88.9 REMARK 620 4 HOH A1002 O 96.9 94.1 170.2 REMARK 620 5 HOH A1003 O 178.2 92.3 88.1 82.5 REMARK 620 6 HOH B1003 O 88.4 169.2 82.0 95.7 93.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 2 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 55 OD1 REMARK 620 2 HOH A1002 O 89.8 REMARK 620 3 HOH A1004 O 101.0 87.8 REMARK 620 4 HOH A1005 O 157.2 73.0 93.5 REMARK 620 5 HOH B1004 O 106.5 163.0 84.4 92.3 REMARK 620 6 HOH B1005 O 77.4 99.0 172.9 90.2 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 3 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1006 O REMARK 620 2 ASP B 55 OD2 91.5 REMARK 620 3 GLU B 65 OE2 173.5 87.4 REMARK 620 4 THR B 66 O 82.5 91.4 91.1 REMARK 620 5 HOH B1006 O 90.1 101.1 96.5 165.7 REMARK 620 6 HOH B1007 O 88.1 179.6 93.0 88.6 78.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 4 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1007 O REMARK 620 2 HOH A1008 O 103.0 REMARK 620 3 ASP B 55 OD1 116.6 79.9 REMARK 620 4 HOH B1006 O 148.6 95.4 91.4 REMARK 620 5 HOH B1008 O 72.2 175.0 103.4 88.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 5 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 55 OD2 REMARK 620 2 ASP C 55 OD1 55.8 REMARK 620 3 GLU C 65 OE2 91.1 115.9 REMARK 620 4 THR C 66 O 100.3 140.0 93.9 REMARK 620 5 HOH C1004 O 123.8 73.4 90.6 135.6 REMARK 620 6 HOH C1005 O 178.4 124.6 90.1 78.5 57.3 REMARK 620 7 HOH C1006 O 103.2 76.9 164.9 79.0 85.4 75.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 6 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 55 OD1 REMARK 620 2 HOH C1004 O 93.6 REMARK 620 3 HOH C1007 O 111.4 94.0 REMARK 620 4 HOH C1008 O 141.3 55.0 94.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 7 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C1009 O REMARK 620 2 ASP D 55 OD2 90.4 REMARK 620 3 GLU D 65 OE2 171.4 87.5 REMARK 620 4 THR D 66 O 83.2 93.9 88.7 REMARK 620 5 HOH D1005 O 96.4 105.6 92.2 160.4 REMARK 620 6 HOH D1006 O 90.8 178.8 91.4 86.1 74.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 8 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C1010 O REMARK 620 2 HOH C1011 O 97.6 REMARK 620 3 ASP D 55 OD1 108.5 88.2 REMARK 620 4 HOH D1005 O 149.2 98.5 98.1 REMARK 620 5 HOH D1007 O 79.3 173.5 98.2 81.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN D 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN D 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FZR RELATED DB: PDB REMARK 900 BACTERIOPHAGE T7 ENDONUCLEASE I E65K MUTANT REMARK 900 RELATED ID: 1M0I RELATED DB: PDB REMARK 900 BACTERIOPHAGE T7 ENDONUCLEASE I WITH A WILD-TYPE ACTIVE SITE DBREF 1M0D A 12 149 UNP P00641 ENRN_BPT7 12 149 DBREF 1M0D B 12 149 UNP P00641 ENRN_BPT7 12 149 DBREF 1M0D C 12 149 UNP P00641 ENRN_BPT7 12 149 DBREF 1M0D D 12 149 UNP P00641 ENRN_BPT7 12 149 SEQRES 1 A 138 VAL GLY ALA PHE ARG SER