HEADER VIRAL PROTEIN 12-OCT-09 3K7B TITLE THE STRUCTURE OF THE POXVIRUS A33 PROTEIN REVEALS A DIMER OF UNIQUE C- TITLE 2 TYPE LECTIN-LIKE DOMAINS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN A33; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 90-185; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS WR; SOURCE 3 ORGANISM_COMMON: VACV; SOURCE 4 ORGANISM_TAXID: 10254; SOURCE 5 STRAIN: WESTERN RESERVE (WR); SOURCE 6 GENE: A33R, SALL3R; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3)-RIL-X; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PNAN KEYWDS C-TYPE LECTIN-LIKE DOMAIN, HOMODIMER, POXVIRUS, EEV, EV, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.P.SU,D.N.GARBOCZI REVDAT 5 13-OCT-21 3K7B 1 SEQADV LINK REVDAT 4 01-NOV-17 3K7B 1 REMARK REVDAT 3 30-NOV-11 3K7B 1 TITLE VERSN REVDAT 2 09-MAR-10 3K7B 1 JRNL REVDAT 1 19-JAN-10 3K7B 0 JRNL AUTH H.P.SU,K.SINGH,A.G.GITTIS,D.N.GARBOCZI JRNL TITL THE STRUCTURE OF THE POXVIRUS A33 PROTEIN REVEALS A DIMER OF JRNL TITL 2 UNIQUE C-TYPE LECTIN-LIKE DOMAINS. JRNL REF J.VIROL. V. 84 2502 2010 JRNL REFN ISSN 0022-538X JRNL PMID 20032175 JRNL DOI 10.1128/JVI.02247-09 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1129284.980 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 10073 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) : 0.218 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 500 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1521 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 32 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1342 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.91000 REMARK 3 B22 (A**2) : -2.08000 REMARK 3 B33 (A**2) : -6.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 41.56 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3K7B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97622 REMARK 200 MONOCHROMATOR : SI 220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.30400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 10% ISOPROPANOL, 0.1M REMARK 280 SODIUM ACETATE, PH 4.30, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 40.47000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.47000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.16000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 SER A 90 REMARK 465 THR A 91 REMARK 465 THR A 92 REMARK 465 GLN A 93 REMARK 465 TYR A 94 REMARK 465 ASP A 95 REMARK 465 HIS A 96 REMARK 465 LYS A 97 REMARK 465 TYR A 166 REMARK 465 GLN A 167 REMARK 465 ASP A 168 REMARK 465 SER B 90 REMARK 465 THR B 91 REMARK 465 THR B 92 REMARK 465 GLN B 93 REMARK 465 TYR B 94 REMARK 465 ASP B 95 REMARK 465 TYR B 166 REMARK 465 GLN B 167 REMARK 465 ASP B 168 REMARK 465 ASN B 185 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 SER A 164 -173.27 -54.98 REMARK 500 MSE A 184 -159.12 -88.