HEADER VIRAL PROTEIN 22-MAR-24 9EQN TITLE N-TERMINAL DOMAIN OF INFECTIOUS BURSAL DISEASE VIRUS (IBDV) VP3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STRUCTURAL POLYPROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFECTIOUS BURSAL DISEASE VIRUS; SOURCE 3 ORGANISM_COMMON: GUMBORO VIRUS; SOURCE 4 ORGANISM_TAXID: 10995; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PREST-C KEYWDS DSRNA BINDING PROTEIN, BIRNAVIRUS, IBDV, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.S.FERRERO,N.VERDAGUER REVDAT 1 09-OCT-24 9EQN 0 JRNL AUTH D.S.FERRERO,N.VERDAGUER JRNL TITL STRUCTURE OF THE AMINO TERMINAL DOMAIN OF THE BIRNAVIRAL JRNL TITL 2 MULTIFUNCTIONAL VP3 PROTEIN AND ITS UNEXPLORED CRITICAL ROLE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_4788: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 43928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2162 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.7000 - 3.6000 1.00 3022 151 0.1942 0.2198 REMARK 3 2 3.6000 - 2.8600 1.00 2973 130 0.1745 0.1967 REMARK 3 3 2.8600 - 2.5000 1.00 2957 149 0.1684 0.1994 REMARK 3 4 2.5000 - 2.2700 1.00 2911 186 0.1521 0.1671 REMARK 3 5 2.2700 - 2.1100 1.00 2910 165 0.1566 0.1769 REMARK 3 6 2.1100 - 1.9800 1.00 2919 170 0.1646 0.2406 REMARK 3 7 1.9800 - 1.8800 1.00 2905 153 0.1712 0.2239 REMARK 3 8 1.8800 - 1.8000 1.00 2944 142 0.1611 0.2061 REMARK 3 9 1.8000 - 1.7300 1.00 2908 156 0.1643 0.2278 REMARK 3 10 1.7300 - 1.6700 1.00 2921 142 0.1603 0.2422 REMARK 3 11 1.6700 - 1.6200 0.99 2901 139 0.1745 0.1846 REMARK 3 12 1.6200 - 1.5700 0.98 2863 122 0.1938 0.2510 REMARK 3 13 1.5700 - 1.5300 0.89 2615 146 0.2062 0.2620 REMARK 3 14 1.5300 - 1.4900 0.75 2196 107 0.2152 0.2641 REMARK 3 15 1.4900 - 1.4600 0.63 1821 104 0.2359 0.2871 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.13 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 NULL REMARK 3 ANGLE : 0.993 NULL REMARK 3 CHIRALITY : 0.067 332 REMARK 3 PLANARITY : 0.007 410 REMARK 3 DIHEDRAL : 13.670 804 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9EQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1292137416. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 45.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08931 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.82150 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M NACL, 0.1M SODIUM ACETATE PH4.5, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 27.88050 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 66 REMARK 465 PRO A 67 REMARK 465 GLN A 68 REMARK 465 GLN B -6 REMARK 465 LEU B -5 REMARK 465 VAL B -4 REMARK 465 PRO B -3 REMARK 465 TRP B -2 REMARK 465 ALA B -1 REMARK 465 ALA B 0 REMARK 465 ALA B 1 REMARK 465 GLN C -6 REMARK 465 LEU C -5 REMARK 465 VAL C -4 REMARK 465 PRO C -3 REMARK 465 TRP C -2 REMARK 465 