HEADER HYDROLASE (PROTEINASE) 27-JUN-77 1ACT OBSLTE 07-MAR-80 1ACT 2ACT TITLE STRUCTURE OF ACTINIDIN,DETAILS OF THE POLYPEPTIDE CHAIN TITLE 2 CONFORMATION AND ACTIVE SITE FROM AN ELECTRON DENSITY MAP TITLE 3 AT 2.8 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS HYDROLASE (PROTEINASE) EXPDTA X-RAY DIFFRACTION AUTHOR E.N.BAKER REVDAT 1 1ACT 0 JRNL AUTH E.N.BAKER JRNL TITL STRUCTURE OF ACTINIDIN,DETAILS OF THE POLYPEPTIDE JRNL TITL 2 CHAIN CONFORMATION AND ACTIVE SITE FROM AN JRNL TITL 3 ELECTRON DENSITY MAP AT 2.8 ANGSTROMS RESOLUTION JRNL REF J.MOL.BIOL. V. 115 263 1977 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.N.BAKER REMARK 1 TITL THE STRUCTURE OF ACTINIDIN AT 5.5 ANGSTROMS REMARK 1 TITL 2 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 101 185 1976 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.N.BAKER REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC DATA FOR ACTINIDIN, A REMARK 1 TITL 2 THIOL PROTEASE FROM ACTINIDIA CHINENSIS REMARK 1 REF J.MOL.BIOL. V. 74 411 1973 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : NULL 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) : 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 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 : 1649 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 1ACT COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-19) 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 (%): 45.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-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 SMTRY1 2 -1.000000 0.000000 0.000000 39.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.52500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.52500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.90000 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN 19 OE1 NE2 REMARK 470 ASN 38 OD1 ND2 REMARK 470 GLN 51 OE1 NE2 REMARK 470 GLN 60 OE1 NE2 REMARK 470 ASN 61 OD1 ND2 REMARK 470 GLN 75 OE1 NE2 REMARK 470 ASN 79 OD1 ND2 REMARK 470 ASN 84 OD1 ND2 REMARK 470 ASN 88 OD1 ND2 REMARK 470 GLN 94 OE1 NE2 REMARK 470 ASN 101 OD1 ND2 REMARK 470 GLN 103 OE1 NE2 REMARK 470 GLN 105 OE1 NE2 REMARK 470 ASN 115 OD1 ND2 REMARK 470 ASN 119 OD1 ND2 REMARK 470 ASN 120 OD1 ND2 REMARK 470 GLN 125 OE1 NE2 REMARK 470 GLN 131 OE1 NE2 REMARK 470 GLN 146 OE1 NE2 REMARK 470 ASN 182 OD1 ND2 REMARK 470 ASN 199 OD1 ND2 REMARK 470 TYR 219 CA C O CB CG CD1 CD2 REMARK 470 TYR 219 CE1 CE2 CZ OH 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 REMARK 500 O VAL 5 N TYR 169 1.86 REMARK 500 OD1 ASP 111 N TYR 218 1.97 REMARK 500 OE2 GLU 121 NE1 TRP 178 1.98 REMARK 500 O GLY 207 OG1 THR 210 2.13 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 AE2 GLN 60 O ASP 80 2654 2.11 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 206 -30.01 99.27 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR 4 VAL 5 149.70 REMARK 500 GLY 154 PRO 155 -30.88 SEQRES 1 219 LEU PRO SER TYR VAL ASP TRP ARG SER ALA GLY ALA VAL SEQRES 2 219 VAL ASP ILE LYS SER GLN GLY GLU CYS GLY GLY CYS TRP SEQRES 3 219 ALA PHE SER ALA ILE ALA THR VAL GLU GLY ILE ASN LYS SEQRES 4 219 ILE THR SER GLY SER LEU ILE SER LEU SER GLU GLN GLU SEQRES 5 219 LEU ILE ASP CYS GLY ARG THR GLN ASN THR ARG GLY CYS SEQRES 6 219 ASP GLY GLY TYR ILE THR ASP GLY PHE GLN PHE ILE ILE SEQRES 7 219 ASN ASP GLY GLY ILE ASN THR ASP GLU ASN TYR PRO TYR SEQRES 8 219 THR ALA GLN ASP GLY ALA CYS ASP VAL ASN LEU GLN ASP SEQRES 9 219 GLN LYS TYR VAL THR ILE ASP THR TYR GLU ASN VAL PRO SEQRES 10 219 TYR ASN ASN GLU TRP ALA LEU GLN THR ALA VAL THR TYR SEQRES 11 219 GLN PRO VAL SER VAL ALA LEU ASP ALA ALA GLY ASP ALA SEQRES 12 219 PHE LYS GLN TYR ALA SER GLY ILE PHE THR GLY PRO CYS SEQRES 13 219 GLY THR ALA VAL ASP HIS ALA ILE VAL ILE VAL GLY TYR SEQRES 14 219 GLY THR GLU GLY GLY VAL ASP TYR TRP ILE VAL LYS ASN SEQRES 15 219 SER TRP ASP THR THR TRP GLY GLU GLU GLY TYR MET ARG SEQRES 16 219 ILE LEU ARG ASN VAL GLY GLY ALA GLY THR CYS GLY ILE SEQRES 17 219 ALA THR MET PRO SER TYR PRO VAL LYS TYR TYR FTNOTE 1 RESIDUE 97 IS ASP IN SEQUENCE BUT NO DENSITY BEYOND CB. FTNOTE 1 THIS RESIDUE IS REGARDED AS ALA IN THE SEQRES RECORDS AND FTNOTE 1 COORDINATE LIST. FTNOTE 2 RESIDUE 101 IS ALA IN SEQUENCE BUT LOOKS LARGER IN MAP. FTNOTE 2 THIS RESIDUE IS REGARDED AS ASN IN THE SEQRES RECORDS AND FTNOTE 2 COORDINATE LIST. FTNOTE 3 RESIDUE ALA 93 HAS NO DENSITY FOR CB. FTNOTE 4 RESIDUE 155 IS A CIS-PROLINE. HELIX 1 A CYS 25 SER 42 1 18 HELIX 2 B GLU 50 GLY 57 1 8 HELIX 3 C TYR 69 GLY 81 1 13 HELIX 4 D ASP 99 ASP 104 1ONLY 2 HYDROGEN BONDS 6 HELIX 5 E ASN 120 THR 129 1 10 HELIX 6 F GLY 141 GLN 146 1ONLY 2 HYDROGEN BONDS 6 SHEET 1 S1 4 VAL 133 LEU 137 0 SHEET 2 S1 4 HIS 162 GLU 172 -1 N VAL 133 O ILE 166 SHEET 3 S1 4 VAL 175 ASN 182 -1 N VAL 165 O LYS 181 SHEET 4 S1 4 GLY 192 ARG 198 -1 O ASP 176 N ARG 198 TURN 1 A GLY 201 GLY 204 TURN 2 B GLY 207 THR 210 SSBOND 1 CYS 22 CYS 65 SSBOND 2 CYS 56 CYS 98 SSBOND 3 CYS 156 CYS 206 SITE 1 CAT 4 CYS 25 HIS 162 ASN 182 TRP 184 SITE 1 BIN 6 TYR 69 ILE 70 MET 211 ALA 136 SITE 2 BIN 6 ALA 163 VAL 160 CRYST1 78.200 81.800 33.050 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 0.012788 0.000000 0.000000 0.00000 ORIGX2 0.000000 0.012225 0.000000 0.00000 ORIGX3 0.000000 0.000000 0.030257 0.00000 SCALE1 0.012788 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030257 0.00000