HEADER RIBONUCLEASE INHIBITOR 20-JAN-94 1BNH OBSLTE 12-MAR-97 1BNH 2BNH TITLE CRYSTAL STRUCTURE OF PORCINE RIBONUCLEASE INHIBITOR, A TITLE 2 PROTEIN WITH LEUCINE-RICH REPEATS COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS RIBONUCLEASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR B.KOBE,J.DEISENHOFER REVDAT 1 30-APR-94 1BNH 0 JRNL AUTH B.KOBE,J.DEISENHOFER JRNL TITL CRYSTAL STRUCTURE OF PORCINE RIBONUCLEASE JRNL TITL 2 INHIBITOR, A PROTEIN WITH LEUCINE-RICH REPEATS JRNL REF NATURE V. 366 751 1993 JRNL REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.KOBE,J.DEISENHOFER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF REMARK 1 TITL 2 PORCINE RIBONUCLEASE INHIBITOR, A PROTEIN WITH REMARK 1 TITL 3 LEUCINE-RICH REPEATS REMARK 1 REF J.MOL.BIOL. V. 231 137 1993 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 1BNH REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 21310 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 3411 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.68 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BNH COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 1/2+X,1/2+Y,1/2+Z REMARK 290 6555 1/2-X,1/2-Y,1/2+Z REMARK 290 7555 1/2-Y,1/2+X,1/2+Z REMARK 290 8555 1/2+Y,1/2-X,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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 67.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.80000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 67.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.80000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 67.45000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 67.45000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.80000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 67.45000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 67.45000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.80000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET 331 SD MET 331 CE -0.186 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN 175 N - CA - C ANGL. DEV. =-10.3 DEGREES REMARK 500 CYS 243 N - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 LEU 348 CA - CB - CG ANGL. DEV. =-10.6 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 CYS 7 -31.03 70.89 SEQRES 1 456 MET ASN LEU ASP ILE HIS CYS GLU GLN LEU SER ASP ALA SEQRES 2 456 ARG TRP THR GLU LEU LEU PRO LEU LEU GLN GLN TYR GLU SEQRES 3 456 VAL VAL ARG LEU ASP ASP CYS GLY LEU THR GLU GLU HIS SEQRES 4 456 CYS LYS ASP ILE GLY SER ALA LEU ARG ALA ASN PRO SER SEQRES 5 456 LEU THR GLU LEU CYS LEU ARG THR ASN GLU LEU GLY ASP SEQRES 6 456 ALA GLY VAL HIS LEU VAL LEU GLN GLY LEU GLN SER PRO SEQRES 7 456 THR CYS LYS ILE GLN LYS LEU SER LEU GLN ASN CYS SER SEQRES 8 456 LEU THR GLU ALA GLY CYS GLY VAL LEU PRO SER THR LEU SEQRES 9 456 ARG SER LEU PRO THR LEU ARG GLU LEU HIS LEU SER ASP SEQRES 10 456 ASN PRO LEU GLY ASP ALA GLY LEU ARG LEU LEU CYS GLU SEQRES 