10 20 30 40 50 60 70 80 1LPD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIVIRAL PROTEIN 07-MAY-02 1LPD
TITLE HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL TITLE 2 PROTEIN-POTENT ANTI-HIV AGENT (COMPLEX WITH ADENINE)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIANTHIN 30; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTIVIRAL PROTEIN DAP-30, RRNA N-GLYCOSYLASE, COMPND 5 RRNA N-GLYCOSIDASE, RIBOSOME-INACTIVATING PROTEIN; COMPND 6 EC: 3.2.2.22; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DIANTHUS CARYOPHYLLUS; SOURCE 3 ORGANISM_COMMON: CLOVE PINK; SOURCE 4 ORGANISM_TAXID: 3570; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS DIANTHIN ANTIVIRAL PROTEIN, RIBOSOME INACTIVATING PROTEIN, KEYWDS 2 ANTI-HIV AGENT, HIV-1 INTEGRASE INHIBITOR, KEYWDS 3 POLYNUCLEOTIDE:ADENOSINE GLYCOSIDASE
EXPDTA X-RAY DIFFRACTION
AUTHOR I.V.KURINOV,F.RAJAMOHAN,F.M.UCKUN
REVDAT 3 24-FEB-09 1LPD 1 VERSN REVDAT 2 29-MAR-05 1LPD 1 JRNL REVDAT 1 11-MAY-04 1LPD 0
JRNL AUTH I.V.KURINOV,F.RAJAMOHAN,F.M.UCKUN JRNL TITL HIGH RESOLUTION X-RAY STRUCTURE AND POTENT JRNL TITL 2 ANTI-HIV ACTIVITY OF RECOMBINANT DIANTHIN JRNL TITL 3 ANTIVIRAL PROTEIN. JRNL REF ARZNEIMITTELFORSCHUNG V. 54 692 2004 JRNL REFN ISSN 0004-4172 JRNL PMID 15553110
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 25000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2497 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 : 2012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.80 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.13 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 0.95 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1LPD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB016159.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 290. REMARK 200 PH : 8 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25427 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 43.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1LP8 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG3350, 0.1M CACL2, PH 8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
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 39.23200 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: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 40 CG CD OE1 OE2
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 THR A 48 -74.62 -87.60 REMARK 500 THR A 175 -78.24 -117.32 REMARK 500 ASP A 219 37.44 -144.91 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 651 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH A 693 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH A 703 DISTANCE = 5.15 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADE A 901
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LP8 RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL REMARK 900 PROTEIN-POTENT ANTI-HIV AGENT REMARK 900 RELATED ID: 1LPC RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL REMARK 900 PROTEIN-POTENT ANTI-HIV AGENT (COMPLEX WITH CYCLIC AMP)
