HEADER HYDROLASE/HYDROLASE INHIBITOR 06-JAN-00 1DS2 TITLE CRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEINASE B (SGPB); COMPND 3 CHAIN: E; COMPND 4 SYNONYM: STREPTOGRISIN B; COMPND 5 EC: 3.4.21.81; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: OVOMUCOID; COMPND 8 CHAIN: I; COMPND 9 FRAGMENT: THIRD DOMAIN (OMTKY3); COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES GRISEUS; SOURCE 3 ORGANISM_TAXID: 1911; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MELEAGRIS GALLOPAVO; SOURCE 6 ORGANISM_COMMON: TURKEY; SOURCE 7 ORGANISM_TAXID: 9103; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 OTHER_DETAILS: THE PEPTIDE LINKAGE BETWEEN THR17I AND LEU18I(1LU) SOURCE 11 HAS BEEN REPLACED BY AN ESTER BOND. KEYWDS SERINE PROTEINASE, PROTEIN INHIBITOR, OVOMUCOID, CANONICAL INHIBITOR, KEYWDS 2 ESTER BOND, SGPB, OMTKY3, HYDROLASE-HYDROLASE INHIBITOR COMPLEX 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 4 13-JUL-11 1DS2 1 VERSN REVDAT 3 24-FEB-09 1DS2 1 VERSN REVDAT 2 01-APR-03 1DS2 1 JRNL REVDAT 1 31-JAN-01 1DS2 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. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT V. 5-E REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 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 : 18894 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL 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 : 1697 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 140 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) : 0.011 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 0.985 ; 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 1DS2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-00. REMARK 100 THE RCSB ID CODE IS RCSB010322. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.1 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 : 61078 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 87.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM POTASSIUM PHOSPHATE, REMARK 280 PH 7.1, VAPOR 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 27.32350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, 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 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 PRO E 99A -152.58 -79.26 REMARK 500 ASN E 100 -58.49 78.13 REMARK 500 ASP E 102 71.33 -150.59 REMARK 500 LYS E 115 77.27 -117.23 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 E 349 DISTANCE = 5.29 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SGB 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 1DS2 E 16 242 UNP P00777 PRTB_STRGR 115 299 DBREF 1DS2 I 6 56 UNP P68390 IOVO_MELGA 135 185 SEQADV 1DS2 VAL E 235A UNP P00777 SER 292 CONFLICT SEQADV 1DS2 1LU I 18 UNP P68390 LEU 147 ENGINEERED SEQRES 1 E 185 ILE SER GLY GLY ASP ALA ILE TYR SER SER THR GLY ARG SEQRES 2 E 185 CYS SER LEU GLY PHE ASN VAL ARG SER GLY SER THR TYR SEQRES 3 E 185 TYR PHE LEU THR ALA GLY HIS CYS THR ASP GLY ALA THR SEQRES 4 E 185 THR TRP TRP ALA ASN SER ALA ARG THR THR VAL LEU GLY SEQRES 5 E 185 THR THR SER GLY SER SER PHE PRO ASN ASN ASP TYR GLY SEQRES 6 E 185 ILE VAL ARG TYR THR ASN THR THR ILE PRO LYS ASP GLY SEQRES 7 E 185 THR VAL GLY GLY GLN ASP ILE THR SER ALA ALA ASN ALA SEQRES 8 E 185 THR VAL GLY MET ALA VAL THR ARG ARG GLY SER THR THR SEQRES 9 E 185 GLY THR HIS SER GLY SER VAL THR ALA LEU ASN ALA THR SEQRES 10 E 185 VAL ASN TYR GLY GLY GLY ASP VAL VAL TYR GLY MET ILE SEQRES 11 E 185 ARG THR ASN VAL CYS ALA GLU PRO GLY ASP SER GLY GLY SEQRES 12 E 185 PRO LEU TYR SER GLY THR ARG ALA ILE GLY LEU THR SER SEQRES 13 E 185 GLY GLY SER GLY ASN CYS SER SER GLY GLY THR THR PHE SEQRES 14 E 185 PHE GLN PRO VAL THR GLU ALA LEU VAL ALA TYR GLY VAL SEQRES 15 E 185 SER VAL TYR SEQRES 1 I 51 VAL ASP CYS SER GLU TYR PRO LYS PRO ALA CYS THR 1LU SEQRES 2 I 51 GLU 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 MODRES 1DS2 1LU I 18 LEU 4-METHYL-PENTANOIC ACID-2-OXYL GROUP HET 1LU I 18 8 HETNAM 1LU (2S)-2-HYDROXY-4-METHYL-PENTANOIC ACID FORMUL 2 1LU C6 H12 O3 FORMUL 3 HOH *140(H2 O) HELIX 1 1 ALA E 55 ASP E 60 1 6 HELIX 2 2 VAL E 231 GLY E 238 1 9 HELIX 3 3 ASN I 33 SER I 44 1 12 SHEET 1 A 2 ALA E 30 TYR E 32 0 SHEET 2 A 2 ARG E 41 SER E 43 -1 N CYS E 42 O ILE E 31 SHEET 1 B 6 THR E 65 TRP E 67 0 SHEET 2 B 6 VAL E 84 SER E 93 -1 N LEU E 85 O TRP E 66 SHEET 3 B 6 TYR E 103 TYR E 108 -1 O TYR E 103 N SER E 93 SHEET 4 B 6 THR E 49 THR E 54 -1 O TYR E 50 N TYR E 108 SHEET 5 B 6 PHE E 46 SER E 48B-1 O PHE E 46 N LEU E 53 SHEET 6 B 6 SER E 240 VAL E 241 -1 O SER E 240 N ARG E 48A SHEET 1 C 2 THR E 118 VAL E 119 0 SHEET 2 C 2 GLN E 122 ASP E 123 -1 N GLN E 122 O VAL E 119 SHEET 1 D 3 THR I 30 TYR I 31 0 SHEET 2 D 3 LEU I 23 GLY I 25 -1 O LEU I 23 N TYR I 31 SHEET 3 D 3 LEU I 50 PHE I 53 -1 N SER I 51 O CYS I 24 SSBOND 1 CYS E 42 CYS E 58 1555 1555 2.03 SSBOND 2 CYS E 191 CYS E 220 1555 1555 2.03 SSBOND 3 CYS I 8 CYS I 38 1555 1555 2.03 SSBOND 4 CYS I 16 CYS I 35 1555 1555 2.02 SSBOND 5 CYS I 24 CYS I 56 1555 1555 2.04 LINK OS 1LU I 18 C THR I 17 1555 1555 1.28 LINK C 1LU I 18 N GLU I 19 1555 1555 1.33 CISPEP 1 PHE E 94 PRO E 99A 0 -1.46 CISPEP 2 TYR I 11 PRO I 12 0 4.48 CRYST1 45.413 54.647 45.525 90.00 119.13 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 0.022020 0.000000 0.012269 0.00000 SCALE2 0.000000 0.018299 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025145 0.00000 MASTER 215 0 1 3 13 0 0 6 0 0 0 19 END