HEADER HYDROLASE 22-SEP-03 1UM2 TITLE CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE WITH THE LIGATED TITLE 2 EXTEIN SEGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE PI-SCEI; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VMA1-DERIVED ENDONUCLEASE X10SNS; COMPND 5 EC: 3.6.3.14; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 21-MER FROM VACUOLAR ATP SYNTHASE CATALYTIC SUBUNIT A; COMPND 10 CHAIN: C, D; COMPND 11 SYNONYM: 21-MER FROM VMA1-DERIVED ENDONUCLEASE X10SNS; COMPND 12 EC: 3.6.3.14; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 OTHER_DETAILS: THE N-EXTEIN SEGMENTS: RESIDUES 273-283 AND C-EXTEIN COMPND 16 SEGMENTS: 738-747 WERE LIGATED BY PROTEIN SPLICING. RESIDUE 283 LINKS COMPND 17 WITH RESIDUE 738 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: VMA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-17B-VDE-X10SNS; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 GENE: VMA1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET-17B-VDE-X10SNS KEYWDS PROTEIN SPLICING, VMA1-DERIVED ENDONUCLEASE, VDE, INTEIN, EXTEIN, KEYWDS 2 THIAZOLIDINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.MIZUTANI,Y.ANRAKU,Y.SATOW REVDAT 6 25-OCT-23 1UM2 1 REMARK REVDAT 5 10-NOV-21 1UM2 1 SEQADV REVDAT 4 09-OCT-19 1UM2 1 JRNL REVDAT 3 23-AUG-17 1UM2 1 SOURCE REMARK REVDAT 2 24-FEB-09 1UM2 1 VERSN REVDAT 1 22-SEP-04 1UM2 0 JRNL AUTH R.MIZUTANI,Y.ANRAKU,Y.SATOW JRNL TITL PROTEIN SPLICING OF YEAST VMA1-DERIVED ENDONUCLEASE VIA JRNL TITL 2 THIAZOLIDINE INTERMEDIATES. JRNL REF J.SYNCHROTRON RADIAT. V. 11 109 2004 JRNL REFN ISSN 0909-0495 JRNL PMID 14646148 JRNL DOI 10.1107/S0909049503023495 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.MIZUTANI,S.NOGAMI,M.KAWASAKI,Y.OHYA,Y.ANRAKU,Y.SATOW REMARK 1 TITL PROTEIN-SPLICING REACTION VIA A THIAZOLIDINE INTERMEDIATE: REMARK 1 TITL 2 CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING REMARK 1 TITL 3 THE N AND C-TERMINAL PROPEPTIDES REMARK 1 REF J.MOL.BIOL. V. 316 919 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11884132 REMARK 1 DOI 10.1006/JMBI.2001.5357 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 20700 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) : 0.214 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 922 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 6712 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 153 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) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : NULL 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.720 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1UM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000005976. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR AND REMARK 200 BENT-CYLINDER MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20700 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.05100 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) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14100 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1JVA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, BISTRISHCL, 2 REMARK 280 -MERCAPTOETHANOL, MAGNESIUM CHLORIDE, CADMIUM CHLORIDE, PH 6.2, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 APPLY THE FOLLOWING TO CHAINS: B, 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 GLN A 338 REMARK 465 HIS A 339 REMARK 465 ARG A 340 REMARK 465 ALA A 341 REMARK 465 HIS A 342 REMARK 465 LYS A 343 REMARK 465 SER A 344 REMARK 465 ASP A 345 REMARK 465 SER A 346 REMARK 465 SER A 347 REMARK 465 ARG A 348 REMARK 465 GLU A 349 REMARK 465 VAL A 350 REMARK 465 VAL A 553 REMARK 465 VAL A 554 REMARK 465 ARG A 555 REMARK 465 GLY A 556 REMARK 465 ASN A 557 REMARK 465 GLY A 558 REMARK 465 ILE A 559 REMARK 465 ARG A 560 REMARK 465 ASN A 561 REMARK 465 ASN A 562 REMARK 465 LEU A 563 REMARK 465 ASN A 564 REMARK 465 THR A 565 REMARK 465 ALA A 651 REMARK 465 LYS A 652 REMARK 465 VAL A 653 REMARK 465 ASP A 654 REMARK 465 MET A 655 REMARK 465 ASN A 656 REMARK 465 GLY A 657 REMARK 465 THR A 658 REMARK 465 LYS A 659 REMARK 465 HIS A 660 REMARK 465 LYS A 661 REMARK 465 SER B 337 REMARK 465 GLN B 338 REMARK 465 HIS B 339 REMARK 465 ARG B 340 REMARK 465 ALA B 341 REMARK 465 HIS B 342 REMARK 465 LYS B 343 REMARK 465 SER B 344 REMARK 465 ASP B 345 REMARK 465 SER B 346 REMARK 465 SER B 347 REMARK 465 ARG B 348 REMARK 465 GLU B 349 REMARK 465 VAL B 350 REMARK 465 PRO B 351 REMARK 465 LYS B 552 REMARK 465 VAL B 553 REMARK 465 VAL B 554 REMARK 465 ARG B 555 REMARK 465 GLY B 556 REMARK 465 ASN B 557 REMARK 465 GLY B 558 REMARK 465 ILE B 559 REMARK 465 ARG B 560 REMARK 465 ASN B 561 REMARK 465 ASN B 562 REMARK 465 ALA B 651 REMARK 465 LYS B 652 REMARK 465 VAL B 653 REMARK 465 ASP B 654 REMARK 465 MET B 655 REMARK 465 ASN B 656 REMARK 465 GLY B 657 REMARK 465 THR B 658 REMARK 465 LYS B 659 REMARK 465 MET C 273 REMARK 465 SER C 274 REMARK 465 ASN C 275 REMARK 465 SER C 276 REMARK 465 ASP C 277 REMARK 465 ALA C 278 REMARK 465 ILE C 279 REMARK 465 ILE C 280 REMARK 465 GLY C 742 REMARK 465 ASN C 743 REMARK 465 GLU C 744 REMARK 465 MET C 745 REMARK 465 ALA C 746 REMARK 465 GLU C 747 REMARK 465 MET D 273 REMARK 465 SER D 274 REMARK 465 ASN D 275 REMARK 465 SER D 276 REMARK 465 ASP D 277 REMARK 465 ALA D 278 REMARK 465 ILE D 279 REMARK 465 ILE D 280 REMARK 465 GLY D 742 REMARK 465 ASN D 743 REMARK 465 GLU D 744 REMARK 465 MET D 745 REMARK 465 ALA D 746 REMARK 465 GLU D 747 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 ASP B 474 N MET B 476 2.14 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 