PDB Short entry for 1DS3 HEADER HYDROLASE INHIBITOR 06-JAN-00 1DS3 TITLE CRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I COMPND MOL_ID: 1; COMPND 2 MOLECULE: OVOMUCOID; COMPND 3 CHAIN: I; COMPND 4 FRAGMENT: THIRD DOMAIN (OMTKY3); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MELEAGRIS GALLOPAVO; SOURCE 3 ORGANISM_COMMON: TURKEY; SOURCE 4 ORGANISM_TAXID: 9103; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 OTHER_DETAILS: THE PEPTIDE BOND BETWEEN LEU18I(2LU) AND ASP19I HAS SOURCE 8 BEEN REDUCED. KEYWDS CANONICAL PROTEIN INHIBITOR, OVOMUCOID, REDUCED PEPTIDE BOND, OMTKY3, KEYWDS 2 HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR K.S.BATEMAN,K.HUANG,S.ANDERSON,W.LU,M.A.QASIM,M.LASKOWSKI JR., AUTHOR 2 M.N.G.JAMES REVDAT 5 03-NOV-21 1DS3 1 SEQADV LINK REVDAT 4 17-AUG-11 1DS3 1 HETNAM VERSN REVDAT 3 24-FEB-09 1DS3 1 VERSN REVDAT 2 01-APR-03 1DS3 1 JRNL REVDAT 1 31-JAN-01 1DS3 0 JRNL AUTH K.S.BATEMAN,K.HUANG,S.ANDERSON,W.LU,M.A.QASIM, JRNL AUTH 2 M.LASKOWSKI JR.,M.N.JAMES JRNL TITL CONTRIBUTION OF PEPTIDE BONDS TO INHIBITOR-PROTEASE BINDING: JRNL TITL 2 CRYSTAL STRUCTURES OF THE TURKEY OVOMUCOID THIRD DOMAIN JRNL TITL 3 BACKBONE VARIANTS OMTKY3-PRO18I AND OMTKY3-PSI[COO]-LEU18I JRNL TITL 4 IN COMPLEX WITH STREPTOMYCES GRISEUS PROTEINASE B (SGPB) AND JRNL TITL 5 THE STRUCTURE OF THE FREE INHIBITOR, JRNL TITL 6 OMTKY-3-PSI[CH2NH2+]-ASP19I JRNL REF J.MOL.BIOL. V. 305 839 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11162096 JRNL DOI 10.1006/JMBI.2000.4343 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4800 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM. 5% REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 385 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.115 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 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 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DS3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL 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) : 1.5417 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XPRESS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16933 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 92.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, NO BUFFER, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K 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 18.04600 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: I 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SGP RELATED DB: PDB REMARK 900 SGPB:OMTKY3(WILD TYPE) REMARK 900 RELATED ID: 1SGR RELATED DB: PDB REMARK 900 SGPB:OMTKY3-LEU18I REMARK 900 RELATED ID: 1SGQ RELATED DB: PDB REMARK 900 SGPB:OMTKY3-GLY18I REMARK 900 RELATED ID: 1SGP RELATED DB: PDB REMARK 900 SGPB:OMTKY3-ALA18I REMARK 900 RELATED ID: 2SGP RELATED DB: PDB REMARK 900 SGPB:OMTKY3-PRO18I DBREF 1DS3 I 6 56 UNP P68390 IOVO_MELGA 135 185 SEQADV 1DS3 DCL I 18 UNP P68390 LEU 147 ENGINEERED MUTATION SEQADV 1DS3 ASP I 19 UNP P68390 GLU 148 ENGINEERED MUTATION SEQRES 1 I 51 VAL ASP CYS SER GLU TYR PRO LYS PRO ALA CYS THR DCL SEQRES 2 I 51 ASP TYR ARG PRO LEU CYS GLY SER ASP ASN LYS THR TYR SEQRES 3 I 51 GLY ASN LYS CYS ASN PHE CYS ASN ALA VAL VAL GLU SER SEQRES 4 I 51 ASN GLY THR LEU THR LEU SER HIS PHE GLY LYS CYS HET DCL I 18 7 HETNAM DCL 2-AMINO-4-METHYL-PENTAN-1-OL HETSYN DCL LEUCINOL FORMUL 1 DCL C6 H15 N O FORMUL 2 HOH *41(H2 O) HELIX 1 1 ASN I 33 SER I 44 1 12 SHEET 1 A 3 THR I 30 TYR I 31 0 SHEET 2 A 3 LEU I 23 GLY I 25 -1 O LEU I 23 N TYR I 31 SHEET 3 A 3 LEU I 50 PHE I 53 -1 N SER I 51 O CYS I 24 SSBOND 1 CYS I 8 CYS I 38 1555 1555 2.03 SSBOND 2 CYS I 16 CYS I 35 1555 1555 2.02 SSBOND 3 CYS I 24 CYS I 56 1555 1555 2.02 LINK C THR I 17 N DCL I 18 1555 1555 1.33 LINK C DCL I 18 N ASP I 19 1555 1555 1.45 CISPEP 1 TYR I 11 PRO I 12 0 2.38 CRYST1 23.152 36.092 26.135 90.00 97.51 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 0.043193 0.000000 0.005692 0.00000 SCALE2 0.000000 0.027707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038594 0.00000