PDB Short entry for 1PPD HEADER HYDROLASE (SULFHYDRYL PROTEINASE) 06-NOV-84 1PPD TITLE RESTRAINED LEAST-SQUARES REFINEMENT OF THE SULFHYDRYL PROTEASE PAPAIN TITLE 2 TO 2.0 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-HYDROXYETHYL-THIOPAPAIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 ORGANISM_TAXID: 3649 KEYWDS HYDROLASE (SULFHYDRYL PROTEINASE) EXPDTA X-RAY DIFFRACTION AUTHOR J.N.JANSONIUS REVDAT 3 29-NOV-17 1PPD 1 HELIX REVDAT 2 24-FEB-09 1PPD 1 VERSN REVDAT 1 02-JAN-85 1PPD 0 JRNL AUTH J.P.PRIESTLE,G.C.FORD,M.GLOR,E.L.MEHLER,J.D.G.SMIT, JRNL AUTH 2 C.THALLER,J.N.JANSONIUS JRNL TITL RESTRAINED LEAST-SQUARES REFINEMENT OF THE SULFHYDRYL JRNL TITL 2 PROTEASE PAPAIN TO 2.0 ANGSTROMS JRNL REF ACTA CRYSTALLOGR.,SECT.A V. 40 17 1984 JRNL REFN ISSN 0108-7673 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.DRENTH,J.N.JANSONIUS,R.KOEKOEK,B.G.WOLTHERS REMARK 1 TITL THE STRUCTURE OF PAPAIN REMARK 1 REF ADV.PROTEIN CHEM. V. 25 79 1971 REMARK 1 REFN ISSN 0065-3233 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13394 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 + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 211 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.007 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: REMARK 3 THE CRYSTALS USED ARE OF THE *D* TYPE, COURTESY OF REMARK 3 PROF. J. DRENTH OF THE UNIVERSITY OF GRONINGEN, GRONINGEN, REMARK 3 THE NETHERLANDS. REMARK 4 REMARK 4 1PPD 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_1000175783. 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 <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) : 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 <I/SIGMA(I)> 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 (%): 43.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.85000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.85000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.85000 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 400 REMARK 400 COMPOUND REMARK 400 RESIDUE CYS 25, THE ACTIVE SULPHYDRYL IS INHIBITED WITH 2- REMARK 400 MERCAPTOETHANOL 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 ASP A 57 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 58 NE - CZ - NH2 ANGL. DEV. = 4.6 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 SER A 21 57.02 -97.46 REMARK 500 ASP A 158 6.57 -157.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ACTIVE SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 213 DBREF 1PPD A 1 212 UNP P00784 PAPA1_CARPA 134 345 SEQADV 1PPD GLN A 47 UNP P00784 GLU 180 CONFLICT SEQADV 1PPD GLN A 118 UNP P00784 GLU 251 CONFLICT SEQADV 1PPD GLN A 135 UNP P00784 GLU 268 CONFLICT SEQRES 1 A 212 ILE PRO GLU TYR VAL ASP TRP ARG GLN LYS GLY ALA VAL SEQRES 2 A 212 THR PRO VAL LYS ASN GLN GLY SER CYS GLY SER CYS TRP SEQRES 3 A 212 ALA PHE SER ALA VAL VAL THR ILE GLU GLY ILE ILE LYS SEQRES 4 A 212 ILE ARG THR GLY ASN LEU ASN GLN TYR SER GLU GLN GLU SEQRES 5 A 212 LEU LEU ASP CYS ASP ARG ARG SER TYR GLY CYS ASN GLY SEQRES 6 A 212 GLY TYR PRO TRP SER ALA LEU GLN LEU VAL ALA GLN TYR SEQRES 7 A 212 GLY ILE HIS TYR ARG ASN THR TYR PRO TYR GLU GLY VAL SEQRES 8 A 212 GLN ARG TYR CYS ARG SER ARG GLU LYS GLY PRO TYR ALA SEQRES 9 A 212 ALA LYS THR ASP GLY VAL ARG GLN VAL GLN PRO TYR ASN SEQRES 10 A 212 GLN GLY ALA LEU LEU TYR SER ILE ALA ASN GLN PRO VAL SEQRES 11 A 212 SER VAL VAL LEU GLN ALA ALA GLY LYS ASP PHE GLN LEU SEQRES 12 A 212 TYR ARG GLY GLY ILE PHE VAL GLY PRO CYS GLY ASN LYS SEQRES 13 A 212 VAL ASP HIS ALA VAL ALA ALA VAL GLY TYR GLY PRO ASN SEQRES 14 A 212 TYR ILE LEU ILE LYS ASN SER TRP GLY THR GLY TRP GLY SEQRES 15 A 212 GLU ASN GLY TYR ILE ARG ILE LYS ARG GLY THR GLY ASN SEQRES 16 A 212 SER TYR GLY VAL CYS GLY LEU TYR THR SER SER PHE TYR SEQRES 17 A 212 PRO VAL LYS ASN HET BME A 213 4 HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 BME C2 H6 O S FORMUL 3 HOH *211(H2 O) HELIX 1 H1 SER A 24 THR A 42 1BENT SLIGHTLY BETWEEN 29 - 31 19 HELIX 2 H2 GLU A 50 CYS A 56 1 7 HELIX 3 H3 PRO A 68 TYR A 78 1 11 HELIX 4 H4 GLN A 118 ASN A 127 1 10 HELIX 5 H5 LYS A 139 LEU A 143 1 5 SHEET 1 S1A 6 GLY A 109 ARG A 111 0 SHEET 2 S1A 6 PHE A 207 VAL A 210 -1 SHEET 3 S1A 6 VAL A 130 LEU A 134 -1 SHEET 4 S1A 6 ASP A 158 GLY A 167 -1 SHEET 5 S1A 6 ASN A 169 ASN A 175 -1 SHEET 6 S1A 6 GLY A 185 ARG A 191 -1 SHEET 1 S1B 4 VAL A 5 TRP A 7 0 SHEET 2 S1B 4 ASP A 158 GLY A 167 -1 SHEET 3 S1B 4 ASN A 169 ASN A 175 -1 SHEET 4 S1B 4 GLY A 185 ARG A 191 -1 SSBOND 1 CYS A 22 CYS A 63 1555 1555 1.96 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.02 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.08 LINK SG CYS A 25 S2 BME A 213 1555 1555 2.02 CISPEP 1 GLY A 151 PRO A 152 0 2.99 SITE 1 ACT 7 GLN A 19 GLY A 23 CYS A 25 HIS A 159 SITE 2 ACT 7 ASN A 175 SER A 176 TRP A 177 SITE 1 AC1 3 GLN A 19 CYS A 25 HIS A 159 CRYST1 42.800 95.700 49.700 90.00 90.00 90.00 P 21 21 21 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 0.023360 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020120 0.00000