HEADER HYDROLASE 20-JUN-96 1YAL TITLE CARICA PAPAYA CHYMOPAPAIN AT 1.7 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHYMOPAPAIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.6; COMPND 5 OTHER_DETAILS: THE ACTIVE SITE CYS 25 AS WELL AS CYS 117 ARE COMPND 6 PROTECTED WITH A THIOMETHYL GROUP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 ORGANISM_TAXID: 3649; SOURCE 5 ORGAN: FRUIT KEYWDS HYDROLASE, THIOL PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR D.MAES,J.BOUCKAERT,F.POORTMANS,L.WYNS,Y.LOOZE REVDAT 5 09-AUG-23 1YAL 1 REMARK SEQADV LINK REVDAT 4 18-APR-18 1YAL 1 REMARK REVDAT 3 04-APR-18 1YAL 1 REMARK REVDAT 2 24-FEB-09 1YAL 1 VERSN REVDAT 1 23-DEC-96 1YAL 0 JRNL AUTH D.MAES,J.BOUCKAERT,F.POORTMANS,L.WYNS,Y.LOOZE JRNL TITL STRUCTURE OF CHYMOPAPAIN AT 1.7 A RESOLUTION. JRNL REF BIOCHEMISTRY V. 35 16292 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8973203 JRNL DOI 10.1021/BI961491W REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.AZARKAN,D.MAES,J.BOUCKAERT,M.-H.D.THI,L.WYNS,Y.LOOZE REMARK 1 TITL PREPARATION OF CRYSTALS OF CHYMOPAPAIN DIFFRACTING TO 1.4 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.50 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) (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 20060 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) : 0.192 REMARK 3 FREE R VALUE : NULL 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2017 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 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 : 1670 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.74 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) : 0.10 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 9.50 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.540 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.63 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.440 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 1YAL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CCP4, MADNES REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20199 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.30 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1PPO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.6 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 72.59000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.59000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.17500 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -6.90269 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.91491 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 GLN A 3 CD OE1 NE2 REMARK 480 LYS A 58 CG CD CE NZ REMARK 480 LYS A 64 NZ REMARK 480 LYS A 84 CD CE NZ REMARK 480 LYS A 91 CD CE NZ REMARK 480 LYS A 94 CE NZ REMARK 480 ASP A 99 CA C O CB CG OD1 OD2 REMARK 480 LYS A 145 CD CE NZ 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 TYR A 93 -169.02 -126.68 REMARK 500 PRO A 101 -155.79 -98.62 REMARK 500 ASP A 158 9.32 -150.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 1YAL A 1 218 UNP P14080 PAPA2_CARPA 135 352 SEQADV 1YAL SCH A 25 UNP P14080 CYS 159 CONFLICT SEQADV 1YAL SCH A 117 UNP P14080 CYS 251 CONFLICT SEQRES 1 A 218 TYR PRO GLN SER ILE ASP TRP ARG ALA LYS GLY ALA VAL SEQRES 2 A 218 THR PRO VAL LYS ASN GLN GLY ALA CYS GLY SER SCH TRP SEQRES 3 A 218 ALA PHE SER THR ILE ALA THR VAL GLU GLY ILE ASN LYS SEQRES 4 A 218 ILE VAL THR GLY ASN LEU LEU GLU LEU SER GLU GLN GLU SEQRES 5 A 218 LEU VAL ASP CYS ASP LYS HIS SER TYR GLY CYS LYS GLY SEQRES 6 A 218 GLY TYR GLN THR THR SER LEU GLN TYR VAL ALA ASN ASN SEQRES 7 A 218 GLY VAL HIS THR SER LYS VAL TYR PRO TYR GLN ALA LYS SEQRES 8 A 218 GLN TYR LYS CYS ARG ALA THR ASP LYS PRO GLY PRO LYS SEQRES 9 A 218 VAL LYS ILE THR GLY TYR LYS ARG VAL PRO SER ASN SCH SEQRES 10 A 218 GLU THR SER PHE LEU GLY ALA LEU ALA ASN GLN PRO LEU SEQRES 11 A 218 SER VAL LEU VAL GLU ALA GLY GLY LYS PRO PHE GLN LEU SEQRES 12 A 218 TYR LYS SER GLY VAL PHE ASP GLY PRO CYS GLY THR LYS SEQRES 13 A 218 LEU ASP HIS ALA VAL THR ALA VAL GLY TYR GLY THR SER SEQRES 14 A 218 ASP GLY LYS ASN TYR ILE ILE ILE LYS ASN SER TRP GLY SEQRES 15 A 218 PRO ASN TRP GLY GLU LYS GLY TYR MET ARG LEU LYS ARG SEQRES 16 A 218 GLN SER GLY ASN SER GLN GLY THR CYS GLY VAL TYR LYS SEQRES 17 A 218 SER SER TYR TYR PRO PHE LYS GLY PHE ALA MODRES 1YAL SCH A 25 CYS S-METHYL-THIO-CYSTEINE MODRES 1YAL SCH A 117 CYS S-METHYL-THIO-CYSTEINE HET SCH A 25 8 HET SCH A 117 8 HETNAM SCH S-METHYL-THIO-CYSTEINE FORMUL 1 SCH 2(C4 H9 N O2 S2) FORMUL 2 HOH *222(H2 O) HELIX 1 1 SCH A 25 THR A 42 1 18 HELIX 2 2 GLU A 50 CYS A 56 1 7 HELIX 3 3 GLY A 62 LYS A 64 5 3 HELIX 4 4 GLN A 68 ASN A 78 1 11 HELIX 5 5 ALA A 97 ASP A 99 5 3 HELIX 6 6 GLU A 118 LEU A 125 1 8 HELIX 7 7 LYS A 139 GLN A 142 1 4 HELIX 8 8 THR A 203 GLY A 205 5 3 SHEET 1 A 2 GLY A 109 ARG A 112 0 SHEET 2 A 2 TYR A 211 PHE A 214 -1 N PHE A 214 O GLY A 109 SHEET 1 B 4 LEU A 130 VAL A 134 0 SHEET 2 B 4 HIS A 159 SER A 169 -1 N ALA A 163 O LEU A 130 SHEET 3 B 4 LYS A 172 LYS A 178 -1 N LYS A 178 O THR A 162 SHEET 4 B 4 TYR A 190 LYS A 194 -1 N LEU A 193 O ILE A 175 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.02 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.03 SSBOND 3 CYS A 153 CYS A 204 1555 1555 2.04 LINK C SER A 24 N SCH A 25 1555 1555 1.33 LINK C SCH A 25 N TRP A 26 1555 1555 1.34 LINK C ASN A 116 N SCH A 117 1555 1555 1.33 LINK C SCH A 117 N GLU A 118 1555 1555 1.33 CISPEP 1 GLY A 151 PRO A 152 0 0.84 CRYST1 145.180 32.350 47.420 90.00 98.37 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 0.006888 0.000000 0.001013 0.00000 SCALE2 0.000000 0.030912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021315 0.00000