HEADER INTRON-ENCODED 03-DEC-98 1B24 TITLE I-DMOI, INTRON-ENCODED ENDONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMING ENDONUCLEASE I-DMOI; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SELENOMETHIONYL PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFUROCOCCUS MOBILIS; SOURCE 3 ORGANISM_TAXID: 2275; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: DL41(DE3); SOURCE 7 OTHER_DETAILS: SELENOMETHIONINE AUXOTROPH KEYWDS INTRON-ENCODED, ENDONUCLEASE, HOMING, THERMOSTABLE EXPDTA X-RAY DIFFRACTION AUTHOR P.VAN ROEY,G.H.SILVA REVDAT 5 13-NOV-24 1B24 1 REMARK REVDAT 4 21-DEC-22 1B24 1 COMPND SOURCE DBREF SEQADV REVDAT 4 2 1 LINK REVDAT 3 24-FEB-09 1B24 1 VERSN REVDAT 2 01-APR-03 1B24 1 JRNL REVDAT 1 24-MAR-99 1B24 0 JRNL AUTH G.H.SILVA,J.Z.DALGAARD,M.BELFORT,P.VAN ROEY JRNL TITL CRYSTAL STRUCTURE OF THE THERMOSTABLE ARCHAEAL JRNL TITL 2 INTRON-ENCODED ENDONUCLEASE I-DMOI. JRNL REF J.MOL.BIOL. V. 286 1123 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10047486 JRNL DOI 10.1006/JMBI.1998.2519 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 8878 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) : 0.218 REMARK 3 FREE R VALUE : 0.324 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 887 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 737 REMARK 3 BIN R VALUE (WORKING SET) : 0.2996 REMARK 3 BIN FREE R VALUE : 0.3613 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 80 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 : 1427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.285 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.23 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.609 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : TOPH19.PEP REMARK 3 PARAMETER FILE 4 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-98. REMARK 100 THE DEPOSITION ID IS D_1000000208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9300,0.9785,0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8884 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.3000 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) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 24.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: MAD DATA TREATED AS A SPECIAL CASE OF MIR REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOR-DIFFUSION METHOD: REMARK 280 4UL I-DMOI PROTEIN 1UL 20MM N-OCTYL-B- GLUCOPYRANOSIDE 4UL REMARK 280 PRECIPITATING BUFFER: 30% PEG 3350 200MM SODIUM ACETATE 100MM REMARK 280 TRIS-HCL PH 8.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 46.86500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.86500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.61000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 1 REMARK 465 HIS A 2 REMARK 465 ASN A 3 REMARK 465 ASN A 4 REMARK 465 GLU A 5 REMARK 465 ASN A 6 REMARK 465 SER A 180 REMARK 465 HIS A 181 REMARK 465 LEU A 182 REMARK 465 ASN A 183 REMARK 465 PRO A 184 REMARK 465 LEU A 185 REMARK 465 PRO A 186 REMARK 465 PRO A 187 REMARK 465 GLU A 188 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 SER A 179 CA C O CB OG 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 A 210 O HOH A 255 1.86 REMARK 500 O HOH A 229 O HOH A 234 1.88 REMARK 500 O HOH A 237 O HOH A 257 1.95 REMARK 500 O HOH A 203 O HOH A 230 2.03 REMARK 500 O HOH A 230 O HOH A 255 2.19 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 ASP A 21 88.02 -158.15 REMARK 500 TYR A 29 -77.37 -91.46 REMARK 500 HIS A 51 -62.66 -130.99 REMARK 500 THR A 76 -38.74 84.47 REMARK 500 ARG A 97 42.29 -96.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 1B24 A 1 188 UNP P21505 DMO1_DESMO 1 188 SEQRES 1 A 188 MET HIS ASN ASN GLU ASN VAL SER GLY ILE SER ALA TYR SEQRES 2 A 188 LEU LEU GLY LEU ILE ILE GLY ASP GLY GLY LEU TYR LYS SEQRES 3 A 188 LEU LYS TYR LYS GLY ASN ARG SER GLU TYR ARG VAL VAL SEQRES 4 A 188 ILE THR GLN LYS SER GLU ASN LEU ILE LYS GLN HIS ILE SEQRES 5 A 188 ALA PRO LEU MSE GLN PHE LEU ILE ASP GLU LEU ASN VAL SEQRES 6 A 188 LYS SER LYS ILE GLN ILE VAL LYS GLY ASP THR ARG TYR SEQRES 7 A 188 GLU LEU ARG VAL SER SER LYS LYS LEU TYR TYR TYR PHE SEQRES 8 A 188 ALA ASN MSE LEU GLU ARG ILE ARG LEU PHE ASN MSE ARG SEQRES 9 A 188 GLU GLN ILE ALA PHE ILE LYS GLY LEU TYR VAL ALA GLU SEQRES 10 A 188 GLY ASP LYS THR LEU LYS ARG LEU ARG ILE TRP ASN LYS SEQRES 11 A 188 ASN LYS ALA LEU LEU GLU ILE VAL SER ARG TRP LEU ASN SEQRES 12 A 188 ASN LEU GLY VAL ARG ASN THR ILE HIS LEU ASP ASP HIS SEQRES 13 A 188 ARG HIS GLY VAL TYR VAL LEU ASN ILE SER LEU ARG ASP SEQRES 14 A 188 ARG ILE LYS PHE VAL HIS THR ILE LEU SER SER HIS LEU SEQRES 15 A 188 ASN PRO LEU PRO PRO GLU MODRES 1B24 MSE A 56 MET MODIFIED RESIDUE MODRES 1B24 MSE A 94 MET MODIFIED RESIDUE MODRES 1B24 MSE A 103 MET MODIFIED RESIDUE HET MSE A 56 8 HET MSE A 94 8 HET MSE A 103 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *78(H2 O) HELIX 1 1 SER A 8 GLY A 20 1 13 HELIX 2 2 GLU A 45 GLN A 50 1 6 HELIX 3 3 PRO A 54 GLU A 62 5 9 HELIX 4 4 LYS A 85 ALA A 92 1 8 HELIX 5 5 ILE A 98 LEU A 100 5 3 HELIX 6 6 GLU A 105 GLU A 117 1 13 HELIX 7 7 LYS A 132 LEU A 145 1 14 HELIX 8 8 LEU A 167 THR A 176 5 10 SHEET 1 A 4 GLY A 22 LYS A 28 0 SHEET 2 A 4 SER A 34 GLN A 42 -1 N VAL A 39 O GLY A 23 SHEET 3 A 4 TYR A 78 SER A 83 -1 N VAL A 82 O VAL A 38 SHEET 4 A 4 GLN A 70 LYS A 73 -1 N VAL A 72 O GLU A 79 SHEET 1 B 3 ARG A 126 ASN A 129 0 SHEET 2 B 3 VAL A 160 ILE A 165 -1 N LEU A 163 O ILE A 127 SHEET 3 B 3 ASN A 149 ASP A 155 -1 N ASP A 155 O VAL A 160 LINK C LEU A 55 N MSE A 56 1555 1555 1.33 LINK C MSE A 56 N GLN A 57 1555 1555 1.33 LINK C ASN A 93 N MSE A 94 1555 1555 1.34 LINK C MSE A 94 N LEU A 95 1555 1555 1.33 LINK C ASN A 102 N MSE A 103 1555 1555 1.32 LINK C MSE A 103 N ARG A 104 1555 1555 1.33 CRYST1 93.730 37.220 56.280 90.00 112.80 90.00 C 1 2 1 4 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 0.010669 0.000000 0.004485 0.00000 SCALE2 0.000000 0.026867 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019274 0.00000