DBREF 1LPD A 1 254 UNP P24476 RIP0_DIACA 24 277
SEQRES 1 A 254 ALA THR ALA TYR THR LEU ASN LEU ALA ASN PRO SER ALA SEQRES 2 A 254 SER GLN TYR SER SER PHE LEU ASP GLN ILE ARG ASN ASN SEQRES 3 A 254 VAL ARG ASP THR SER LEU ILE TYR GLY GLY THR ASP VAL SEQRES 4 A 254 GLU VAL ILE GLY ALA PRO SER THR THR ASP LYS PHE LEU SEQRES 5 A 254 ARG LEU ASN PHE GLN GLY PRO ARG GLY THR VAL SER LEU SEQRES 6 A 254 GLY LEU ARG ARG GLU ASN LEU TYR VAL VAL ALA TYR LEU SEQRES 7 A 254 ALA MET ASP ASN ALA ASN VAL ASN ARG ALA TYR TYR PHE SEQRES 8 A 254 LYS ASN GLN ILE THR SER ALA GLU LEU THR ALA LEU PHE SEQRES 9 A 254 PRO GLU VAL VAL VAL ALA ASN GLN LYS GLN LEU GLU TYR SEQRES 10 A 254 GLY GLU ASP TYR GLN ALA ILE GLU LYS ASN ALA LYS ILE SEQRES 11 A 254 THR THR GLY ASP GLN SER ARG LYS GLU LEU GLY LEU GLY SEQRES 12 A 254 ILE ASN LEU LEU ILE THR MET ILE ASP GLY VAL ASN LYS SEQRES 13 A 254 LYS VAL ARG VAL VAL LYS ASP GLU ALA ARG PHE LEU LEU SEQRES 14 A 254 ILE ALA ILE GLN MET THR ALA GLU ALA ALA ARG PHE ARG SEQRES 15 A 254 TYR ILE GLN ASN LEU VAL THR LYS ASN PHE PRO ASN LYS SEQRES 16 A 254 PHE ASP SER GLU ASN LYS VAL ILE GLN PHE GLN VAL SER SEQRES 17 A 254 TRP SER LYS ILE SER THR ALA ILE PHE GLY ASP CYS LYS SEQRES 18 A 254 ASN GLY VAL PHE ASN LYS ASP TYR ASP PHE GLY PHE GLY SEQRES 19 A 254 LYS VAL ARG GLN ALA LYS ASP LEU GLN MET GLY LEU LEU SEQRES 20 A 254 LYS TYR LEU GLY ARG PRO LYS
HET ADE A 901 10
HETNAM ADE ADENINE
FORMUL 2 ADE C5 H5 N5 FORMUL 3 HOH *190(H2 O)
HELIX 1 1 SER A 12 ARG A 28 1 17 HELIX 2 2 LYS A 92 ILE A 95 5 4 HELIX 3 3 THR A 96 PHE A 104 1 9 HELIX 4 4 VAL A 108 ALA A 110 5 3 HELIX 5 5 ASP A 120 ALA A 128 1 9 HELIX 6 6 SER A 136 GLY A 141 5 6 HELIX 7 7 GLY A 143 GLY A 153 1 11 HELIX 8 8 VAL A 160 THR A 175 1 16 HELIX 9 9 THR A 175 PHE A 181 1 7 HELIX 10 10 PHE A 181 ASN A 191 1 11 HELIX 11 11 GLU A 199 SER A 208 1 10 HELIX 12 12 SER A 208 ASP A 219 1 12 HELIX 13 13 LYS A 240 GLN A 243 5 4
SHEET 1 A 6 THR A 2 ASN A 7 0 SHEET 2 A 6 PHE A 51 GLY A 58 1 O ASN A 55 N LEU A 6 SHEET 3 A 6 GLY A 61 ARG A 68 -1 O VAL A 63 N PHE A 56 SHEET 4 A 6 VAL A 74 MET A 80 -1 O VAL A 75 N GLY A 66 SHEET 5 A 6 ASN A 86 TYR A 90 -1 O TYR A 89 N TYR A 77 SHEET 6 A 6 GLN A 112 GLN A 114 1 O LYS A 113 N ALA A 88 SHEET 1 B 2 GLU A 40 VAL A 41 0 SHEET 2 B 2 LEU A 246 LEU A 247 1 O LEU A 247 N GLU A 40 SHEET 1 C 3 CYS A 220 LYS A 221 0 SHEET 2 C 3 VAL A 224 ASP A 230 -1 O VAL A 224 N LYS A 221 SHEET 3 C 3 LYS A 235 GLN A 238 -1 O VAL A 236 N TYR A 229
CISPEP 1 PHE A 192 PRO A 193 0 0.30
SITE 1 AC1 6 LEU A 72 TYR A 73 VAL A 74 GLU A 119 SITE 2 AC1 6 ILE A 172 ARG A 180
CRYST1 37.093 78.464 42.721 90.00 105.26 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 0.026959 0.000000 0.007355 0.00000
SCALE2 0.000000 0.012745 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024263 0.00000