HEADER ANTIVIRAL PROTEIN 21-SEP-93 1APA TITLE X-RAY STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN, CODED BY A NEW TITLE 2 GENOMIC CLONE, AT 0.23 NM RESOLUTION. A MODEL STRUCTURE PROVIDES A TITLE 3 SUITABLE ELECTROSTATIC FIELD FOR SUBSTRATE BINDING. COMPND MOL_ID: 1; COMPND 2 MOLECULE: POKEWEED ANTIVIRAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYTOLACCA AMERICANA; SOURCE 3 ORGANISM_COMMON: AMERICAN POKEWEED; SOURCE 4 ORGANISM_TAXID: 3527 KEYWDS ANTIVIRAL PROTEIN, GENOMIC CLONE EXPDTA X-RAY DIFFRACTION AUTHOR H.AGO,J.KATAOKA,H.TSUGE,N.HABUKA,E.INAGAKI,M.NOMA,M.MIYANO REVDAT 5 16-OCT-24 1APA 1 SEQADV REVDAT 4 29-NOV-17 1APA 1 HELIX REVDAT 3 24-FEB-09 1APA 1 VERSN REVDAT 2 11-AUG-00 1APA 1 TITLE EXPDTA JRNL KEYWOR REVDAT 1 31-JAN-94 1APA 0 JRNL AUTH H.AGO,J.KATAOKA,H.TSUGE,N.HABUKA,E.INAGAKI,M.NOMA,M.MIYANO JRNL TITL X-RAY STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN, CODED BY A JRNL TITL 2 NEW GENOMIC CLONE, AT 0.23 NM RESOLUTION. A MODEL STRUCTURE JRNL TITL 3 PROVIDES A SUITABLE ELECTROSTATIC FIELD FOR SUBSTRATE JRNL TITL 4 BINDING. JRNL REF EUR.J.BIOCHEM. V. 225 369 1994 JRNL REFN ISSN 0014-2956 JRNL PMID 7925458 JRNL DOI 10.1111/J.1432-1033.1994.00369.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.KATAOKA,H.AGO,N.HABUKA,M.FURUNO,C.MASUTA,M.MIYANO,A.KOIWAI REMARK 1 TITL EXPRESSION OF A POKEWEED ANTIVIRAL PROTEIN IN ESCHERICHIA REMARK 1 TITL 2 COLI AND ITS CHARACTERIZATION REMARK 1 REF FEBS LETT. V. 320 31 1993 REMARK 1 REFN ISSN 0014-5793 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.KATAOKA,N.HABUKA,C.MASUTA,M.MIYANO,A.KOIWAI REMARK 1 TITL ISOLATION AND ANALYSIS OF A GENOMIC CLONE ENCODING A REMARK 1 TITL 2 POKEWEED ANTIVIRAL PROTEIN REMARK 1 REF PLANT MOL.BIOL. V. 20 879 1992 REMARK 1 REFN ISSN 0167-4412 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL 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) : 0.172 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 : 2054 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 95 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) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 2.200 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 1APA 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_1000171090. 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL 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 (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 23.55000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.55000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.15000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 LEU A 4 REMARK 465 GLU A 5 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 ASN A 7 N - CA - C ANGL. DEV. = -22.4 DEGREES REMARK 500 LEU A 71 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 64 9.85 58.39 REMARK 500 ASN A 75 -8.16 -146.46 REMARK 500 ASN A 86 -104.67 74.73 REMARK 500 PRO A 114 173.61 -56.82 REMARK 500 SER A 115 60.90 28.47 REMARK 500 SER A 116 37.82 177.30 REMARK 500 ASN A 121 150.51 -45.57 REMARK 500 ASN A 123 26.01 -71.90 REMARK 500 SER A 126 58.89 -91.59 REMARK 500 ARG A 137 135.04 161.90 REMARK 500 THR A 163 139.72 119.03 REMARK 500 VAL A 178 -64.21 -127.47 REMARK 500 PRO A 230 155.07 -41.