GLY LEU GLU ASP LYS VAL SER SEQRES 2 A 138 LYS GLN LEU GLU SER LYS GLY ILE LYS PHE GLU TYR GLU SEQRES 3 A 138 GLU TRP LYS VAL PRO TYR VAL ILE PRO ALA SER ASN HIS SEQRES 4 A 138 THR TYR THR PRO ASP PHE LEU LEU PRO ASN GLY ILE PHE SEQRES 5 A 138 VAL GLU THR LYS GLY LEU TRP GLU SER ASP ASP ARG LYS SEQRES 6 A 138 LYS HIS LEU LEU ILE ARG GLU GLN HIS PRO GLU LEU ASP SEQRES 7 A 138 ILE ARG ILE VAL PHE SER SER SER ARG THR LYS LEU TYR SEQRES 8 A 138 LYS GLY SER PRO THR SER TYR GLY GLU PHE CYS GLU LYS SEQRES 9 A 138 HIS GLY ILE LYS PHE ALA ASP LYS LEU ILE PRO ALA GLU SEQRES 10 A 138 TRP ILE LYS GLU PRO LYS LYS GLU VAL PRO PHE ASP ARG SEQRES 11 A 138 LEU LYS ARG LYS GLY GLY LYS LYS SEQRES 1 B 138 VAL GLY ALA PHE ARG SER GLY LEU GLU ASP LYS VAL SER SEQRES 2 B 138 LYS GLN LEU GLU SER LYS GLY ILE LYS PHE GLU TYR GLU SEQRES 3 B 138 GLU TRP LYS VAL PRO TYR VAL ILE PRO ALA SER ASN HIS SEQRES 4 B 138 THR TYR THR PRO ASP PHE LEU LEU PRO ASN GLY ILE PHE SEQRES 5 B 138 VAL GLU THR LYS GLY LEU TRP GLU SER ASP ASP ARG LYS SEQRES 6 B 138 LYS HIS LEU LEU ILE ARG GLU GLN HIS PRO GLU LEU ASP SEQRES 7 B 138 ILE ARG ILE VAL PHE SER SER SER ARG THR LYS LEU TYR SEQRES 8 B 138 LYS GLY SER PRO THR SER TYR GLY GLU PHE CYS GLU LYS SEQRES 9 B 138 HIS GLY ILE LYS PHE ALA ASP LYS LEU ILE PRO ALA GLU SEQRES 10 B 138 TRP ILE LYS GLU PRO LYS LYS GLU VAL PRO PHE ASP ARG SEQRES 11 B 138 LEU LYS ARG LYS GLY GLY LYS LYS SEQRES 1 C 138 VAL GLY ALA PHE ARG SER GLY LEU GLU ASP LYS VAL SER SEQRES 2 C 138 LYS GLN LEU GLU SER LYS GLY ILE LYS PHE GLU TYR GLU SEQRES 3 C 138 GLU TRP LYS VAL PRO TYR VAL ILE PRO ALA SER ASN HIS SEQRES 4 C 138 THR TYR THR PRO ASP PHE LEU LEU PRO ASN GLY ILE PHE SEQRES 5 C 138 VAL GLU THR LYS GLY LEU TRP GLU SER ASP ASP ARG LYS SEQRES 6 C 138 LYS HIS LEU LEU ILE ARG GLU GLN HIS PRO GLU LEU ASP SEQRES 7 C 138 ILE ARG ILE VAL PHE SER SER SER ARG THR LYS LEU TYR SEQRES 8 C 138 LYS GLY SER PRO THR SER TYR GLY GLU PHE CYS GLU LYS SEQRES 9 C 138 HIS GLY ILE LYS PHE ALA ASP LYS LEU ILE PRO ALA GLU SEQRES 10 C 138 TRP ILE LYS GLU PRO LYS LYS GLU VAL PRO PHE ASP ARG SEQRES 11 C 138 LEU LYS ARG LYS GLY GLY LYS LYS SEQRES 1 D 138 VAL GLY ALA PHE ARG SER GLY LEU GLU ASP LYS VAL SER SEQRES 2 D 138 LYS GLN LEU GLU SER LYS GLY ILE LYS PHE GLU TYR GLU SEQRES 3 D 138 GLU TRP LYS VAL PRO TYR VAL ILE PRO ALA SER ASN HIS SEQRES 4 D 138 THR TYR THR PRO ASP PHE LEU LEU PRO ASN GLY ILE PHE SEQRES 5 D 138 VAL GLU THR LYS GLY LEU TRP GLU SER ASP ASP ARG LYS SEQRES 6 D 138 LYS HIS LEU LEU ILE ARG GLU GLN HIS PRO GLU LEU ASP SEQRES 7 D 138 ILE ARG ILE VAL PHE SER SER SER ARG THR LYS LEU TYR SEQRES 8 D 138 LYS GLY SER PRO THR SER TYR GLY GLU PHE CYS GLU LYS SEQRES 9 D 138 HIS GLY ILE LYS PHE ALA ASP LYS LEU ILE PRO ALA GLU SEQRES 10 D 138 TRP ILE LYS GLU PRO LYS LYS GLU VAL PRO PHE ASP ARG SEQRES 11 D 138 LEU LYS ARG LYS GLY