HEADER PROTEIN BINDING 03-MAR-04 1VBW TITLE CRYSTAL STRUCTURE OF BITTER GOURD TRYPSIN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN INHIBITOR BGIT; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MOMORDICA CHARANTIA; SOURCE 3 ORGANISM_COMMON: BALSAM PEAR; SOURCE 4 ORGANISM_TAXID: 3673; SOURCE 5 TISSUE: PEELED SEEDS KEYWDS BGTI, TRYPSIN INHIBITOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.SUTO,M.FURUICHI,E.NISHIMOTO,K.MENO,K.HORII,H.MIZUNO REVDAT 4 30-OCT-24 1VBW 1 REMARK REVDAT 3 25-OCT-23 1VBW 1 REMARK LINK REVDAT 2 24-FEB-09 1VBW 1 VERSN REVDAT 1 22-MAR-05 1VBW 0 JRNL AUTH K.SUTO,M.FURUICHI,E.NISHIMOTO,K.MENO,K.HORII,H.MIZUNO JRNL TITL CRYSTAL STRUCTURE OF BITTER GOURD TRYPSIN INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.93 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.114 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1660 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 33916 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.108 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1456 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 29750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 516 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.330 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.095 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.106 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.028 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VBW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006443. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34146 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.930 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.28200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 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 2CI2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 10.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTRATE, PH 8.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,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 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: 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 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 26 NE - CZ - NH2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 52 CD - NE - CZ ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG A 52 NH1 - CZ - NH2 ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG A 52 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -6.2 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 CYS A 3 4.70 82.45 REMARK 500 LYS A 44 47.64 -90.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 11 O REMARK 620 2 VAL A 13 O 92.5 REMARK 620 3 PRO A 29 O 79.9 111.2 REMARK 620 4 HOH A3006 O 161.3 92.4 81.5 REMARK 620 5 HOH A3035 O 146.5 71.0 132.8 51.6 REMARK 620 6 HOH A3074 O 88.7 76.5 166.4 110.0 59.7 REMARK 620 7 HOH A3075 O 89.8 147.6 101.0 95.6 89.8 71.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 52 N REMARK 620 2 THR A 66 O 95.1 REMARK 620 3 GLY A 68 O 119.9 121.0 REMARK 620 4 HOH A3037 O 116.8 76.8 117.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLA A 1101 DBREF 1VBW A 1 68 UNP Q7M1Q1 Q7M1Q1_MOMCH 1 68 SEQRES 1 A 68 SER ARG CYS GLN GLY LYS SER SER TRP PRO GLN LEU VAL SEQRES 2 A 68 GLY SER THR GLY ALA ALA ALA LYS ALA VAL ILE GLU ARG SEQRES 3 A 68 GLU ASN PRO ARG VAL ARG ALA VAL ILE ILE LYS VAL GLY SEQRES 4 A 68 SER GLY ALA THR LYS ASP PHE ARG CYS ASP ARG VAL ARG SEQRES 5 A 68 VAL TRP VAL THR GLU ARG GLY ILE VAL ALA ARG PRO PRO SEQRES 6 A 68 THR ILE GLY HET K A1102 1 HET NA A1103 1 HET NA A1104 1 HET TLA A1101 10 HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETNAM TLA L(+)-TARTARIC ACID FORMUL 2 K K 1+ FORMUL 3 NA 2(NA 1+) FORMUL 5 TLA C4 H6 O6 FORMUL 6 HOH *140(H2 O) HELIX 1 1 TRP A 9 VAL A 13 5 5 HELIX 2 2 THR A 16 ASN A 28 1 13 SHEET 1 A 3 ARG A 32 LYS A 37 0 SHEET 2 A 3 ARG A 50 VAL A 55 1 O VAL A 53 N VAL A 34 SHEET 3 A 3 THR A 66 ILE A 67 -1 O THR A 66 N ARG A 52 SSBOND 1 CYS A 3 CYS A 48 1555 1555 2.08 LINK O GLN A 11 K K A1102 1555 1555 2.52 LINK O VAL A 13 K K A1102 1555 1555 2.55 LINK O PRO A 29 K K A1102 1545 1555 2.51 LINK N ARG A 52 NA NA A1103 1555 1555 2.87 LINK O THR A 66 NA NA A1103 1555 1555 2.70 LINK O GLY A 68 NA NA A1103 1555 1555 2.69 LINK K K A1102 O HOH A3006 1555 1555 2.58 LINK K K A1102 O HOH A3035 1555 1645 3.57 LINK K K A1102 O HOH A3074 1555 1555 2.68 LINK K K A1102 O HOH A3075 1555 1555 2.43 LINK NA NA A1103 O HOH A3037 1555 1555 2.73 LINK NA NA A1104 O HOH A3076 1555 1555 2.89 SITE 1 AC1 6 GLN A 11 VAL A 13 PRO A 29 HOH A3006 SITE 2 AC1 6 HOH A3074 HOH A3075 SITE 1 AC2 6 ARG A 50 VAL A 51 ARG A 52 THR A 66 SITE 2 AC2 6 GLY A 68 HOH A3037 SITE 1 AC3 5 LYS A 6 TRP A 9 PRO A 10 GLN A 11 SITE 2 AC3 5 HOH A3076 SITE 1 AC4 8 ARG A 2 LYS A 21 ARG A 32 ARG A 47 SITE 2 AC4 8 CYS A 48 ARG A 58 HOH A3012 HOH A3023 CRYST1 22.662 23.023 27.685 92.05 100.11 101.80 P 1 1 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 0.044127 0.009219 0.008578 0.00000 SCALE2 0.000000 0.044373 0.003309 0.00000 SCALE3 0.000000 0.000000 0.036792 0.00000