PRO B 568 C - N - CA ANGL. DEV. = 12.2 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 ALA A 286 160.68 -46.27 REMARK 500 THR A 289 99.00 -69.62 REMARK 500 LYS A 313 24.92 -61.09 REMARK 500 ILE A 321 -45.65 -132.35 REMARK 500 LEU A 323 64.73 -154.47 REMARK 500 GLU A 328 -169.04 170.24 REMARK 500 GLU A 352 43.33 -76.52 REMARK 500 PHE A 356 135.64 -170.32 REMARK 500 SER A 371 139.07 -175.00 REMARK 500 LEU A 375 -157.65 -91.12 REMARK 500 LYS A 380 86.47 52.06 REMARK 500 ARG A 401 155.30 -35.22 REMARK 500 ILE A 415 -79.73 -55.32 REMARK 500 SER A 416 -34.80 -17.31 REMARK 500 GLU A 417 5.19 -68.24 REMARK 500 PRO A 419 9.11 -62.15 REMARK 500 ALA A 422 -37.90 -39.86 REMARK 500 ALA A 436 32.36 -96.60 REMARK 500 ALA A 444 -39.60 -36.26 REMARK 500 SER A 452 -88.29 -1.98 REMARK 500 ASN A 469 -131.83 -88.11 REMARK 500 ASP A 470 11.47 170.73 REMARK 500 HIS A 471 -14.10 -47.37 REMARK 500 TYR A 475 -22.71 -39.09 REMARK 500 GLN A 477 47.60 -67.78 REMARK 500 SER A 479 -34.33 -132.49 REMARK 500 PHE A 481 21.53 -167.96 REMARK 500 HIS A 482 65.10 -169.91 REMARK 500 THR A 484 151.47 -33.37 REMARK 500 ASP A 505 -6.00 160.12 REMARK 500 ALA A 507 35.85 -72.72 REMARK 500 SER A 510 89.94 -49.58 REMARK 500 THR A 516 37.68 -78.99 REMARK 500 SER A 517 -36.83 -139.89 REMARK 500 ASN A 530 78.39 139.66 REMARK 500 LEU A 531 136.48 -170.38 REMARK 500 ALA A 533 70.66 -102.07 REMARK 500 TYR A 535 -150.90 -171.92 REMARK 500 LYS A 536 -125.90 -96.65 REMARK 500 ASP A 537 148.25 92.17 REMARK 500 ARG A 538 41.96 33.19 REMARK 500 LYS A 539 108.91 164.33 REMARK 500 GLU A 540 74.00 119.70 REMARK 500 GLN A 542 175.41 163.45 REMARK 500 PRO A 568 -16.43 -33.73 REMARK 500 LEU A 579 59.92 -156.49 REMARK 500 ASP A 581 88.64 40.87 REMARK 500 LYS A 584 170.37 -56.14 REMARK 500 ILE A 595 -74.33 -33.86 REMARK 500 LYS A 619 138.21 -173.25 REMARK 500 REMARK 500 THIS ENTRY HAS 119 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JVA RELATED DB: PDB REMARK 900 PROTEIN-SPLICING PRECURSOR OF THE VMA1-DERIVED ENDONUCLEASE DBREF 1UM2 A 284 737 UNP P17255 VATA_YEAST 284 737 DBREF 1UM2 B 284 737 UNP P17255 VATA_YEAST 284 737 DBREF 1UM2 C 274 283 UNP P17255 VATA_YEAST 274 283 DBREF 1UM2 C 738 747 UNP P17255 VATA_YEAST 738 747 DBREF 1UM2 D 274 283 UNP P17255 VATA_YEAST 274 283 DBREF 1UM2 D 738 747 UNP P17255 VATA_YEAST 738 747 SEQADV 1UM2 SER A 284 UNP P17255 CYS 284 ENGINEERED MUTATION SEQADV 1UM2 ASN A 362 UNP P17255 HIS 362 ENGINEERED MUTATION SEQADV 1UM2 SER B 284 UNP P17255 CYS 284 ENGINEERED MUTATION SEQADV 1UM2 ASN B 362 UNP P17255 HIS 362 ENGINEERED MUTATION SEQADV 1UM2 MET C 273 UNP P17255 INITIATING METHIONINE SEQADV 1UM2 SER C 738 UNP P17255 CYS 738 ENGINEERED MUTATION SEQADV 1UM2 MET D 273 UNP P17255 INITIATING METHIONINE SEQADV 1UM2 SER D 738 UNP P17255 CYS 738 ENGINEERED