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 3K7B A 90 185 UNP P68617 VA33_VACCW 90 185 DBREF 3K7B B 90 185 UNP P68617 VA33_VACCW 90 185 SEQADV 3K7B MSE A 118 UNP P68617 LEU 118 ENGINEERED MUTATION SEQADV 3K7B ALA A 123 UNP P68617 LYS 123 ENGINEERED MUTATION SEQADV 3K7B MSE A 140 UNP P68617 LEU 140 ENGINEERED MUTATION SEQADV 3K7B MSE B 118 UNP P68617 LEU 118 ENGINEERED MUTATION SEQADV 3K7B ALA B 123 UNP P68617 LYS 123 ENGINEERED MUTATION SEQADV 3K7B MSE B 140 UNP P68617 LEU 140 ENGINEERED MUTATION SEQRES 1 A 96 SER THR THR GLN TYR ASP HIS LYS GLU SER CYS ASN GLY SEQRES 2 A 96 LEU TYR TYR GLN GLY SER CYS TYR ILE LEU HIS SER ASP SEQRES 3 A 96 TYR GLN MSE PHE SER ASP ALA ALA ALA ASN CYS THR ALA SEQRES 4 A 96 GLU SER SER THR LEU PRO ASN LYS SER ASP VAL MSE ILE SEQRES 5 A 96 THR TRP LEU ILE ASP TYR VAL GLU ASP THR TRP GLY SER SEQRES 6 A 96 ASP GLY ASN PRO ILE THR LYS THR THR SER ASP TYR GLN SEQRES 7 A 96 ASP SER ASP VAL SER GLN GLU VAL ARG LYS TYR PHE CYS SEQRES 8 A 96 VAL LYS THR MSE ASN SEQRES 1 B 96 SER THR THR GLN TYR ASP HIS LYS GLU SER CYS ASN GLY SEQRES 2 B 96 LEU TYR TYR GLN GLY SER CYS TYR ILE LEU HIS SER ASP SEQRES 3 B 96 TYR GLN MSE PHE SER ASP ALA ALA ALA ASN CYS THR ALA SEQRES 4 B 96 GLU SER SER THR LEU PRO ASN LYS SER ASP VAL MSE ILE SEQRES 5 B 96 THR TRP LEU ILE ASP TYR VAL GLU ASP THR TRP GLY SER SEQRES 6 B 96 ASP GLY ASN PRO ILE THR LYS THR THR SER ASP TYR GLN SEQRES 7 B 96 ASP SER ASP VAL SER GLN GLU VAL ARG LYS TYR PHE CYS SEQRES 8 B 96 VAL LYS THR MSE ASN MODRES 3K7B MSE A 118 MET SELENOMETHIONINE MODRES 3K7B MSE A 140 MET SELENOMETHIONINE MODRES 3K7B MSE A 184 MET SELENOMETHIONINE MODRES 3K7B MSE B 118 MET SELENOMETHIONINE MODRES 3K7B MSE B 140 MET SELENOMETHIONINE MODRES 3K7B MSE B 184 MET SELENOMETHIONINE HET MSE A 118 8 HET MSE A 140 8 HET MSE A 184 8 HET MSE B 118 8 HET MSE B 140 8 HET MSE B 184 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 HOH *42(H2 O) HELIX 1 1 MSE A 118 GLU A 129 1 12 HELIX 2 2 ASN A 135 MSE A 140 1 6 HELIX 3 3 LEU A 144 GLU A 149 1 6 HELIX 4 4 PHE B 119 GLU B 129 1 11 HELIX 5 5 ASN B 135 MSE B 140 1 6 HELIX 6 6 LEU B 144 GLU B 149 1 6 HELIX 7 7 ASP B 170 GLN B 173 5 4 SHEET 1 A 3 LEU A 103 TYR A 105 0 SHEET 2 A 3 SER A 108 GLN A 117 -1 O TYR A 110 N LEU A 103 SHEET 3 A 3 ARG A 176 THR A 183 -1 O LYS A 182 N CYS A 109 SHEET 1 B 3 LEU B 103 TYR B 104 0 SHEET 2 B 3 CYS B 109 MSE B 118 -1 O TYR B 110 N LEU B 103 SHEET 3 B 3 VAL B 175 LYS B 182 -1 O LYS B 182 N CYS B 109 SSBOND 1 CYS A 100 CYS A 109 1555 1555 2.04 SSBOND 2 CYS A 126 CYS A 180 1555 1555 2.05 SSBOND 3 CYS B 100 CYS B 109 1555 1555 2.04 SSBOND 4 CYS B 126 CYS B 180 1555 1555 2.05 LINK C GLN A 117 N MSE A 118 1555 1555 1.33 LINK C MSE A 118 N PHE A 119 1555 1555 1.32 LINK C VAL A 139 N MSE A 140 1555 1555 1.33 LINK C MSE A 140 N ILE A 141 1555 1555 1.33 LINK C THR A 183 N MSE A 184 1555 1555 1.33 LINK C MSE A 184 N ASN A 185 1555 1555 1.34 LINK C GLN B 117 N MSE B 118 1555 1555 1.33 LINK C MSE B 118 N PHE B 119 1555 1555 1.33 LINK C VAL B 139 N MSE B 140 1555 1555 1.33 LINK C MSE B 140 N ILE B 141 1555 1555 1.33 LINK C THR B 183 N MSE B 184 1555 1555 1.33 CRYST1 80.940 56.320 41.680 90.00 110.68 90.00 C 1 2 1 8 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 0.012355 0.000000 0.004664 0.00000 SCALE2 0.000000 0.017756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025645 0.00000