PDB Short entry for 2NU0 HEADER HYDROLASE 08-NOV-06 2NU0 TITLE MOLECULAR STRUCTURES OF THE COMPLEXES OF SGPB WITH OMTKY3 AROMATIC P1 TITLE 2 VARIANTS TRP18I, HIS18I, PHE18I, AND TYR18I COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTOGRISIN B, PROTEASE B; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: RESIDUES 115-299; COMPND 5 SYNONYM: 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 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 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PEZZ318.TKY KEYWDS ENZYME-INHIBITOR COMPLEX, AROMATIC P1 RESIDUE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.S.BATEMAN,S.ANDERSON,W.LU,M.A.QASIM,K.HUANG,M.LASKOWSKI JR., AUTHOR 2 M.N.G.JAMES REVDAT 4 30-AUG-23 2NU0 1 REMARK REVDAT 3 20-OCT-21 2NU0 1 SEQADV REVDAT 2 24-FEB-09 2NU0 1 VERSN REVDAT 1 21-NOV-06 2NU0 0 JRNL AUTH K.S.BATEMAN,S.ANDERSON,W.LU,M.A.QASIM,K.HUANG, JRNL AUTH 2 M.LASKOWSKI JR.,M.N.G.JAMES JRNL TITL MOLECULAR STRUCTURES OF THE COMPLEXES OF SGPB WITH OMTKY3 JRNL TITL 2 AROMATIC P1 VARIANTS TRP18I, HIS18I, PHE18I, AND TYR18I JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 13629 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 0 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 : 1702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 139 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) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.155 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 16.108; 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 2NU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-94 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) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE MONOCHROMETER REMARK 200 OPTICS : GRAPHITE MONOCHROMETER REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SDMS REMARK 200 DATA SCALING SOFTWARE : SDMS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13629 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REPLACEMENT 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 (%): 39.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM POTASSIUM PHOSPHATE, REMARK 280 PH 7.1, VAPOR DIFFUSION, HANGING DROP, 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 27.26000 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 -166.70 -108.78 REMARK 500 PRO E 99A -154.45 -79.10 REMARK 500 ASN E 100 -58.28 81.63 REMARK 500 ASP E 102 70.45 -152.40 REMARK 500 LYS E 115 77.84 -119.77 REMARK 500 ARG I 21 79.50 -152.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SGY RELATED DB: PDB REMARK 900 TYR 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED REMARK 900 WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 REMARK 900 RELATED ID: 2SGF RELATED DB: PDB REMARK 900 PHE 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED REMARK 900 WITH STREPTOMYCES GRISEUS PROTEINASE B 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: 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: 2NU4 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 DBREF 2NU0 E 16 242 UNP P00777 PRTB_STRGR 115 299 DBREF 2NU0 I 6 56 UNP P68390 IOVO_MELGA 135 185 SEQADV 2NU0 TRP I 18 UNP P68390 LEU 18 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 TRP 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 *139(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 ARG E 107 N THR E 87 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 VAL E 48 O TYR E 51 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 ARG E 182 N ALA E 164 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 HIS I 52 N 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 2.03 CISPEP 1 PHE E 94 PRO E 99A 0 -1.12 CISPEP 2 TYR I 11 PRO I 12 0 3.06 CRYST1 45.350 54.520 45.650 90.00 119.20 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 0.022051 0.000000 0.012324 0.00000 SCALE2 0.000000 0.018342 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025095 0.00000