11 456 GLY LEU LEU ASP PRO GLN CYS HIS LEU GLU LYS LEU GLN SEQRES 12 456 LEU GLU TYR CYS ARG LEU THR ALA ALA SER CYS GLU PRO SEQRES 13 456 LEU ALA SER VAL LEU ARG ALA THR ARG ALA LEU LYS GLU SEQRES 14 456 LEU THR VAL SER ASN ASN ASP ILE GLY GLU ALA GLY ALA SEQRES 15 456 ARG VAL LEU GLY GLN GLY LEU ALA ASP SER ALA CYS GLN SEQRES 16 456 LEU GLU THR LEU ARG LEU GLU ASN CYS GLY LEU THR PRO SEQRES 17 456 ALA ASN CYS LYS ASP LEU CYS GLY ILE VAL ALA SER GLN SEQRES 18 456 ALA SER LEU ARG GLU LEU ASP LEU GLY SER ASN GLY LEU SEQRES 19 456 GLY ASP ALA GLY ILE ALA GLU LEU CYS PRO GLY LEU LEU SEQRES 20 456 SER PRO ALA SER ARG LEU LYS THR LEU TRP LEU TRP GLU SEQRES 21 456 CYS ASP ILE THR ALA SER GLY CYS ARG ASP LEU CYS ARG SEQRES 22 456 VAL LEU GLN ALA LYS GLU THR LEU LYS GLU LEU SER LEU SEQRES 23 456 ALA GLY ASN LYS LEU GLY ASP GLU GLY ALA ARG LEU LEU SEQRES 24 456 CYS GLU SER LEU LEU GLN PRO GLY CYS GLN LEU GLU SER SEQRES 25 456 LEU TRP VAL LYS SER CYS SER LEU THR ALA ALA CYS CYS SEQRES 26 456 GLN HIS VAL SER LEU MET LEU THR GLN ASN LYS HIS LEU SEQRES 27 456 LEU GLU LEU GLN LEU SER SER ASN LYS LEU GLY ASP SER SEQRES 28 456 GLY ILE GLN GLU LEU CYS GLN ALA LEU SER GLN PRO GLY SEQRES 29 456 THR THR LEU ARG VAL LEU CYS LEU GLY ASP CYS GLU VAL SEQRES 30 456 THR ASN SER GLY CYS SER SER LEU ALA SER LEU LEU LEU SEQRES 31 456 ALA ASN ARG SER LEU ARG GLU LEU ASP LEU SER ASN ASN SEQRES 32 456 CYS VAL GLY ASP PRO GLY VAL LEU GLN LEU LEU GLY SER SEQRES 33 456 LEU GLU GLN PRO GLY CYS ALA LEU GLU GLN LEU VAL LEU SEQRES 34 456 TYR ASP THR TYR TRP THR GLU GLU VAL GLU ASP ARG LEU SEQRES 35 456 GLN ALA LEU GLU GLY SER LYS PRO GLY LEU ARG VAL ILE SEQRES 36 456 SER HELIX 1 1 ASP 12 LEU 22 1 11 HELIX 2 2 GLU 37 LEU 47 1 11 HELIX 3 3 GLY 64 LEU 75 1 12 HELIX 4 4A GLU 94 VAL 99 5 6 HELIX 5 4 LEU 100 SER 106 1 7 HELIX 6 5 GLY 121 LEU 133 1 13 HELIX 7 6 ALA 151 ALA 163 1 13 HELIX 8 7 GLY 178 ALA 190 1 13 HELIX 9 8 PRO 208 SER 220 1 13 HELIX 10 9 GLY 235 LEU 246 1 12 HELIX 11 10 ALA 265 ALA 277 1 13 HELIX 12 11 GLY 292 LEU 303 1 12 HELIX 13 12A ALA 322 CYS 324 5 3 HELIX 14 12 CYS 325 GLN 334 1 10 HELIX 15 13 GLY 349 ALA 359 1 11 HELIX 16 14 ASN 379 ALA 391 1 13 HELIX 17 15 ASP 407 LEU 417 1 11 HELIX 18 16 GLU 436 SER 448 1 13 SHEET 1 S117 ILE 5 HIS 6 0 SHEET 2 S117 VAL 27 ASP 31 1 SHEET 3 S117 GLU 55 CYS 57 1 SHEET 4 S117 LYS 84 SER 86 1 SHEET 5 S117 GLU 112 HIS 114 1 SHEET 6 S117 LYS 141 GLN 143 1 SHEET 7 S117 GLU 169 THR 171 1 SHEET 8 S117 THR 198 ARG 200 1 SHEET 9 S117 GLU 226 ASP 228 1 SHEET 10 S117 THR 255 TRP 257 1 SHEET 11 S117 GLU 283 SER 285 1 SHEET 12 S117 SER 312 TRP 314 1 SHEET 13 S117 GLU 340 GLN 342 1 SHEET 14 S117 VAL 369 CYS 371 1 SHEET 15 S117 GLU 397 ASP 399 1 SHEET 16 S117 GLN 426 VAL 428 1 SHEET 17 S117 ARG 453 ILE 455 1 CRYST1 134.900 134.900 83.600 90.00 90.00 90.00 I 4 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 0.007413 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011962 0.00000