HEADER HYDROLASE INHIBITOR 23-NOV-98 1B1U TITLE CRYSTAL STRUCTURE OF THE BIFUNCTIONAL INHIBITOR RAGI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ALPHA-AMYLASE/TRYPSIN INHIBITOR RATI); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAGI BIFUNCTIONAL INHIBITOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ELEUSINE CORACANA; SOURCE 3 ORGANISM_COMMON: FINGER MILLET; SOURCE 4 ORGANISM_TAXID: 4511; SOURCE 5 ORGAN: SEED KEYWDS ALPHA-AMYLASE/TRYPSIN INHIBITOR (RATI), BIFUNCTIONAL, HYDROLASE KEYWDS 2 INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR S.GOURINATH,A.SRINIVASAN,T.P.SINGH REVDAT 7 09-AUG-23 1B1U 1 REMARK REVDAT 6 24-FEB-09 1B1U 1 VERSN REVDAT 5 08-APR-03 1B1U 1 REMARK MASTER REVDAT 4 08-MAR-00 1B1U 1 JRNL REVDAT 3 22-DEC-99 1B1U 1 JRNL REVDAT 2 15-DEC-99 1B1U 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 02-DEC-98 1B1U 0 SPRSDE 02-DEC-98 1B1U 1JFO JRNL AUTH S.GOURINATH,N.ALAM,A.SRINIVASAN,C.BETZEL,T.P.SINGH JRNL TITL STRUCTURE OF THE BIFUNCTIONAL INHIBITOR OF TRYPSIN AND JRNL TITL 2 ALPHA-AMYLASE FROM RAGI SEEDS AT 2.2 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 287 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 10713515 JRNL DOI 10.1107/S0907444999016601 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.STROBL,P.MUHLHAHN,R.BERNSTEIN,R.WILTSCHECK,K.MASKOS, REMARK 1 AUTH 2 M.WUNDERLICH,R.HUBER,R.GLOCKSHUBER,T.A.HOLAK REMARK 1 TITL DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE REMARK 1 TITL 2 BIFUNCTIONAL ALPHA-AMYLASE/TRYPSIN INHIBITOR FROM RAGI SEEDS REMARK 1 TITL 3 BY NMR SPECTROSCOPY REMARK 1 REF BIOCHEMISTRY V. 34 8281 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.SRINIVASAN,A.RAMAN,T.P.SINGH REMARK 1 TITL PRELIMINARY X-RAY INVESTIGATION OF A BIFUNCTIONAL INHIBITOR REMARK 1 TITL 2 FROM INDIAN FINGER MILLET (RAGI) REMARK 1 REF J.MOL.BIOL. V. 222 1 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH F.A.P.CAMPOS,M.RICHARDSON REMARK 1 TITL THE COMPLETE AMINO ACID SEQUENCE OF THE BIFUNCTIONAL REMARK 1 TITL 2 ALPHA-AMYLASE/TRYPSIN INHIBITOR FROM SEEDS OF RAGI (INDIAN REMARK 1 TITL 3 FINGER MILLET, ELEUSINE CORACANA GAERTN.) REMARK 1 REF FEBS LETT. V. 152 300 1983 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.7 REMARK 3 NUMBER OF REFLECTIONS : 4451 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) : 0.222 REMARK 3 FREE R VALUE : 0.321 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 251 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.023 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 498 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 26 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.083 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 880 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.80 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 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) : 2.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.570 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.160 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARA-1.DAT REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPO-1.DAT REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 173.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5684 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29900 REMARK 200 FOR SHELL : 2.270 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE (CCP4), CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 1BIP, MODEL 20 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.15M AMMONIUM SULFATE, 0.2M AMMONIUM REMARK 280 PHOSPHATE PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 23.69000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.69000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.24000 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 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 SER A 1 REMARK 465 VAL A 2 REMARK 465 ALA A 120 REMARK 465 GLY A 121 REMARK 465 GLU A 122 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 DISTANCE REMARK 500 O GLY A 3 OH TYR A 54 2.19 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 MET A 10 -74.55 -108.77 REMARK 500 ALA A 11 -39.00 -37.88 REMARK 500 PRO A 13 170.03 -57.10 REMARK 500 ASN A 15 63.19 67.79 REMARK 500 PRO A 33 -70.44 -79.50 REMARK 500 ARG A 34 -17.98 -159.45 REMARK 500 THR A 37 -39.05 -31.80 REMARK 500 ASP A 81 152.31 -38.87 REMARK 500 ALA A 94 -59.96 -20.58 REMARK 500 PRO A 95 7.40 -62.22 REMARK 500 GLU A 102 -125.96 -96.11 REMARK 500 ASN A 104 76.28 45.99 REMARK 500 PRO A 112 57.62 -69.88 REMARK 500 SER A 116 35.69 -91.16 REMARK 500 LEU A 118 88.94 -69.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 1B1U A 1 122 UNP P01087 IAAT_ELECO 1 122 SEQRES 1 A 122 SER VAL GLY THR SER CYS ILE PRO GLY MET ALA ILE PRO SEQRES 2 A 122 HIS ASN PRO LEU ASP SER CYS ARG TRP TYR VAL SER THR SEQRES 3 A 122 ARG THR CYS GLY VAL GLY PRO ARG LEU ALA THR GLN GLU SEQRES 4 A 122 MET LYS ALA ARG CYS CYS ARG GLN LEU GLU ALA ILE PRO SEQRES 5 A 122 ALA TYR CYS ARG CYS GLU ALA VAL ARG ILE LEU MET ASP SEQRES 6 A 122 GLY VAL VAL THR PRO SER GLY GLN HIS GLU GLY ARG LEU SEQRES 7 A 122 LEU GLN ASP LEU PRO GLY CYS PRO ARG GLN VAL GLN ARG SEQRES 8 A 122 ALA PHE ALA PRO LYS LEU VAL THR GLU VAL GLU CYS ASN SEQRES 9 A 122 LEU ALA THR ILE HIS GLY GLY PRO PHE CYS LEU SER LEU SEQRES 10 A 122 LEU GLY ALA GLY GLU FORMUL 2 HOH *88(H2 O) HELIX 1 1 ASP A 18 CYS A 29 5 12 HELIX 2 2 THR A 37 ALA A 50 1 14 HELIX 3 3 ALA A 53 MET A 64 1 12 HELIX 4 4 ARG A 87 LYS A 96 1 10 SHEET 1 A 2 VAL A 67 VAL A 68 0 SHEET 2 A 2 HIS A 74 GLU A 75 -1 N GLU A 75 O VAL A 67 SSBOND 1 CYS A 6 CYS A 55 1555 1555 2.03 SSBOND 2 CYS A 20 CYS A 44 1555 1555 2.04 SSBOND 3 CYS A 29 CYS A 85 1555 1555 2.05 SSBOND 4 CYS A 45 CYS A 103 1555 1555 2.04 SSBOND 5 CYS A 57 CYS A 114 1555 1555 2.03 CRYST1 47.380 54.480 40.350 90.00 90.00 90.00 P 21 21 2 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 0.021106 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024783 0.00000