HEADER ENDONUCLEASE 07-NOV-01 1GPP TITLE CRYSTAL STRUCTURE OF THE S.CEREVISIAE HOMING ENDONUCLEASE PI-SCEI TITLE 2 DOMAIN I COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE PI-SCEI; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEIN SPLICING DOMAIN, RESIDUES 284-466,693-736, SEE COMPND 5 REMARK 999; COMPND 6 SYNONYM: HOMING ENDONUCLEASE PI-SCEI, VMA1-DERIVED ENDONUCLEASE; COMPND 7 EC: 3.6.3.14; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: GLY183 LINKS ILE182 AND ALA410, WHERE IN THE FULL COMPND 11 LENGTH PROTEIN IS DOMAIN II SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDONUCLEASE, HOMING, PROTEIN SPLICING EXPDTA X-RAY DIFFRACTION AUTHOR E.WERNER,W.WENDE,A.PINGOUD,U.HEINEMANN REVDAT 4 13-DEC-23 1GPP 1 REMARK REVDAT 3 24-JUL-19 1GPP 1 REMARK REVDAT 2 24-FEB-09 1GPP 1 VERSN REVDAT 1 19-SEP-02 1GPP 0 JRNL AUTH E.WERNER,W.WENDE,A.PINGOUD,U.HEINEMANN JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF DOMAIN I OF THE JRNL TITL 2 SACCHAROMYCES CEREVISIAE HOMING ENDONUCLEASE PI-SCEI JRNL REF NUCLEIC ACIDS RES. V. 30 3962 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 12235380 JRNL DOI 10.1093/NAR/GKF523 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 47840 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 3744 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2498 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 197 REMARK 3 BIN FREE R VALUE : 0.2370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1726 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.97000 REMARK 3 B22 (A**2) : 1.92000 REMARK 3 B33 (A**2) : -0.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.249 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1769 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1610 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2391 ; 1.834 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3751 ; 0.952 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 216 ; 5.345 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 327 ;15.100 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 272 ; 0.159 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1952 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 363 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 318 ; 0.262 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1537 ; 0.200 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 275 ; 0.241 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 3 ; 0.089 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.245 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.192 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.440 ; 0.500 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): 1087 ; 2.004 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1764 ; 2.979 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 682 ; 3.838 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 626 ; 5.758 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. FIRST 8 RESIDUES OF THE HIS-TAG AND RESIDUES 55 - 66 REMARK 3 ARE NOT VISIBLE IN ELECTRON DENSITY. REMARK 4 REMARK 4 1GPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1290008824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8453 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51602 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.16400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1VDE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG4000, 