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 1APA A 3 266 UNP Q03464 RIPA_PHYAM 22 285 SEQADV 1APA LEU A 4 UNP Q03464 TRP 23 CONFLICT SEQADV 1APA GLU A 5 UNP Q03464 ALA 24 CONFLICT SEQRES 1 A 266 ALA PRO THR LEU GLU ILE ASN THR ILE THR PHE ASP VAL SEQRES 2 A 266 GLY ASN ALA THR ILE ASN LYS TYR ALA THR PHE MET LYS SEQRES 3 A 266 SER ILE HIS ASN GLN ALA LYS ASP PRO THR LEU LYS CYS SEQRES 4 A 266 TYR GLY ILE PRO MET LEU PRO ASN THR ASN LEU THR PRO SEQRES 5 A 266 LYS TYR LEU LEU VAL THR LEU GLN ASP SER SER LEU LYS SEQRES 6 A 266 THR ILE THR LEU MET LEU LYS ARG ASN ASN LEU TYR VAL SEQRES 7 A 266 MET GLY TYR ALA ASP THR TYR ASN GLY LYS CYS ARG TYR SEQRES 8 A 266 HIS ILE PHE LYS ASP ILE SER ASN THR THR GLU ARG ASN SEQRES 9 A 266 ASP VAL MET THR THR LEU CYS PRO ASN PRO SER SER ARG SEQRES 10 A 266 VAL GLY LYS ASN ILE ASN TYR ASP SER SER TYR PRO ALA SEQRES 11 A 266 LEU GLU LYS LYS VAL GLY ARG PRO ARG SER GLN VAL GLN SEQRES 12 A 266 LEU GLY ILE GLN ILE LEU ASN SER GLY ILE GLY LYS ILE SEQRES 13 A 266 TYR GLY VAL ASP SER PHE THR GLU LYS THR GLU ALA GLU SEQRES 14 A 266 PHE LEU LEU VAL ALA ILE GLN MET VAL SER GLU ALA ALA SEQRES 15 A 266 ARG PHE LYS TYR ILE GLU ASN GLN VAL LYS THR ASN PHE SEQRES 16 A 266 ASN ARG ALA PHE TYR PRO ASN ALA LYS VAL LEU ASN LEU SEQRES 17 A 266 GLU GLU SER TRP GLY LYS ILE SER THR ALA ILE HIS ASN SEQRES 18 A 266 ALA LYS ASN GLY ALA LEU THR SER PRO LEU GLU LEU LYS SEQRES 19 A 266 ASN ALA ASN GLY SER LYS TRP ILE VAL LEU ARG VAL ASP SEQRES 20 A 266 ASP ILE GLU PRO ASP VAL GLY LEU LEU LYS TYR VAL ASN SEQRES 21 A 266 GLY THR CYS GLN ALA THR FORMUL 2 HOH *95(H2 O) HELIX 1 H1 ILE A 18 ALA A 32 1 15 HELIX 2 H2 THR A 100 LEU A 110 1 11 HELIX 3 H3 TYR A 128 VAL A 135 1 8 HELIX 4 H4 ILE A 146 ILE A 156 1 11 HELIX 5 H5 GLU A 164 ARG A 183 1 20 HELIX 6 H6 TYR A 186 THR A 193 1 8 HELIX 7 H7 ALA A 203 ASN A 221 1 19 HELIX 8 H8 VAL A 246 ASP A 252 1 7 SHEET 1 S1 6 ILE A 9 VAL A 13 0 SHEET 2 S1 6 TYR A 54 GLN A 60 1 SHEET 3 S1 6 THR A 66 LYS A 72 -1 SHEET 4 S1 6 VAL A 78 THR A 84 -1 SHEET 5 S1 6 CYS A 89 PHE A 94 -1 SHEET 6 S1 6 ARG A 117 GLY A 119 1 SHEET 1 S2 2 LEU A 231 LYS A 234 0 SHEET 2 S2 2 LYS A 240 VAL A 243 -1 SSBOND 1 CYS A 39 CYS A 263 1555 1555 2.03 SSBOND 2 CYS A 89 CYS A 111 1555 1555 2.02 CISPEP 1 THR A 51 PRO A 52 0 0.49 CRYST1 47.100 116.300 49.600 90.00 90.00 90.00 P 21 21 2 4 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 0.021231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020161 0.00000