GLY LYS LYS HET MN A 1 1 HET MN A 2 1 HET SO4 A1001 5 HET MN B 3 1 HET MN B 4 1 HET SO4 B1002 5 HET MN C 5 1 HET MN C 6 1 HET SO4 C1003 5 HET MN D 7 1 HET MN D 8 1 HET SO4 D1004 5 HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 5 MN 8(MN 2+) FORMUL 7 SO4 4(O4 S 2-) FORMUL 17 HOH *473(H2 O) HELIX 1 1 SER A 17 LYS A 30 1 14 HELIX 2 2 GLU A 71 HIS A 85 1 15 HELIX 3 3 SER A 108 GLY A 117 1 10 HELIX 4 4 PRO A 126 GLU A 132 1 7 HELIX 5 5 PRO A 138 LEU A 142 5 5 HELIX 6 6 SER B 17 LYS B 30 1 14 HELIX 7 7 GLU B 71 HIS B 85 1 15 HELIX 8 8 SER B 108 GLY B 117 1 10 HELIX 9 9 PRO B 126 GLU B 132 1 7 HELIX 10 10 PRO B 138 LEU B 142 5 5 HELIX 11 11 SER C 17 LYS C 30 1 14 HELIX 12 12 GLU C 71 HIS C 85 1 15 HELIX 13 13 SER C 108 HIS C 116 1 9 HELIX 14 14 PRO C 126 LYS C 131 1 6 HELIX 15 15 PRO C 138 LEU C 142 5 5 HELIX 16 16 SER D 17 SER D 29 1 13 HELIX 17 17 GLU D 71 HIS D 85 1 15 HELIX 18 18 SER D 108 GLY D 117 1 10 HELIX 19 19 PRO D 126 LYS D 131 1 6 HELIX 20 20 PRO D 138 LEU D 142 5 5 SHEET 1 A 5 GLU A 35 TYR A 36 0 SHEET 2 A 5 PHE B 56 LEU B 57 -1 O LEU B 57 N GLU A 35 SHEET 3 A 5 PHE B 63 LYS B 67 -1 O VAL B 64 N PHE B 56 SHEET 4 A 5 ILE B 90 PHE B 94 1 O VAL B 93 N LYS B 67 SHEET 5 A 5 PHE B 120 ASP B 122 1 O ALA B 121 N PHE B 94 SHEET 1 B 3 SER B 48 TYR B 52 0 SHEET 2 B 3 TRP A 39 ILE A 45 -1 N VAL A 41 O TYR B 52 SHEET 3 B 3 LYS B 143 ARG B 144 -1 O LYS B 143 N LYS A 40 SHEET 1 C 3 SER A 48 TYR A 52 0 SHEET 2 C 3 TRP B 39 ILE B 45 -1 O VAL B 41 N TYR A 52 SHEET 3 C 3 LYS A 143 ARG A 144 -1 N LYS A 143 O LYS B 40 SHEET 1 D 5 PHE A 120 ASP A 122 0 SHEET 2 D 5 ILE A 90 PHE A 94 1 N PHE A 94 O ALA A 121 SHEET 3 D 5 PHE A 63 LYS A 67 1 N GLU A 65 O ARG A 91 SHEET 4 D 5 PHE A 56 LEU A 57 -1 N PHE A 56 O VAL A 64 SHEET 5 D 5 GLU B 35 TYR B 36 -1 O GLU B 35 N LEU A 57 SHEET 1 E 5 GLU C 35 TYR C 36 0 SHEET 2 E 5 PHE D 56 LEU D 57 -1 O LEU D 57 N GLU C 35 SHEET 3 E 5 PHE D 63 LYS D 67 -1 O VAL D 64 N PHE D 56 SHEET 4 E 5 ILE D 90 PHE D 94 1 O ARG D 91 N GLU D 65 SHEET 5 E 5 PHE D 120 ASP D 122 1 O ALA D 121 N PHE D 94 SHEET 1 F 3 SER D 48 TYR D 52 0 SHEET 2 F 3 TRP C 39 ILE C 45 -1 N VAL C 41 O TYR D 52 SHEET 3 F 3 LYS D 143 ARG D 144 -1 O LYS D 143 N LYS C 40 SHEET 1 G 2 SER C 48 TYR C 52 0 SHEET 2 G 2 VAL D 41 ILE D 45 -1 O VAL D 41 N TYR C 52 SHEET 1 H 4 PHE C 56 LEU C 57 0 SHEET 2 H 4 PHE C 63 LYS C 67 -1 O VAL C 64 N PHE C 56 SHEET 3 H 4 ILE C 90 PHE C 94 1 O ARG C 91 N GLU C 65 SHEET 4 H 4 PHE C 120 ASP C 122 1 O ALA C 121 N PHE C 94 LINK MN MN A 1 OD2 ASP A 55 1555 1555 2.13 LINK MN MN A 1 OE2 GLU A 65 1555 1555 2.07 LINK MN MN A 1 O THR A 66 1555 1555 2.22 LINK MN MN A 1 O HOH A1002 1555 1555 2.17 LINK MN MN A 1 O HOH A1003 1555 1555 2.41 LINK MN MN A 1 O HOH B1003 1555 1555 2.26 LINK MN MN A 2 OD1 ASP A 55 1555 1555 2.20 LINK MN MN A 2 O HOH A1002 1555 1555 1.82 LINK MN MN A 2 