PDB Short entry for 1IY5 HEADER HYDROLASE 23-JUL-02 1IY5 TITLE SOLUTION STRUCTURE OF WILD TYPE OMSVP3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OMSVP3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIRD DOMAIN; COMPND 5 SYNONYM: OVOMUCOID; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LOPHURA NYCTHEMERA; SOURCE 3 ORGANISM_COMMON: SILVER PHEASANT; SOURCE 4 ORGANISM_TAXID: 9046; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS SOLUTION STRUCTURE, CSH MOTIF, OMSVP3, OVOMUCOID THIRD DOMAIN, KEYWDS 2 PROTEASE INHIBITOR, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR H.HEMMI,T.KUMAZAKI,T.YAMAZAKI,S.KOJIMA,T.YOSHIDA,Y.KYOGOKU,M.KATSU, AUTHOR 2 H.YOKOSAWA,K.MIURA,Y.KOBAYASHI REVDAT 4 27-DEC-23 1IY5 1 REMARK REVDAT 3 23-FEB-22 1IY5 1 REMARK REVDAT 2 24-FEB-09 1IY5 1 VERSN REVDAT 1 11-MAR-03 1IY5 0 JRNL AUTH H.HEMMI,T.KUMAZAKI,T.YAMAZAKI,S.KOJIMA,T.YOSHIDA,Y.KYOGOKU, JRNL AUTH 2 M.KATSU,F.SHINOHARA,H.YOKOSAWA,K.MIURA,Y.KOBAYASHI JRNL TITL INHIBITORY SPECIFICITY CHANGE OF OVOMUCOID THIRD DOMAIN OF JRNL TITL 2 THE SILVER PHEASANT UPON INTRODUCTION OF AN ENGINEERED JRNL TITL 3 CYS14-CYS39 BOND JRNL REF BIOCHEMISTRY V. 42 2524 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12614146 JRNL DOI 10.1021/BI026727C REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IY5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000005395. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 4.0MM OMSVP3; 90%H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRPIPP 4.3.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOW TOTAL ENERGY AND LOW REMARK 210 DEVIATION FROM MEAN STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 1 VAL A 6 164.80 55.72 REMARK 500 1 CYS A 8 55.04 -102.25 REMARK 500 1 ALA A 15 146.89 169.06 REMARK 500 1 TYR A 20 45.72 -97.66 REMARK 500 1 ASN A 33 173.88 177.71 REMARK 500 1 THR A 49 -165.04 -120.36 REMARK 500 1 HIS A 52 108.33 178.98 REMARK 500 1 PHE A 53 92.48 -43.63 REMARK 500 2 SER A 5 -57.16 161.20 REMARK 500 2 CYS A 8 53.35 -99.67 REMARK 500 2 GLU A 10 44.34 -89.33 REMARK 500 2 ASN A 33 -165.32 176.37 REMARK 500 2 THR A 49 -149.98 -132.20 REMARK 500 2 HIS A 52 104.84 177.61 REMARK 500 2 PHE A 53 93.83 -44.84 REMARK 500 3 ASP A 7 86.48 -69.50 REMARK 500 3 CYS A 8 31.75 -89.15 REMARK 500 3 GLU A 10 35.00 -90.87 REMARK 500 3 GLU A 19 173.07 -54.95 REMARK 500 3 TYR A 20 37.18 -140.80 REMARK 500 3 ASN A 33 172.09 172.87 REMARK 500 3 THR A 49 -152.03 -123.85 REMARK 500 3 HIS A 52 110.07 176.99 REMARK 500 3 PHE A 53 93.72 -42.27 REMARK 500 4 VAL A 4 -48.53 -137.41 REMARK 500 4 SER A 5 -58.25 175.57 REMARK 500 4 ASN A 33 169.77 173.71 REMARK 500 4 ASN A 45 -0.47 75.51 REMARK 500 4 THR A 47 42.48 -101.46 REMARK 500 4 THR