HEADER VIRAL PROTEIN 17-OCT-05 2BBR TITLE CRYSTAL STRUCTURE OF MC159 REVEALS MOLECULAR MECHANISM OF DISC TITLE 2 ASSEMBLY AND VFLIP INHIBITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRAL CASP8 AND FADD-LIKE APOPTOSIS REGULATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DEATH EFFECTOR DOMAIN (RESIDUES 1-187); COMPND 5 SYNONYM: V-CFLAR, VIRAL FLICE-INHIBITORY PROTEIN, V-FLIP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MOLLUSCUM CONTAGIOSUM VIRUS SUBTYPE 1; SOURCE 3 ORGANISM_TAXID: 10280; SOURCE 4 STRAIN: SUBTYPE 1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RIPL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET28B KEYWDS VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.K.YANG,L.WANG,L.ZHENG,F.WAN,M.AHMED,M.J.LENARDO,H.WU REVDAT 3 23-AUG-23 2BBR 1 REMARK SEQADV REVDAT 2 24-FEB-09 2BBR 1 VERSN REVDAT 1 14-FEB-06 2BBR 0 JRNL AUTH J.K.YANG,L.WANG,L.ZHENG,F.WAN,M.AHMED,M.J.LENARDO,H.WU JRNL TITL CRYSTAL STRUCTURE OF MC159 REVEALS MOLECULAR MECHANISM OF JRNL TITL 2 DISC ASSEMBLY AND FLIP INHIBITION. JRNL REF MOL.CELL V. 20 939 2005 JRNL REFN ISSN 1097-2765 JRNL PMID 16364918 JRNL DOI 10.1016/J.MOLCEL.2005.10.023 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 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 : 50964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 5154 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 : 1492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 319 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) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.000 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 2BBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000034913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52241 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 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) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2BBZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 - 1.2 M SODIUM ACETATE, 0.1 M REMARK 280 IMIDAZOLE , PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.48950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.90300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.43350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.90300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.48950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.43350 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 MET A 1 REMARK 465 GLU A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 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 ALA A 36 75.93 -116.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BBZ RELATED DB: PDB DBREF 2BBR A 1 187 UNP Q98325 CFLA_MCV1 1 187 SEQADV 2BBR LEU A 188 UNP Q98325 EXPRESSION TAG SEQADV 2BBR GLU A 189 UNP Q98325 EXPRESSION TAG SEQADV 2BBR HIS A 190 UNP Q98325 EXPRESSION TAG SEQADV 2BBR HIS A 191 UNP Q98325 EXPRESSION TAG SEQADV 2BBR HIS A 192 UNP Q98325 EXPRESSION TAG SEQADV 2BBR HIS A 193 UNP Q98325 EXPRESSION TAG SEQADV 2BBR HIS A 194 UNP Q98325 EXPRESSION TAG SEQADV 2BBR HIS A 195 UNP Q98325 EXPRESSION TAG SEQRES 1 A 195 MET SER ASP SER LYS GLU VAL PRO SER LEU PRO PHE LEU SEQRES 2 A 195 ARG HIS LEU LEU GLU GLU LEU ASP SER HIS GLU ASP SER SEQRES 3 A 195 LEU LEU LEU PHE LEU CYS HIS ASP ALA ALA PRO GLY CYS SEQRES 4 A 195 THR THR VAL THR GLN ALA LEU CYS SER LEU SER GLN GLN SEQRES 5 A 195 ARG LYS LEU THR LEU ALA ALA LEU VAL GLU MET LEU TYR SEQRES 6 A 195 VAL LEU GLN ARG MET ASP LEU LEU LYS SER ARG PHE GLY SEQRES 7 A 195 LEU SER LYS GLU GLY ALA GLU GLN LEU LEU GLY THR SER SEQRES 8 A 195 PHE LEU THR ARG TYR ARG LYS LEU MET VAL CYS VAL GLY SEQRES 9 A 195 GLU GLU LEU ASP SER SER GLU LEU ARG ALA LEU ARG LEU SEQRES 10 A 195 PHE ALA CYS ASN LEU ASN PRO SER LEU SER THR ALA LEU SEQRES 11 A 195 SER GLU SER SER ARG PHE VAL GLU LEU VAL LEU ALA LEU SEQRES 12 A 195 GLU ASN VAL GLY LEU VAL SER PRO SER SER VAL SER VAL SEQRES 13 A 195 LEU ALA ASP MET LEU ARG THR LEU ARG ARG LEU ASP LEU SEQRES 14 A 195 CYS GLN GLN LEU VAL GLU TYR GLU GLN GLN GLU GLN ALA SEQRES 15 A 195 ARG TYR ARG TYR CYS LEU GLU HIS HIS HIS HIS HIS HIS HET AZI A 201 3 HETNAM AZI AZIDE ION FORMUL 2 AZI N3 1- FORMUL 3 HOH *319(H2 O) HELIX 1 1 ASP A 3 VAL A 7 5 5 HELIX 2 2 SER A 9 GLU A 18 1 10 HELIX 3 3 ASP A 21 CYS A 32 1 12 HELIX 4 4 THR A 41 GLN A 52 1 12 HELIX 5 5 THR A 56 LEU A 67 1 12 HELIX 6 6 ARG A 69 GLY A 78 1 10 HELIX 7 7 SER A 80 GLN A 86 1 7 HELIX 8 8 THR A 94 GLU A 105 1 12 HELIX 9 9 ASP A 108 ASN A 123 1 16 HELIX 10 10 PRO A 124 LEU A 130 5 7 HELIX 11 11 ARG A 135 VAL A 146 1 12 HELIX 12 12 VAL A 154 LEU A 164 1 11 HELIX 13 13 ARG A 166 LEU A 188 1 23 SITE 1 AC1 5 LEU A 88 ARG A 95 LYS A 98 ARG A 185 SITE 2 AC1 5 TYR A 186 CRYST1 34.979 62.867 75.806 90.00 90.00 90.00 P 21 21 21 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 0.028589 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013192 0.00000