O HOH A1004 1555 1555 2.24 LINK MN MN A 2 O HOH A1005 1555 1555 2.46 LINK MN MN A 2 O HOH B1004 1555 1555 2.16 LINK MN MN A 2 O HOH B1005 1555 1555 2.20 LINK O HOH A1006 MN MN B 3 1555 1555 2.17 LINK O HOH A1007 MN MN B 4 1555 1555 2.53 LINK O HOH A1008 MN MN B 4 1555 1555 2.29 LINK MN MN B 3 OD2 ASP B 55 1555 1555 2.20 LINK MN MN B 3 OE2 GLU B 65 1555 1555 2.10 LINK MN MN B 3 O THR B 66 1555 1555 2.26 LINK MN MN B 3 O HOH B1006 1555 1555 2.08 LINK MN MN B 3 O HOH B1007 1555 1555 2.32 LINK MN MN B 4 OD1 ASP B 55 1555 1555 2.16 LINK MN MN B 4 O HOH B1006 1555 1555 1.92 LINK MN MN B 4 O HOH B1008 1555 1555 2.50 LINK MN MN C 5 OD2 ASP C 55 1555 1555 1.68 LINK MN MN C 5 OD1 ASP C 55 1555 1555 2.64 LINK MN MN C 5 OE2 GLU C 65 1555 1555 2.21 LINK MN MN C 5 O THR C 66 1555 1555 2.38 LINK MN MN C 5 O HOH C1004 1555 1555 2.67 LINK MN MN C 5 O HOH C1005 1555 1555 1.65 LINK MN MN C 5 O HOH C1006 1555 1555 2.40 LINK MN MN C 6 OD1 ASP C 55 1555 1555 2.02 LINK MN MN C 6 O HOH C1004 1555 1555 2.32 LINK MN MN C 6 O HOH C1007 1555 1555 2.32 LINK MN MN C 6 O HOH C1008 1555 1555 2.38 LINK O HOH C1009 MN MN D 7 1555 1555 2.23 LINK O HOH C1010 MN MN D 8 1555 1555 2.57 LINK O HOH C1011 MN MN D 8 1555 1555 2.31 LINK MN MN D 7 OD2 ASP D 55 1555 1555 2.10 LINK MN MN D 7 OE2 GLU D 65 1555 1555 2.07 LINK MN MN D 7 O THR D 66 1555 1555 2.29 LINK MN MN D 7 O HOH D1005 1555 1555 2.23 LINK MN MN D 7 O HOH D1006 1555 1555 2.28 LINK MN MN D 8 OD1 ASP D 55 1555 1555 2.09 LINK MN MN D 8 O HOH D1005 1555 1555 1.97 LINK MN MN D 8 O HOH D1007 1555 1555 2.50 SITE 1 AC1 7 MN A 2 ASP A 55 GLU A 65 THR A 66 SITE 2 AC1 7 HOH A1002 HOH A1003 HOH B1003 SITE 1 AC2 8 MN A 1 ASP A 55 HOH A1002 HOH A1004 SITE 2 AC2 8 HOH A1005 GLU B 37 HOH B1004 HOH B1005 SITE 1 AC3 7 HOH A1006 MN B 4 ASP B 55 GLU B 65 SITE 2 AC3 7 THR B 66 HOH B1006 HOH B1007 SITE 1 AC4 7 GLU A 37 HOH A1007 HOH A1008 MN B 3 SITE 2 AC4 7 ASP B 55 HOH B1006 HOH B1008 SITE 1 AC5 7 MN C 6 ASP C 55 GLU C 65 THR C 66 SITE 2 AC5 7 HOH C1004 HOH C1005 HOH C1006 SITE 1 AC6 5 MN C 5 ASP C 55 HOH C1004 HOH C1007 SITE 2 AC6 5 HOH C1008 SITE 1 AC7 7 HOH C1009 MN D 8 ASP D 55 GLU D 65 SITE 2 AC7 7 THR D 66 HOH D1005 HOH D1006 SITE 1 AC8 6 HOH C1010 HOH C1011 MN D 7 ASP D 55 SITE 2 AC8 6 HOH D1005 HOH D1007 SITE 1 AC9 6 LYS A 67 GLY A 68 HOH A1003 HOH A1062 SITE 2 AC9 6 SER B 17 HOH B1003 SITE 1 BC1 7 SER A 17 HOH A1006 LYS B 67 GLY B 68 SITE 2 BC1 7 HOH B1007 HOH B1051 HOH B1146 SITE 1 BC2 6 THR C 66 LYS C 67 GLY C 68 HOH C1005 SITE 2 BC2 6 HOH C1006 SER D 17 SITE 1 BC3 9 SER C 17 HOH C1009 LYS D 67 GLY D 68 SITE 2 BC3 9 HOH D1006 HOH D1032 HOH D1127 HOH D1142 SITE 3 BC3 9 HOH D1147 CRYST1 123.810 133.960 61.460 90.00 90.00 90.00 P 21 21 2 16 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 0.008077 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016271 0.00000