HEADER HYDROLASE INHIBITOR 31-MAY-00 1F32 TITLE CRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PEPSIN INHIBITOR PI-3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASCARIS SUUM; SOURCE 3 ORGANISM_COMMON: PIG ROUNDWORM; SOURCE 4 ORGANISM_TAXID: 6253; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-3D KEYWDS PROTEINASE INHIBITOR, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR K.K.NG,J.F.PETERSEN,M.M.CHERNEY,C.GAREN,M.N.JAMES REVDAT 3 04-APR-18 1F32 1 REMARK REVDAT 2 24-FEB-09 1F32 1 VERSN REVDAT 1 01-FEB-01 1F32 0 JRNL AUTH K.K.NG,J.F.PETERSEN,M.M.CHERNEY,C.GAREN,J.J.ZALATORIS, JRNL AUTH 2 C.RAO-NAIK,B.M.DUNN,M.R.MARTZEN,R.J.PEANASKY,M.N.JAMES JRNL TITL STRUCTURAL BASIS FOR THE INHIBITION OF PORCINE PEPSIN BY JRNL TITL 2 ASCARIS PEPSIN INHIBITOR-3. JRNL REF NAT.STRUCT.BIOL. V. 7 653 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10932249 JRNL DOI 10.1038/77950 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 578945.700 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 13394 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) : 0.211 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1362 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1985 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 200 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 995 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.76000 REMARK 3 B22 (A**2) : -2.71000 REMARK 3 B33 (A**2) : -3.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.99000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.380 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.380 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 64.74 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_PI3.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F32 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030B REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13394 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, POTASSIUM FLUORIDE, REMARK 280 SPERMIDINE-HCL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.35850 REMARK 290 SMTRY3 2 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 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 1 REMARK 465 GLN A 118 REMARK 465 GLU A 119 REMARK 465 ASN A 120 REMARK 465 GLN A 121 REMARK 465 PRO A 122 REMARK 465 PRO A 123 REMARK 465 SER A 124 REMARK 465 SER A 125 REMARK 465 GLY A 126 REMARK 465 MET A 127 REMARK 465 PRO A 128 REMARK 465 HIS A 129 REMARK 465 GLY A 130 REMARK 465 ALA A 131 REMARK 465 VAL A 132 REMARK 465 PRO A 133 REMARK 465 ALA A 134 REMARK 465 GLY A 135 REMARK 465 GLY A 136 REMARK 465 LEU A 137 REMARK 465 GLN A 149 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 ASN A 18 -9.75 75.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F34 RELATED DB: PDB REMARK 900 SCARIS PEPSIN INHIBITOR-3 BOUND TO PORCINE PEPSIN DBREF 1F32 A 1 149 UNP P19400 API3_ASCSU 21 169 SEQRES 1 A 149 GLN PHE LEU PHE SER MET SER THR GLY PRO PHE ILE CYS SEQRES 2 A 149 THR VAL LYS ASP ASN GLN VAL PHE VAL ALA ASN LEU PRO SEQRES 3 A 149 TRP THR MET LEU GLU GLY ASP ASP ILE GLN VAL GLY LYS SEQRES 4 A 149 GLU PHE ALA ALA ARG VAL GLU ASP CYS THR ASN VAL LYS SEQRES 5 A 149 HIS ASP MET ALA PRO THR CYS THR LYS PRO PRO PRO PHE SEQRES 6 A 149 CYS GLY PRO GLN ASP MET LYS MET PHE ASN PHE VAL GLY SEQRES 7 A 149 CYS SER VAL LEU GLY ASN LYS LEU PHE ILE ASP GLN LYS SEQRES 8 A 149 TYR VAL ARG ASP LEU THR ALA LYS ASP HIS ALA GLU VAL SEQRES 9 A 149 GLN THR PHE ARG GLU LYS ILE ALA ALA PHE GLU GLU GLN SEQRES 10 A 149 GLN GLU ASN GLN PRO PRO SER SER GLY MET PRO HIS GLY SEQRES 11 A 149 ALA VAL PRO ALA GLY GLY LEU SER PRO PRO PRO PRO PRO SEQRES 12 A 149 SER PHE CYS THR VAL GLN FORMUL 2 HOH *136(H2 O) HELIX 1 1 GLU A 31 ASP A 33 5 3 HELIX 2 2 ASP A 34 VAL A 51 1 18 HELIX 3 3 ALA A 56 LYS A 61 1 6 HELIX 4 4 PRO A 63 GLY A 67 5 5 HELIX 5 5 THR A 97 GLN A 117 1 21 HELIX 6 6 PRO A 143 THR A 147 5 5 SHEET 1 A 5 SER A 5 THR A 8 0 SHEET 2 A 5 LYS A 72 PHE A 76 -1 N MET A 73 O SER A 7 SHEET 3 A 5 CYS A 79 LEU A 82 -1 O CYS A 79 N PHE A 76 SHEET 4 A 5 LYS A 85 ILE A 88 -1 O LYS A 85 N LEU A 82 SHEET 5 A 5 LYS A 91 ASP A 95 -1 O LYS A 91 N ILE A 88 SHEET 1 B 3 CYS A 13 LYS A 16 0 SHEET 2 B 3 GLN A 19 VAL A 22 -1 O GLN A 19 N LYS A 16 SHEET 3 B 3 LEU A 25 MET A 29 -1 O LEU A 25 N VAL A 22 SSBOND 1 CYS A 13 CYS A 66 1555 1555 2.03 SSBOND 2 CYS A 48 CYS A 59 1555 1555 2.03 SSBOND 3 CYS A 79 CYS A 146 1555 1555 2.03 CISPEP 1 GLY A 9 PRO A 10 0 0.07 CRYST1 30.455 72.717 31.137 90.00 101.03 90.00 P 1 21 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 0.032835 0.000000 0.006399 0.00000 SCALE2 0.000000 0.013752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032720 0.00000