A 49 -157.09 -109.60 REMARK 500 4 HIS A 52 105.15 167.55 REMARK 500 4 PHE A 53 99.88 -47.00 REMARK 500 5 SER A 5 -91.70 49.46 REMARK 500 5 CYS A 8 45.17 -81.90 REMARK 500 5 ALA A 15 144.11 -176.62 REMARK 500 5 CYS A 16 -166.54 -126.31 REMARK 500 5 SER A 26 -18.17 -48.84 REMARK 500 5 ASN A 33 -172.47 175.09 REMARK 500 5 ASN A 45 -0.47 76.90 REMARK 500 5 THR A 49 -153.55 -137.75 REMARK 500 5 HIS A 52 109.55 178.09 REMARK 500 5 PHE A 53 103.67 -44.60 REMARK 500 6 CYS A 8 40.44 -80.66 REMARK 500 6 ALA A 15 -171.36 168.58 REMARK 500 6 ASN A 33 -168.17 172.84 REMARK 500 6 THR A 49 -152.63 -98.22 REMARK 500 6 HIS A 52 111.62 177.73 REMARK 500 6 PHE A 53 93.86 -43.35 REMARK 500 7 SER A 5 -56.48 83.97 REMARK 500 7 CYS A 16 -164.39 -116.44 REMARK 500 REMARK 500 THIS ENTRY HAS 116 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 21 0.32 SIDE CHAIN REMARK 500 2 ARG A 21 0.16 SIDE CHAIN REMARK 500 3 ARG A 21 0.28 SIDE CHAIN REMARK 500 4 ARG A 21 0.21 SIDE CHAIN REMARK 500 5 ARG A 21 0.24 SIDE CHAIN REMARK 500 6 ARG A 21 0.30 SIDE CHAIN REMARK 500 7 ARG A 21 0.29 SIDE CHAIN REMARK 500 8 ARG A 21 0.18 SIDE CHAIN REMARK 500 9 ARG A 21 0.19 SIDE CHAIN REMARK 500 10 ARG A 21 0.30 SIDE CHAIN REMARK 500 11 ARG A 21 0.31 SIDE CHAIN REMARK 500 12 ARG A 21 0.18 SIDE CHAIN REMARK 500 13 ARG A 21 0.28 SIDE CHAIN REMARK 500 14 ARG A 21 0.31 SIDE CHAIN REMARK 500 15 ARG A 21 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IY6 RELATED DB: PDB REMARK 900 1IY6 CONTAINS OMSVP3 VARIANT, P14C/N39C DBREF 1IY5 A 3 56 UNP P67954 IOVO_LOPNY 3 56 SEQRES 1 A 54 ALA VAL SER VAL ASP CYS SER GLU TYR PRO LYS PRO ALA SEQRES 2 A 54 CYS THR MET GLU TYR ARG PRO LEU CYS GLY SER ASP ASN SEQRES 3 A 54 LYS THR TYR GLY ASN LYS CYS ASN PHE CYS ASN ALA VAL SEQRES 4 A 54 VAL GLU SER ASN GLY THR LEU THR LEU SER HIS PHE GLY SEQRES 5 A 54 LYS CYS HELIX 1 1 ASN A 33 ASN A 45 1 13 SHEET 1 A 3 LYS A 29 TYR A 31 0 SHEET 2 A 3 LEU A 23 GLY A 25 -1 N GLY A 25 O LYS A 29 SHEET 3 A 3 LEU A 50 HIS A 52 -1 O SER A 51 N CYS A 24 SSBOND 1 CYS A 8 CYS A 38 1555 1555 2.02 SSBOND 2 CYS A 16 CYS A 35 1555 1555 2.02 SSBOND 3 CYS A 24 CYS A 56 1555 1555 2.02 CISPEP 1 TYR A 11 PRO A 12 1 1.15 CISPEP 2 TYR A 11 PRO A 12 2 0.28 CISPEP 3 TYR A 11 PRO A 12 3 -0.06 CISPEP 4 TYR A 11 PRO A 12 4 0.55 CISPEP 5 TYR A 11 PRO A 12 5 0.50 CISPEP 6 TYR A 11 PRO A 12 6 0.71 CISPEP 7 TYR A 11 PRO A 12 7 0.37 CISPEP 8 TYR A 11 PRO A 12 8 0.05 CISPEP 9 TYR A 11 PRO A 12 9 0.73 CISPEP 10 TYR A 11 PRO A 12 10 0.35 CISPEP 11 TYR A 11 PRO A 12 11 0.19 CISPEP 12 TYR A 11 PRO A 12 12 0.01 CISPEP 13 TYR A 11 PRO A 12 13 -0.01 CISPEP 14 TYR A 11 PRO A 12 14 1.51 CISPEP 15 TYR A 11 PRO A 12 15 0.82 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000