HEADER HYDROLASE INHIBITOR 27-OCT-03 1R8N TITLE THE CRYSTAL STRUCTURE OF THE KUNITZ (STI) TYPE INHIBITOR FROM SEEDS OF TITLE 2 DELONIX REGIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: KUNITZ TRYPSIN INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STI SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DELONIX REGIA; SOURCE 3 ORGANISM_TAXID: 72433 KEYWDS KUNITZ-TYPE TRYPSIN/KALLIKREIN INHIBITOR, BETA-TREFOIL FOLD, KEYWDS 2 FLAMBOYANT, DELONIX REGIA, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR S.KRAUCHENCO,S.C.PANDO,S.MARANGONI,I.POLIKARPOV REVDAT 3 23-AUG-23 1R8N 1 REMARK REVDAT 2 24-FEB-09 1R8N 1 VERSN REVDAT 1 25-MAY-04 1R8N 0 JRNL AUTH S.KRAUCHENCO,S.C.PANDO,S.MARANGONI,I.POLIKARPOV JRNL TITL CRYSTAL STRUCTURE OF THE KUNITZ (STI)-TYPE INHIBITOR FROM JRNL TITL 2 DELONIX REGIA SEEDS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 312 1303 2003 JRNL REFN ISSN 0006-291X JRNL PMID 14652016 JRNL DOI 10.1016/J.BBRC.2003.11.062 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.POLIKARPOV,A.M.GOLUBEV,L.A.PERLES,S.C.PANDO,J.C.NOVELLO, REMARK 1 AUTH 2 S.MARANGONI REMARK 1 TITL PURIFICATION, CRYSTALLIZATION AND PRELIMINARY REMARK 1 TITL 2 CRYSTALLOGRAPHIC STUDY OF A KUNITZ-TYPE TRYPSIN INHIBITOR REMARK 1 TITL 3 FROM DELONIX REGIA SEEDS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 1611 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444999009361 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.C.PANDO,M.L.V.OLIVA,C.A.M.SAMPAIO,L.DI CIERO,J.C.NOVELLO, REMARK 1 AUTH 2 S.MARANGONI REMARK 1 TITL PRIMARY SEQUENCE DETERMINATION OF A KUNITZ INHIBITOR REMARK 1 TITL 2 ISOLATED FROM DELONIX REGIA SEEDS REMARK 1 REF PHYTOCHEMISTRY V. 57 625 2001 REMARK 1 REFN ISSN 0031-9422 REMARK 1 DOI 10.1016/S0031-9422(01)00080-2 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 19.52 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) (%) : 77.1 REMARK 3 NUMBER OF REFLECTIONS : 23454 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) : 0.215 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1075 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 24.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE : 0.6290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 14 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.168 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1417 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.65000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 10.12000 REMARK 3 B13 (A**2) : -2.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.29 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1R8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.38 REMARK 200 MONOCHROMATOR : TRIANGULAR BENT CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 19.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.1 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 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) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 35.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1AVU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG8000, 0.25M AMMONIUM SULFATE, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 16.06250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.03050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.62450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.03050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.06250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.62450 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 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 ASP A 2 102.10 70.33 REMARK 500 ALA A 3 -141.61 69.57 REMARK 500 ARG A 40 96.93 -51.14 REMARK 500 ASP A 100 40.29 -161.30 REMARK 500 SER A 101 33.16 -172.57 REMARK 500 LEU A 129 63.02 -116.34 REMARK 500 SER A 144 92.07 -60.28 REMARK 500 SER A 146 134.26 -172.37 REMARK 500 GLU A 155 35.02 -158.16 REMARK 500 ARG A 158 65.63 32.55 REMARK 500 VAL A 168 44.94 -142.96 REMARK 500 SER A 179 -145.93 -147.67 REMARK 500 GLU A 184 100.81 -46.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R8O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN UNUSUAL KUNITZ-TYPE TRYPSIN INHIBITOR FROM REMARK 900 COPAIFERA LANGSDORFFII SEEDS DBREF 1R8N A 1 185 UNP P83667 DRTI_DELRE 1 185 SEQRES 1 A 185 SER ASP ALA GLU LYS VAL TYR ASP ILE GLU GLY TYR PRO SEQRES 2 A 185 VAL PHE LEU GLY SER GLU TYR TYR ILE VAL SER ALA ILE SEQRES 3 A 185 ILE GLY ALA GLY GLY GLY GLY VAL ARG PRO GLY ARG THR SEQRES 4 A 185 ARG GLY SER MET CYS PRO MET SER ILE ILE GLN GLU GLN SEQRES 5 A 185 SER ASP LEU GLN MET GLY LEU PRO VAL ARG PHE SER SER SEQRES 6 A 185 PRO GLU GLU LYS GLN GLY LYS ILE TYR THR ASP THR GLU SEQRES 7 A 185 LEU GLU ILE GLU PHE VAL GLU LYS PRO ASP CYS ALA GLU SEQRES 8 A 185 SER SER LYS TRP VAL ILE VAL LYS ASP SER GLY GLU ALA SEQRES 9 A 185 ARG VAL ALA ILE GLY GLY SER GLU ASP HIS PRO GLN GLY SEQRES 10 A 185 GLU LEU VAL ARG GLY PHE PHE LYS ILE GLU LYS LEU GLY SEQRES 11 A 185 SER LEU ALA TYR LYS LEU VAL PHE CYS PRO LYS SER ASP SEQRES 12 A 185 SER GLY SER CYS SER ASP ILE GLY ILE ASN TYR GLU GLY SEQRES 13 A 185 ARG ARG SER LEU VAL LEU LYS SER SER ASP ASP VAL PRO SEQRES 14 A 185 PHE ARG VAL VAL PHE VAL LYS PRO ARG SER GLY SER GLU SEQRES 15 A 185 THR GLU SER FORMUL 2 HOH *183(H2 O) HELIX 1 1 PRO A 115 LEU A 119 5 5 SHEET 1 A 4 GLU A 80 PHE A 83 0 SHEET 2 A 4 VAL A 61 SER A 64 -1 N ARG A 62 O GLU A 82 SHEET 3 A 4 GLU A 19 SER A 24 -1 N TYR A 20 O VAL A 61 SHEET 4 A 4 VAL A 172 VAL A 175 -1 O VAL A 175 N TYR A 21 SHEET 1 B 2 VAL A 34 GLY A 37 0 SHEET 2 B 2 SER A 47 GLN A 50 -1 O SER A 47 N GLY A 37 SHEET 1 C 2 TRP A 95 VAL A 98 0 SHEET 2 C 2 ARG A 105 ILE A 108 -1 O ALA A 107 N VAL A 96 SHEET 1 D 4 GLY A 122 LYS A 128 0 SHEET 2 D 4 TYR A 134 PRO A 140 -1 O CYS A 139 N PHE A 123 SHEET 3 D 4 SER A 148 ASN A 153 -1 O SER A 148 N PHE A 138 SHEET 4 D 4 SER A 159 LEU A 162 -1 O VAL A 161 N GLY A 151 SSBOND 1 CYS A 44 CYS A 89 1555 1555 2.03 SSBOND 2 CYS A 139 CYS A 147 1555 1555 2.03 CRYST1 32.125 67.249 72.061 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 0.031128 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013877 0.00000