MUTATION SEQRES 1 A 454 SER PHE ALA LYS GLY THR ASN VAL LEU MET ALA ASP GLY SEQRES 2 A 454 SER ILE GLU CYS ILE GLU ASN ILE GLU VAL GLY ASN LYS SEQRES 3 A 454 VAL MET GLY LYS ASP GLY ARG PRO ARG GLU VAL ILE LYS SEQRES 4 A 454 LEU PRO ARG GLY ARG GLU THR MET TYR SER VAL VAL GLN SEQRES 5 A 454 LYS SER GLN HIS ARG ALA HIS LYS SER ASP SER SER ARG SEQRES 6 A 454 GLU VAL PRO GLU LEU LEU LYS PHE THR CYS ASN ALA THR SEQRES 7 A 454 ASN GLU LEU VAL VAL ARG THR PRO ARG SER VAL ARG ARG SEQRES 8 A 454 LEU SER ARG THR ILE LYS GLY VAL GLU TYR PHE GLU VAL SEQRES 9 A 454 ILE THR PHE GLU MET GLY GLN LYS LYS ALA PRO ASP GLY SEQRES 10 A 454 ARG ILE VAL GLU LEU VAL LYS GLU VAL SER LYS SER TYR SEQRES 11 A 454 PRO ILE SER GLU GLY PRO GLU ARG ALA ASN GLU LEU VAL SEQRES 12 A 454 GLU SER TYR ARG LYS ALA SER ASN LYS ALA TYR PHE GLU SEQRES 13 A 454 TRP THR ILE GLU ALA ARG ASP LEU SER LEU LEU GLY SER SEQRES 14 A 454 HIS VAL ARG LYS ALA THR TYR GLN THR TYR ALA PRO ILE SEQRES 15 A 454 LEU TYR GLU ASN ASP HIS PHE PHE ASP TYR MET GLN LYS SEQRES 16 A 454 SER LYS PHE HIS LEU THR ILE GLU GLY PRO LYS VAL LEU SEQRES 17 A 454 ALA TYR LEU LEU GLY LEU TRP ILE GLY ASP GLY LEU SER SEQRES 18 A 454 ASP ARG ALA THR PHE SER VAL ASP SER ARG ASP THR SER SEQRES 19 A 454 LEU MET GLU ARG VAL THR GLU TYR ALA GLU LYS LEU ASN SEQRES 20 A 454 LEU CYS ALA GLU TYR LYS ASP ARG LYS GLU PRO GLN VAL SEQRES 21 A 454 ALA LYS THR VAL ASN LEU TYR SER LYS VAL VAL ARG GLY SEQRES 22 A 454 ASN GLY ILE ARG ASN ASN LEU ASN THR GLU ASN PRO LEU SEQRES 23 A 454 TRP ASP ALA ILE VAL GLY LEU GLY PHE LEU LYS ASP GLY SEQRES 24 A 454 VAL LYS ASN ILE PRO SER PHE LEU SER THR ASP ASN ILE SEQRES 25 A 454 GLY THR ARG GLU THR PHE LEU ALA GLY LEU ILE ASP SER SEQRES 26 A 454 ASP GLY TYR VAL THR ASP GLU HIS GLY ILE LYS ALA THR SEQRES 27 A 454 ILE LYS THR ILE HIS THR SER VAL ARG ASP GLY LEU VAL SEQRES 28 A 454 SER LEU ALA ARG SER LEU GLY LEU VAL VAL SER VAL ASN SEQRES 29 A 454 ALA GLU PRO ALA LYS VAL ASP MET ASN GLY THR LYS HIS SEQRES 30 A 454 LYS ILE SER TYR ALA ILE TYR MET SER GLY GLY ASP VAL SEQRES 31 A 454 LEU LEU ASN VAL LEU SER LYS CYS ALA GLY SER LYS LYS SEQRES 32 A 454 PHE ARG PRO ALA PRO ALA ALA ALA PHE ALA ARG GLU CYS SEQRES 33 A 454 ARG GLY PHE TYR PHE GLU LEU GLN GLU LEU LYS GLU ASP SEQRES 34 A 454 ASP TYR TYR GLY ILE THR LEU SER ASP ASP SER ASP HIS SEQRES 35 A 454 GLN PHE LEU LEU ALA ASN GLN VAL VAL VAL HIS ASN SEQRES 1 B 454 SER PHE ALA LYS GLY THR ASN VAL LEU MET ALA ASP GLY SEQRES 2 B 454 SER ILE GLU CYS ILE GLU ASN ILE GLU VAL GLY ASN LYS SEQRES 3 B 454 VAL MET GLY LYS ASP GLY ARG PRO ARG GLU VAL ILE LYS SEQRES 4 B 454 LEU PRO ARG GLY ARG GLU THR MET TYR SER VAL VAL GLN SEQRES 5 B 454 LYS SER GLN HIS ARG ALA HIS LYS SER ASP SER SER ARG SEQRES 6 B 454 GLU VAL PRO GLU LEU LEU LYS PHE THR CYS ASN ALA THR