HEADER HYDROLASE 08-NOV-06 2NU4 TITLE ACCOMMODATION OF POSITIVELY-CHARGED RESIDUES IN A HYDROPHOBIC TITLE 2 SPECIFICITY POCKET: CRYSTAL STRUCTURES OF SGPB IN COMPLEX WITH OMTKY3 TITLE 3 VARIANTS LYS18I AND ARG18I COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTOGRISIN B, PROTEINASE B; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: RESIDUES 115-299; COMPND 5 SYNONYM: PROTEASE B, SGPB, PRONASE ENZYME B; COMPND 6 EC: 3.4.21.81; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: OVOMUCOID; COMPND 9 CHAIN: I; COMPND 10 FRAGMENT: THIRD DOMAIN, RESIDUES 135-185; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES GRISEUS; SOURCE 3 ORGANISM_TAXID: 1911; SOURCE 4 STRAIN: K1; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: MELEAGRIS GALLOPAVO; SOURCE 7 ORGANISM_COMMON: TURKEY; SOURCE 8 ORGANISM_TAXID: 9103; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PEZZ318 KEYWDS ENZYME-INHIBITOR COMPLEX, CHARGED P1 RESIDUE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.S.BATEMAN,S.ANDERSON,W.LU,M.A.QASIM,M.LASKOWSKI JR.,M.N.G.JAMES REVDAT 3 20-OCT-21 2NU4 1 SEQADV REVDAT 2 24-FEB-09 2NU4 1 VERSN REVDAT 1 21-NOV-06 2NU4 0 JRNL AUTH K.S.BATEMAN,S.ANDERSON,W.LU,M.A.QASIM,M.LASKOWSKI JR., JRNL AUTH 2 M.N.G.JAMES JRNL TITL ACCOMMODATION OF POSITIVELY-CHARGED RESIDUES IN A JRNL TITL 2 HYDROPHOBIC SPECIFICITY POCKET: CRYSTAL STRUCTURES OF SGPB JRNL TITL 3 IN COMPLEX WITH OMTKY3 VARIANTS LYS18I AND ARG18I JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 19056 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 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 : 174 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) : 1.016 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 16.273; 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 2NU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040304. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-98 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) : 1.54178 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19056 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.17300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 3SGB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM POTASSIUM PHOSPHATE REMARK 280 AT PH 7.1 24H BEFORE DATA COLLECTION, CRYSTAL WAS TRANSFERRED TO REMARK 280 PEG4000, NAKHPO4 AT PH 10.7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 27.34450 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 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 SER E 33 -163.36 -108.09 REMARK 500 PHE E 94 139.75 -170.03 REMARK 500 PRO E 99A -152.71 -78.71 REMARK 500 ASN E 100 -61.36 78.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SGB RELATED DB: PDB REMARK 900 STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND THE REMARK 900 THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT 1.8 ANGSTROMS REMARK 900 RESOLUTION REMARK 900 RELATED ID: 2NU0 RELATED DB: PDB REMARK 900 MOLECULAR STRUCTURES OF THE COMPLEXES OF SGPB WITH OMTKY3 AROMATIC REMARK 900 P1 VARIANTS TRP18I, HIS18I, PHE18I, AND TYR18I REMARK 900 RELATED ID: 2NU1 RELATED DB: PDB REMARK 900 MOLECULAR STRUCTURES OF THE COMPLEXES OF SGPB WITH OMTKY3 AROMATIC REMARK 900 P1 VARIANTS TRP18I, HIS18I, PHE18I AND TYR18I REMARK 900 RELATED ID: 2NU2 RELATED DB: PDB REMARK 900 ACCOMMODATION OF POSITIVELY-CHARGED RESIDUES IN A HYDROPHOBIC REMARK 900 SPECIFICITY POCKET: CRYSTAL STRUCTURES OF SGPB IN COMPLEX WITH REMARK 900 OMTKY3 VARIANTS LYS18I AND ARG18I REMARK 900 RELATED ID: 2NU3 RELATED DB: PDB REMARK 900 ACCOMMODATION OF POSITIVELY-CHARGED RESIDUES IN A HYDROPHOBIC REMARK 900 SPECIFICITY POCKET: CRYSTAL STRUCTURES OF SGPB IN COMPLEX WITH REMARK 900 OMTKY3 VARIANTS LYS18I AND ARG18I REMARK 900 RELATED ID: 4SGA RELATED DB: PDB REMARK 900 STRUCTURES OF PRODUCT AND INHIBITOR COMPLEXES OF STREPTOMYCES REMARK 900 GRISEUS PROTEASE A AT 1.8 ANGSTROMS RESOLUTION. A MODEL FOR SERINE REMARK 900 PROTEASE CATALYSIS REMARK 900 RELATED ID: 1MCT RELATED DB: PDB REMARK 900 THE REFINED 1.6 ANGSTROMS RESOLUTION CRYSTAL STRUCTURE OF THE REMARK 900 COMPLEX FORMED BETWEEN PORCINE BETA-TRYPSIN AND MCTI-A, A TRYPSIN REMARK 900 INHIBITOR OF SQUASH FAMILY REMARK 900 RELATED ID: 1HJA RELATED DB: PDB REMARK 900 LYS 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED REMARK 900 WITH ALPHA-CHYMOTRYPSIN DBREF 2NU4 E 16 242 UNP P00777 PRTB_STRGR 115 299 DBREF 2NU4 I 6 56 UNP P68390 IOVO_MELGA 135 185 SEQADV 2NU4 LYS I 18 UNP P68390 LEU 147 ENGINEERED MUTATION 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 SER 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 LYS 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 FORMUL 3 HOH *174(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 O CYS E 42 N 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 O LEU E 85 N 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 N PHE E 52 O VAL E 106 SHEET 5 B 6 PHE E 46 SER E 48B-1 N SER E 48B O THR E 49 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 O GLN E 122 N VAL E 119 SHEET 1 D 9 SER E 126 ALA E 127 0 SHEET 2 D 9 CYS I 16 THR I 17 0 SHEET 3 D 9 PRO E 198 SER E 201 0 SHEET 4 D 9 ALA E 135 GLY E 140 -1 N THR E 137 O TYR E 200 SHEET 5 D 9 GLY E 156 ASN E 170 -1 O HIS E 158 N ARG E 138 SHEET 6 D 9 VAL E 176 THR E 183 -1 O MET E 180 N ALA E 167 SHEET 7 D 9 GLY E 223 PRO E 230 -1 O PHE E 228 N ILE E 181 SHEET 8 D 9 ARG E 208 ASN E 219 -1 N GLY E 215 O PHE E 227 SHEET 9 D 9 CYS I 16 THR I 17 -1 O CYS I 16 N GLY E 216 SHEET 1 E 3 THR I 30 TYR I 31 0 SHEET 2 E 3 LEU I 23 GLY I 25 -1 N LEU I 23 O TYR I 31 SHEET 3 E 3 LEU I 50 PHE I 53 -1 O SER I 51 N CYS I 24 SSBOND 1 CYS E 42 CYS E 58 1555 1555 2.04 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 2.03 SSBOND 5 CYS I 24 CYS I 56 1555 1555 2.03 CISPEP 1 PHE E 94 PRO E 99A 0 -1.80 CISPEP 2 TYR I 11 PRO I 12 0 3.52 CRYST1 45.452 54.689 45.633 90.00 119.33 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 0.022001 0.000000 0.012362 0.00000 SCALE2 0.000000 0.018285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025136 0.00000 MASTER 219 0 0 3 22 0 0 6 0 0 0 19 END