HEADER PROTEINASE INHIBITOR (KAZAL) 11-JUN-85 2OVO TITLE THE CRYSTAL AND MOLECULAR STRUCTURE OF THE THIRD DOMAIN OF SILVER TITLE 2 PHEASANT OVOMUCOID (OMSVP3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OVOMUCOID THIRD DOMAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LOPHURA NYCTHEMERA; SOURCE 3 ORGANISM_COMMON: SILVER PHEASANT; SOURCE 4 ORGANISM_TAXID: 9046 KEYWDS PROTEINASE INHIBITOR (KAZAL) EXPDTA X-RAY DIFFRACTION AUTHOR W.BODE,O.EPP REVDAT 6 26-JUL-23 2OVO 1 SCALE ATOM REVDAT 5 29-NOV-17 2OVO 1 HELIX REVDAT 4 13-JUL-11 2OVO 1 VERSN REVDAT 3 24-FEB-09 2OVO 1 VERSN REVDAT 2 01-APR-03 2OVO 1 JRNL REVDAT 1 08-NOV-85 2OVO 0 JRNL AUTH W.BODE,O.EPP,R.HUBER,M.LASKOWSKI JR.,W.ARDELT JRNL TITL THE CRYSTAL AND MOLECULAR STRUCTURE OF THE THIRD DOMAIN OF JRNL TITL 2 SILVER PHEASANT OVOMUCOID (OMSVP3). JRNL REF EUR.J.BIOCHEM. V. 147 387 1985 JRNL REFN ISSN 0014-2956 JRNL PMID 3971987 JRNL DOI 10.1111/J.1432-1033.1985.TB08762.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.W.EMPIE,M.LASKOWSKIJUNIOR REMARK 1 TITL THERMODYNAMICS AND KINETICS OF SINGLE RESIDUE REPLACEMENTS REMARK 1 TITL 2 IN AVIAN OVOMUCOID THIRD DOMAINS. EFFECT ON INHIBITOR REMARK 1 TITL 3 INTERACTIONS WITH SERINE PROTEINASES REMARK 1 REF BIOCHEMISTRY V. 21 2274 1982 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.J.READ,M.FUJINAGA,A.R.SIELECKI,M.N.G.JAMES REMARK 1 TITL STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B REMARK 1 TITL 2 AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT REMARK 1 TITL 3 1.8-ANGSTROMS RESOLUTION REMARK 1 REF BIOCHEMISTRY V. 22 4420 1983 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH E.PAPAMOKOS,E.WEBER,W.BODE,R.HUBER,M.W.EMPIE,I.KATO, REMARK 1 AUTH 2 M.LASKOWSKIJUNIOR REMARK 1 TITL CRYSTALLOGRAPHIC REFINEMENT OF JAPANESE QUAIL OVOMUCOID, A REMARK 1 TITL 2 KAZAL-TYPE INHIBITOR, AND MODEL BUILDING STUDIES OF REMARK 1 TITL 3 COMPLEXES WITH SERINE PROTEASES REMARK 1 REF J.MOL.BIOL. V. 158 515 1982 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.FUJINAGA,R.J.READ,A.SIELECKI,W.ARDELT,M.LASKOWSKIJUNIOR, REMARK 1 AUTH 2 M.N.G.JAMES REMARK 1 TITL REFINED CRYSTAL STRUCTURE OF THE MOLECULAR COMPLEX OF REMARK 1 TITL 2 STREPTOMYCES GRISEUS PROTEASE B, A SERINE PROTEASE, WITH THE REMARK 1 TITL 3 THIRD DOMAIN OF THE OVOMUCOID INHIBITOR FROM TURKEY REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 79 4868 1982 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 5 REMARK 1 AUTH M.LASKOWSKIJUNIOR,M.W.EMPIE,I.KATO,W.J.KOHR,W.ARDELT, REMARK 1 AUTH 2 W.C.BOGARDJUNIOR,E.WEBER,E.PAPAMOKOS,W.BODE,R.HUBER REMARK 1 TITL CORRELATION OF AMINO ACID SEQUENCE WITH INHIBITOR ACTIVITY REMARK 1 TITL 2 AND SPECIFICITY OF PROTEIN INHIBITORS OF SERINE PROTEINASES REMARK 1 REF COLLOQ.GES.BIOL.CHEM. V. 32 136 1981 REMARK 1 REFN ISSN 0366-5887 REMARK 1 REFERENCE 6 REMARK 1 AUTH E.WEBER,E.PAPAMOKOS,W.BODE,R.HUBER,I.KATO,M.LASKOWSKIJUNIOR REMARK 1 TITL CRYSTALLIZATION, CRYSTAL STRUCTURE ANALYSIS AND MOLECULAR REMARK 1 TITL 2 MODEL OF THE THIRD DOMAIN OF JAPANESE QUAIL OVOMUCOID, A REMARK 1 TITL 3 KAZAL TYPE INHIBITOR REMARK 1 REF J.MOL.BIOL. V. 149 109 1981 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : EREF REMARK 3 AUTHORS : JACK,LEVITT REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.199 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 418 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 22.14500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 10.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.14500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 10.57500 REMARK 290 SMTRY3 4 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: 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 11 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 21 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES 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 ASP A 7 0.09 SIDE CHAIN REMARK 500 GLU A 10 0.09 SIDE CHAIN REMARK 500 GLU A 19 0.12 SIDE CHAIN REMARK 500 TYR A 31 0.07 SIDE CHAIN REMARK 500 ASN A 45 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR A 20 10.47 REMARK 500 REMARK 500 REMARK: NULL DBREF 2OVO A 1 56 UNP P67954 IOVO_LOPNY 1 56 SEQRES 1 A 56 LEU ALA ALA VAL SER VAL ASP CYS SER GLU TYR PRO LYS SEQRES 2 A 56 PRO ALA CYS THR MET GLU TYR ARG PRO LEU CYS GLY SER SEQRES 3 A 56 ASP ASN LYS THR TYR GLY ASN LYS CYS ASN PHE CYS ASN SEQRES 4 A 56 ALA VAL VAL GLU SER ASN GLY THR LEU THR LEU SER HIS SEQRES 5 A 56 PHE GLY LYS CYS FORMUL 2 HOH *31(H2 O) HELIX 1 HA ASN A 33 SER A 44 1 12 SHEET 1 SA 3 LYS A 29 GLY A 32 0 SHEET 2 SA 3 ARG A 21 SER A 26 -1 SHEET 3 SA 3 THR A 49 GLY A 54 -1 SSBOND 1 CYS A 8 CYS A 38 1555 1555 2.00 SSBOND 2 CYS A 16 CYS A 35 1555 1555 2.03 SSBOND 3 CYS A 24 CYS A 56 1555 1555 1.99 CISPEP 1 TYR A 11 PRO A 12 0 3.70 CRYST1 44.290 21.150 44.050 90.00 107.00 90.00 C 1 2 1 4 ORIGX1 0.956304 0.000000 0.292372 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 -0.292372 0.000000 0.956304 0.00000 SCALE1 0.022578 0.000000 0.006903 0.00000 SCALE2 0.000000 0.047281 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023739 0.00000