0.1 M SODIUM CITRATE PH REMARK 280 5.6, 0.2 M NH4-ACETATE, PH 4.80 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 51.42800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.79750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.42800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.79750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 MUTATIONS: ARG327SER, VAL350MET, ILE415VAL, LEU466GLY 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 -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 GLY A -3 REMARK 465 GLN A 55 REMARK 465 HIS A 56 REMARK 465 ARG A 57 REMARK 465 ALA A 58 REMARK 465 HIS A 59 REMARK 465 LYS A 60 REMARK 465 SER A 61 REMARK 465 ASP A 62 REMARK 465 SER A 63 REMARK 465 SER A 64 REMARK 465 ARG A 65 REMARK 465 GLU A 66 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 26 CE NZ REMARK 480 LYS A 39 CE NZ REMARK 480 LYS A 53 CE NZ REMARK 480 SER A 54 OG REMARK 480 MET A 67 CB CG SD CE REMARK 480 LYS A 97 CE NZ REMARK 480 LYS A 113 CE NZ REMARK 480 LYS A 124 NZ REMARK 480 LYS A 128 NZ REMARK 480 ARG A 138 NH2 REMARK 480 LYS A 152 CG CD CE NZ REMARK 480 LYS A 173 NZ REMARK 480 GLU A 422 CG CD OE1 OE2 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 2171 O HOH A 2172 0.97 REMARK 500 O HOH A 2029 O HOH A 2030 1.17 REMARK 500 NZ LYS A 72 O HOH A 2118 1.59 REMARK 500 O HOH A 2065 O HOH A 2066 1.72 REMARK 500 O HOH A 2163 O HOH A 2164 1.88 REMARK 500 O HOH A 2211 O HOH A 2212 1.89 REMARK 500 O HOH A 2294 O HOH A 2303 2.00 REMARK 500 O HOH A 2162 O HOH A 2165 2.03 REMARK 500 O ALA A 410 O HOH A 2258 2.04 REMARK 500 O HOH A 2066 O HOH A 2262 2.09 REMARK 500 SG CYS A 416 O HOH A 2255 2.10 REMARK 500 O HOH A 2067 O HOH A 2211 2.16 REMARK 500 O HOH A 2098 O HOH A 2269 2.17 REMARK 500 O HOH A 2043 O HOH A 2045 2.18 REMARK 500 OE1 GLU A 141 O HOH A 2207 2.19 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 O ARG A 42 NZ LYS A 72 4555 2.04 REMARK 500 O HOH A 2115 O HOH A 2153 2655 2.06 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 LYS A 26 CD LYS A 26 CE 0.151 REMARK 500 MET A 67 CB MET A 67 CG -0.473 REMARK 500 LYS A 128 CE LYS A 128 NZ 0.192 REMARK 500 ARG A 138 CZ ARG A 138 NH2 -0.082 REMARK 500 GLU A 422 CB GLU A 422 CG 0.143 REMARK 500 GLU A 422 CD GLU A 422 OE1 0.208 REMARK 500 GLU A 422 CD GLU A 422 OE2 0.211 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 138 NH1 - CZ - NH2 ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = 8.7 DEGREES REMARK 500 ASP A 441 CB - CG - OD2 ANGL. DEV. = 5.7 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 PHE A 412 13.23 56.30 REMARK 500 LEU A 426 -158.06 -103.03 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 A2042 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A2062 DISTANCE = 7.29 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DFA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP REMARK 900 RELATED ID: 1VDE RELATED DB: PDB REMARK 900 PI-SCEI, A HOMING ENDONUCLEASE WITH PROTEIN SPLICING ACTIVITY REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN PI-SCEI IS AN INTEIN OF THE PRIMARY TRANSLATION REMARK 999 PRODUCT OF THE ATP SYNTHASE (SWS ENTRY P17255). IT SPLICES REMARK 999 ITSELF OUT OF THE PRECURSOR. PI-SCEI IS A TWO-DOMAIN REMARK 999 PROTEIN. THE ENTRY 1GPP REPRESENTS DOMAIN I WHICH CONSISTS REMARK 999 OF RESIDUES 1 TO 182 AND 410 TO 453, DOMAIN