SEQRES 7 B 454 ASN GLU LEU VAL VAL ARG THR PRO ARG SER VAL ARG ARG SEQRES 8 B 454 LEU SER ARG THR ILE LYS GLY VAL GLU TYR PHE GLU VAL SEQRES 9 B 454 ILE THR PHE GLU MET GLY GLN LYS LYS ALA PRO ASP GLY SEQRES 10 B 454 ARG ILE VAL GLU LEU VAL LYS GLU VAL SER LYS SER TYR SEQRES 11 B 454 PRO ILE SER GLU GLY PRO GLU ARG ALA ASN GLU LEU VAL SEQRES 12 B 454 GLU SER TYR ARG LYS ALA SER ASN LYS ALA TYR PHE GLU SEQRES 13 B 454 TRP THR ILE GLU ALA ARG ASP LEU SER LEU LEU GLY SER SEQRES 14 B 454 HIS VAL ARG LYS ALA THR TYR GLN THR TYR ALA PRO ILE SEQRES 15 B 454 LEU TYR GLU ASN ASP HIS PHE PHE ASP TYR MET GLN LYS SEQRES 16 B 454 SER LYS PHE HIS LEU THR ILE GLU GLY PRO LYS VAL LEU SEQRES 17 B 454 ALA TYR LEU LEU GLY LEU TRP ILE GLY ASP GLY LEU SER SEQRES 18 B 454 ASP ARG ALA THR PHE SER VAL ASP SER ARG ASP THR SER SEQRES 19 B 454 LEU MET GLU ARG VAL THR GLU TYR ALA GLU LYS LEU ASN SEQRES 20 B 454 LEU CYS ALA GLU TYR LYS ASP ARG LYS GLU PRO GLN VAL SEQRES 21 B 454 ALA LYS THR VAL ASN LEU TYR SER LYS VAL VAL ARG GLY SEQRES 22 B 454 ASN GLY ILE ARG ASN ASN LEU ASN THR GLU ASN PRO LEU SEQRES 23 B 454 TRP ASP ALA ILE VAL GLY LEU GLY PHE LEU LYS ASP GLY SEQRES 24 B 454 VAL LYS ASN ILE PRO SER PHE LEU SER THR ASP ASN ILE SEQRES 25 B 454 GLY THR ARG GLU THR PHE LEU ALA GLY LEU ILE ASP SER SEQRES 26 B 454 ASP GLY TYR VAL THR ASP GLU HIS GLY ILE LYS ALA THR SEQRES 27 B 454 ILE LYS THR ILE HIS THR SER VAL ARG ASP GLY LEU VAL SEQRES 28 B 454 SER LEU ALA ARG SER LEU GLY LEU VAL VAL SER VAL ASN SEQRES 29 B 454 ALA GLU PRO ALA LYS VAL ASP MET ASN GLY THR LYS HIS SEQRES 30 B 454 LYS ILE SER TYR ALA ILE TYR MET SER GLY GLY ASP VAL SEQRES 31 B 454 LEU LEU ASN VAL LEU SER LYS CYS ALA GLY SER LYS LYS SEQRES 32 B 454 PHE ARG PRO ALA PRO ALA ALA ALA PHE ALA ARG GLU CYS SEQRES 33 B 454 ARG GLY PHE TYR PHE GLU LEU GLN GLU LEU LYS GLU ASP SEQRES 34 B 454 ASP TYR TYR GLY ILE THR LEU SER ASP ASP SER ASP HIS SEQRES 35 B 454 GLN PHE LEU LEU ALA ASN GLN VAL VAL VAL HIS ASN SEQRES 1 C 21 MET SER ASN SER ASP ALA ILE ILE TYR VAL GLY SER GLY SEQRES 2 C 21 GLU ARG GLY ASN GLU MET ALA GLU SEQRES 1 D 21 MET SER ASN SER ASP ALA ILE ILE TYR VAL GLY SER GLY SEQRES 2 D 21 GLU ARG GLY ASN GLU MET ALA GLU FORMUL 5 HOH *153(H2 O) HELIX 1 1 PRO A 414 GLY A 418 5 5 HELIX 2 2 PRO A 419 SER A 433 1 15 HELIX 3 3 ARG A 445 LEU A 450 5 6 HELIX 4 4 GLY A 451 ALA A 457 1 7 HELIX 5 5 ASP A 470 GLN A 477 1 8 HELIX 6 6 GLU A 486 GLY A 500 1 15 HELIX 7 7 SER A 517 ASN A 530 1 14 HELIX 8 8 ASN A 567 LEU A 576 1 10 HELIX 9 9 PRO A 587 SER A 591 5 5 HELIX 10 10 ASN A 594 GLY A 610 1 17 HELIX 11 11 HIS A 626 LEU A 640 1 15 HELIX 12 12 GLY A 671 SER A 679 1 9 HELIX 13 13 PRO B 414 PRO B 419 5 6 HELIX 14 14 GLU B 420 LEU B 425 1 6 HELIX 15 15 LEU B 425 LYS B 431 1 7 HELIX 16 16 GLY B 451 THR B 458 1 8 