HEADER PLANT PROTEIN 07-FEB-07 2OT6 OBSLTE 27-NOV-07 2OT6 2R33 TITLE CRYSTAL STRUCTURE OF A BOWMAN-BIRK INHIBITOR FROM VIGNA TITLE 2 UNGUICULATA SEEDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN INHIBITOR; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIGNA SINENSIS; SOURCE 3 ORGANISM_COMMON: COWPEA; SOURCE 4 ORGAN: SEEDS KEYWDS BOWMAN-BIRK PROTEASE INHIBITOR,VIGNA UNGUICULATA,PLANT-PIS, KEYWDS 2 PROTEIN-PROTEIN INTERACTIONS, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.N.RAO,C.G.SURESH REVDAT 2 27-NOV-07 2OT6 1 OBSLTE REVDAT 1 13-MAR-07 2OT6 0 JRNL AUTH K.N.RAO,C.G.SURESH JRNL TITL PURIFICATION, CHARACTERIZATION AND STRUCTURAL JRNL TITL 2 STUDY OF BOWMAN-BIRK PROTEASE INHIBITORS FROM THE JRNL TITL 3 SEEDS OF VIGNA UNGUICULATA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4072 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 177 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; 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) : 3.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.930 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.540 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESOLUTION-DEPENDENT WEIGHTING REMARK 4 REMARK 4 2OT6 COMPLIES WITH FORMAT V. 3.1, 1-AUG-2007 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE RCSB ID CODE IS RCSB041554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-1996 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 4.00 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEIT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4072 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: X-RAY COORDINATES OF BOWMAN-BIRK INHIBITOR FROM REMARK 200 ADZUKI BEAN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% SATURATED AMMONIUM SULFATE 0.1M REMARK 280 CITRATE-PHOSPHATE, PH 4.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.71500 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 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 300 REMARK 300 REMARK: TIGHT DIMER 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: DIMER REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSEQI REMARK 465 GLU A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 ALA A 43 REMARK 465 PRO A 44 REMARK 465 PRO A 62 REMARK 465 GLU B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 PRO B 62 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 SER A 42 OG REMARK 470 HIS B 31 CG ND1 CD2 CE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS B 58 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCELIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 15 CB SER A 15 OG -0.240 REMARK 500 REMARK 500 REMARK: NULL 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 NUCELIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER A 15 N - CA - CB ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG A 26 NE - CZ - NH2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 48 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 48 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 PRO B 44 CA - N - CD ANGL. DEV. = -11.0 DEGREES REMARK 500 PRO B 44 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 PRO B 44 N - CD - CG ANGL. DEV. = 8.6 DEGREES REMARK 500 PRO B 44 C - N - CA ANGL. DEV. = 15.9 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 LYS A 14 26.14 -71.55 REMARK 500 SER B 15 -172.36 -171.00 REMARK 500 ASN B 28 -22.74 67.96 REMARK 500 ALA B 41 -172.61 66.12 REMARK 500 ALA B 43 103.72 -17.09 REMARK 500 PRO B 44 93.72 -54.93 REMARK 500 ASP B 51 128.63 -38.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M=MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 78 DISTANCE = 6.25 ANGSTROMS REMARK 999 REMARK 999 SEQUENCE REMARK 999 Sequence REMARK 999 No suitable database references were REMARK 999 found at time of processing SEQRES 1 A 62 GLU SER SER GLU PRO CYS CYS ASP SER CYS VAL CYS THR SEQRES 2 A 62 LYS SER ILE PRO PRO GLN CYS HIS CYS THR ASN ILE ARG SEQRES 3 A 62 LEU ASN SER CYS HIS SER GLY CYS LYS SER CYS LEU CYS SEQRES 4 A 62 THR ALA SER ALA PRO GLY SER CYS ARG CYS LEU ASP ILE SEQRES 5 A 62 ALA ASN PHE CYS TYR LYS PRO CYS LYS PRO SEQRES 1 B 62 GLU SER SER GLU PRO CYS CYS ASP SER CYS VAL CYS THR SEQRES 2 B 62 LYS SER ILE PRO PRO GLN CYS HIS CYS THR ASN ILE ARG SEQRES 3 B 62 LEU ASN SER CYS HIS SER GLY CYS LYS SER CYS LEU CYS SEQRES 4 B 62 THR ALA SER ALA PRO GLY SER CYS ARG CYS LEU ASP ILE SEQRES 5 B 62 ALA ASN PHE CYS TYR LYS PRO CYS LYS PRO FORMUL 3 HOH *58(H2 O) SHEET 1 A 2 CYS A 10 THR A 13 0 SHEET 2 A 2 GLN A 19 CYS A 22 -1 O GLN A 19 N THR A 13 SHEET 1 B 2 CYS A 37 THR A 40 0 SHEET 2 B 2 SER A 46 CYS A 49 -1 O ARG A 48 N LEU A 38 SHEET 1 C 2 CYS B 10 CYS B 12 0 SHEET 2 C 2 CYS B 20 CYS B 22 -1 O HIS B 21 N VAL B 11 SHEET 1 D 3 ARG B 26 LEU B 27 0 SHEET 2 D 3 SER B 46 CYS B 49 -1 O CYS B 47 N ARG B 26 SHEET 3 D 3 CYS B 37 THR B 40 -1 N LEU B 38 O ARG B 48 SSBOND 1 CYS A 6 CYS A 60 1555 1555 2.04 SSBOND 2 CYS A 7 CYS A 22 1555 1555 2.05 SSBOND 3 CYS A 10 CYS A 56 1555 1555 2.04 SSBOND 4 CYS A 12 CYS A 20 1555 1555 2.83 SSBOND 5 CYS A 30 CYS A 37 1555 1555 2.02 SSBOND 6 CYS A 34 CYS A 49 1555 1555 2.04 SSBOND 7 CYS A 39 CYS A 47 1555 1555 2.02 SSBOND 8 CYS B 6 CYS B 60 1555 1555 2.02 SSBOND 9 CYS B 7 CYS B 22 1555 1555 2.04 SSBOND 10 CYS B 10 CYS B 56 1555 1555 2.01 SSBOND 11 CYS B 12 CYS B 20 1555 1555 2.05 SSBOND 12 CYS B 30 CYS B 37 1555 1555 2.03 SSBOND 13 CYS B 34 CYS B 49 1555 1555 2.07 SSBOND 14 CYS B 39 CYS B 47 1555 1555 2.04 CISPEP 1 ILE A 16 PRO A 17 0 6.33 CISPEP 2 ILE B 16 PRO B 17 0 -3.69 CISPEP 3 ALA B 43 PRO B 44 0 -19.44 CRYST1 32.510 61.430 32.990 90.00 114.87 90.00 P 1 21 1 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 0.030760 0.000000 0.014260 0.00000 SCALE2 0.000000 0.016280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033410 0.00000