II IN THE FULL REMARK 999 LENGTH PROTEIN CONSISTS OF RESIDUES 183 TO 409. GLU183 WAS REMARK 999 ENGINEERD AS LINKER BETWEEN THE TWO PARTS OF THE DOMAIN. REMARK 999 THE MUTATIONS R54S, M67V AND I132V ARE NOT ENGINEERED BUT REMARK 999 TURNED OUT TO BE PRESENT AFTER CLONING FROM BAKERS YEAST REMARK 999 COMMERCIALLY AVAILABLE FOR US. THE SEQADV ONLY SHOWS THE REMARK 999 DIFFERENCE TO THE DATABASE ENTRY. DBREF 1GPP A -10 -1 PDB 1GPP 1GPP -10 -1 DBREF 1GPP A 1 183 UNP P17255 P17255 284 466 DBREF 1GPP A 410 453 UNP P17255 P17255 693 736 SEQADV 1GPP SER A 44 UNP P17255 ARG 327 ENGINEERED MUTATION SEQADV 1GPP MET A 67 UNP P17255 VAL 350 ENGINEERED MUTATION SEQADV 1GPP VAL A 132 UNP P17255 ILE 415 ENGINEERED MUTATION SEQADV 1GPP GLY A 183 UNP P17255 LEU 466 ENGINEERED MUTATION SEQRES 1 A 237 MET HIS HIS HIS HIS HIS HIS GLY SER ALA CYS PHE ALA SEQRES 2 A 237 LYS GLY THR ASN VAL LEU MET ALA ASP GLY SER ILE GLU SEQRES 3 A 237 CYS ILE GLU ASN ILE GLU VAL GLY ASN LYS VAL MET GLY SEQRES 4 A 237 LYS ASP GLY ARG PRO ARG GLU VAL ILE LYS LEU PRO ARG SEQRES 5 A 237 GLY SER GLU THR MET TYR SER VAL VAL GLN LYS SER GLN SEQRES 6 A 237 HIS ARG ALA HIS LYS SER ASP SER SER ARG GLU MET PRO SEQRES 7 A 237 GLU LEU LEU LYS PHE THR CYS ASN ALA THR HIS GLU LEU SEQRES 8 A 237 VAL VAL ARG THR PRO ARG SER VAL ARG ARG LEU SER ARG SEQRES 9 A 237 THR ILE LYS GLY VAL GLU TYR PHE GLU VAL ILE THR PHE SEQRES 10 A 237 GLU MET GLY GLN LYS LYS ALA PRO ASP GLY ARG ILE VAL SEQRES 11 A 237 GLU LEU VAL LYS GLU VAL SER LYS SER TYR PRO VAL SER SEQRES 12 A 237 GLU GLY PRO GLU ARG ALA ASN GLU LEU VAL GLU SER TYR SEQRES 13 A 237 ARG LYS ALA SER ASN LYS ALA TYR PHE GLU TRP THR ILE SEQRES 14 A 237 GLU ALA ARG ASP LEU SER LEU LEU GLY SER HIS VAL ARG SEQRES 15 A 237 LYS ALA THR TYR GLN THR TYR ALA PRO ILE GLY ALA ALA SEQRES 16 A 237 PHE ALA ARG GLU CYS ARG GLY PHE TYR PHE GLU LEU GLN SEQRES 17 A 237 GLU LEU LYS GLU ASP ASP TYR TYR GLY ILE THR LEU SER SEQRES 18 A 237 ASP ASP SER ASP HIS GLN PHE LEU LEU ALA ASN GLN VAL SEQRES 19 A 237 VAL VAL HIS FORMUL 2 HOH *303(H2 O) HELIX 1 1 GLU A 19 ILE A 21 5 3 HELIX 2 2 SER A 133 GLY A 135 5 3 HELIX 3 3 PRO A 136 ALA A 149 1 14 HELIX 4 4 ARG A 162 LEU A 167 5 6 HELIX 5 5 GLY A 168 THR A 175 1 8 HELIX 6 6 GLY A 183 ALA A 413 5 5 SHEET 1 AA 8 ALA A -1 PHE A 2 0 SHEET 2 AA 8 PHE A 421 LEU A 436 -1 O TYR A 432 N PHE A 2 SHEET 3 AA 8 ARG A 42 GLN A 52 -1 O GLY A 43 N TYR A 431 SHEET 4 AA 8 LYS A 72 ASN A 76 -1 O PHE A 73 N VAL A 50 SHEET 5 AA 8 ALA A -1 PHE A 2 -1 O CYS A 1 N ASN A 76 SHEET 6 AA 8 PHE A 421 LEU A 436 -1 O TYR A 432 N PHE A 2 SHEET 7 AA 8 ARG A 42 GLN A 52 -1 O GLY A 43 N TYR A 431 SHEET 8 AA 8 ALA A -1 PHE A 2 0 SHEET 1 AB 2 ASN A 7 LEU A 9 0 SHEET 2 AB 2 ILE A 15 CYS A 17 -1 O GLU A 16 N VAL A 8 SHEET 1 AC 2 GLU A 80 PRO A 86 0 SHEET 2 AC 2 TYR A 154 GLU A 160 -1 O PHE A 155 N THR A 85 SHEET 1 AD 3 VAL A 89 ILE A 96 0 SHEET 2 AD 3 VAL A 99 LYS A 113 -1 O VAL A 99 N ILE A 96 SHEET 3 AD 3 ILE A 119 PRO A 131 -1 O VAL A 120 N LYS A 112 SHEET 1 AE 2 GLN A 177 TYR A 179 0 SHEET 2 AE 2 ARG A 417 PHE A 419 -1 O ARG A 417 N TYR A 179 SHEET 1 AF 2 PHE A 444 LEU A 445 0 SHEET 2 AF 2 VAL A 451 VAL A 452 -1 O VAL A 452 N PHE A 444 CRYST1 102.856 47.595 60.297 90.00 121.41 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 0.009722 0.000000 0.005937 0.00000 SCALE2 0.000000 0.021011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019432 0.00000