HELIX 17 17 ASP B 470 MET B 476 1 7 HELIX 18 18 GLU B 486 GLY B 502 1 17 HELIX 19 19 ASP B 515 GLU B 527 1 13 HELIX 20 20 ASN B 567 LEU B 576 1 10 HELIX 21 21 PRO B 587 ASP B 593 5 7 HELIX 22 22 ASN B 594 ASP B 609 1 16 HELIX 23 23 HIS B 626 LEU B 640 1 15 HELIX 24 24 GLY B 671 SER B 679 1 9 SHEET 1 A 2 LYS A 309 MET A 311 0 SHEET 2 A 2 PRO A 317 GLU A 319 -1 O ARG A 318 N VAL A 310 SHEET 1 B 3 LYS A 355 ASN A 359 0 SHEET 2 B 3 ARG A 325 GLN A 335 -1 N TYR A 331 O CYS A 358 SHEET 3 B 3 PHE A 704 TYR A 715 -1 O GLU A 705 N VAL A 334 SHEET 1 C 2 GLU A 363 PRO A 369 0 SHEET 2 C 2 TYR A 437 GLU A 443 -1 O ILE A 442 N LEU A 364 SHEET 1 D 3 VAL A 372 ARG A 374 0 SHEET 2 D 3 VAL A 387 LYS A 396 -1 O ILE A 388 N ARG A 373 SHEET 3 D 3 ILE A 402 LYS A 411 -1 O LEU A 405 N GLY A 393 SHEET 1 E 2 ARG A 377 THR A 378 0 SHEET 2 E 2 GLU A 383 TYR A 384 -1 O TYR A 384 N ARG A 377 SHEET 1 F 2 GLN A 460 TYR A 462 0 SHEET 2 F 2 ARG A 700 PHE A 702 -1 O ARG A 700 N TYR A 462 SHEET 1 G 4 TYR A 611 THR A 613 0 SHEET 2 G 4 LYS A 619 THR A 624 -1 O THR A 621 N TYR A 611 SHEET 3 G 4 SER A 663 SER A 669 -1 O TYR A 664 N THR A 624 SHEET 4 G 4 VAL A 643 GLU A 649 -1 N GLU A 649 O SER A 663 SHEET 1 H 2 GLN A 726 LEU A 728 0 SHEET 2 H 2 VAL A 734 HIS A 736 -1 O VAL A 735 N PHE A 727 SHEET 1 I 2 ASN B 290 LEU B 292 0 SHEET 2 I 2 ILE B 298 CYS B 300 -1 O GLU B 299 N VAL B 291 SHEET 1 J 2 LYS B 309 MET B 311 0 SHEET 2 J 2 PRO B 317 GLU B 319 -1 O ARG B 318 N VAL B 310 SHEET 1 K 2 ARG B 325 GLU B 328 0 SHEET 2 K 2 ASP B 712 TYR B 715 -1 O ASP B 712 N GLU B 328 SHEET 1 L 3 LYS B 355 ASN B 359 0 SHEET 2 L 3 MET B 330 GLN B 335 -1 N TYR B 331 O CYS B 358 SHEET 3 L 3 PHE B 704 GLU B 708 -1 O GLN B 707 N SER B 332 SHEET 1 M 4 TYR B 437 GLU B 443 0 SHEET 2 M 4 GLU B 363 PRO B 369 -1 N THR B 368 O PHE B 438 SHEET 3 M 4 TYR B 459 TYR B 462 -1 O TYR B 459 N ARG B 367 SHEET 4 M 4 ARG B 700 PHE B 702 -1 O PHE B 702 N GLN B 460 SHEET 1 N 3 VAL B 372 ILE B 379 0 SHEET 2 N 3 VAL B 382 MET B 392 -1 O TYR B 384 N ARG B 377 SHEET 3 N 3 VAL B 406 VAL B 409 -1 O VAL B 409 N THR B 389 SHEET 1 O 2 PHE B 509 ASP B 512 0 SHEET 2 O 2 ALA B 544 VAL B 547 -1 O VAL B 547 N PHE B 509 SHEET 1 P 2 LEU B 579 LYS B 580 0 SHEET 2 P 2 VAL B 583 LYS B 584 -1 O VAL B 583 N LYS B 580 SHEET 1 Q 4 GLY B 610 THR B 613 0 SHEET 2 Q 4 LYS B 619 THR B 624 -1 O THR B 621 N TYR B 611 SHEET 3 Q 4 SER B 663 SER B 669 -1 O TYR B 664 N THR B 624 SHEET 4 Q 4 VAL B 643 GLU B 649 -1 N ASN B 647 O ALA B 665 SHEET 1 R 2 GLN B 726 LEU B 728 0 SHEET 2 R 2 VAL B 734 HIS B 736 -1 O VAL B 735 N PHE B 727 CRYST1 66.400 70.400 58.000 100.40 98.70 78.90 P 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 0.015060 -0.002955 0.001866 0.00000 SCALE2 0.000000 0.014475 0.002287 0.00000 SCALE3 0.000000 0.000000 0.017658 0.00000