ALA C -1 REMARK 465 ALA C 0 REMARK 465 ALA C 1 REMARK 465 PRO C 67 REMARK 465 GLN C 68 REMARK 465 ALA D 66 REMARK 465 PRO D 67 REMARK 465 GLN D 68 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH22 ARG D 15 O HOH D 201 1.55 REMARK 500 HD22 ASN C 22 O HOH C 204 1.57 REMARK 500 O HOH A 143 O HOH C 238 2.02 REMARK 500 OE2 GLU B 3 O HOH B 101 2.09 REMARK 500 O HOH B 141 O HOH B 154 2.17 REMARK 500 O SER B 2 O HOH B 102 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 9EQN A 0 68 UNP P61825 POLS_IBDV 755 823 DBREF 9EQN B 0 68 UNP P61825 POLS_IBDV 755 823 DBREF 9EQN C 0 68 UNP P61825 POLS_IBDV 755 823 DBREF 9EQN D 0 68 UNP P61825 POLS_IBDV 755 823 SEQADV 9EQN GLN A -6 UNP P61825 EXPRESSION TAG SEQADV 9EQN LEU A -5 UNP P61825 EXPRESSION TAG SEQADV 9EQN VAL A -4 UNP P61825 EXPRESSION TAG SEQADV 9EQN PRO A -3 UNP P61825 EXPRESSION TAG SEQADV 9EQN TRP A -2 UNP P61825 EXPRESSION TAG SEQADV 9EQN ALA A -1 UNP P61825 EXPRESSION TAG SEQADV 9EQN GLN B -6 UNP P61825 EXPRESSION TAG SEQADV 9EQN LEU B -5 UNP P61825 EXPRESSION TAG SEQADV 9EQN VAL B -4 UNP P61825 EXPRESSION TAG SEQADV 9EQN PRO B -3 UNP P61825 EXPRESSION TAG SEQADV 9EQN TRP B -2 UNP P61825 EXPRESSION TAG SEQADV 9EQN ALA B -1 UNP P61825 EXPRESSION TAG SEQADV 9EQN GLN C -6 UNP P61825 EXPRESSION TAG SEQADV 9EQN LEU C -5 UNP P61825 EXPRESSION TAG SEQADV 9EQN VAL C -4 UNP P61825 EXPRESSION TAG SEQADV 9EQN PRO C -3 UNP P61825 EXPRESSION TAG SEQADV 9EQN TRP C -2 UNP P61825 EXPRESSION TAG SEQADV 9EQN ALA C -1 UNP P61825 EXPRESSION TAG SEQADV 9EQN GLN D -6 UNP P61825 EXPRESSION TAG SEQADV 9EQN LEU D -5 UNP P61825 EXPRESSION TAG SEQADV 9EQN VAL D -4 UNP P61825 EXPRESSION TAG SEQADV 9EQN PRO D -3 UNP P61825 EXPRESSION TAG SEQADV 9EQN TRP D -2 UNP P61825 EXPRESSION TAG SEQADV 9EQN ALA D -1 UNP P61825 EXPRESSION TAG SEQRES 1 A 75 GLN LEU VAL PRO TRP ALA ALA ALA SER GLU PHE LYS GLU SEQRES 2 A 75 THR PRO GLU LEU GLU SER ALA VAL ARG ALA MET GLU ALA SEQRES 3 A 75 ALA ALA ASN VAL ASP PRO LEU PHE GLN SER ALA LEU SER SEQRES 4 A 75 VAL PHE MET TRP LEU GLU GLU ASN GLY ILE VAL THR ASP SEQRES 5 A 75 MET ALA ASN PHE ALA LEU SER ASP PRO ASN ALA HIS ARG SEQRES 6 A 75 MET ARG ASN PHE LEU ALA ASN ALA PRO GLN SEQRES 1 B 75 GLN LEU VAL PRO TRP ALA ALA ALA SER GLU PHE LYS GLU SEQRES 2 B 75 THR PRO GLU LEU GLU SER ALA VAL ARG ALA MET GLU ALA SEQRES 3 B 75 ALA ALA ASN VAL ASP PRO LEU PHE GLN SER ALA LEU SER SEQRES 4 B 75 VAL PHE MET TRP LEU GLU GLU ASN GLY ILE VAL THR ASP SEQRES 5 B 75 MET ALA ASN PHE ALA LEU SER ASP PRO ASN ALA HIS ARG SEQRES 6 B 75 MET ARG ASN PHE LEU ALA ASN ALA PRO GLN SEQRES 1 C 75 GLN LEU VAL PRO TRP ALA ALA ALA SER GLU PHE LYS GLU SEQRES 2 C 75 THR PRO GLU LEU GLU SER ALA VAL ARG ALA MET GLU ALA SEQRES 3 C 75 ALA ALA ASN VAL ASP PRO LEU PHE GLN SER ALA LEU SER SEQRES 4 C 75 VAL PHE MET TRP LEU GLU GLU ASN GLY ILE VAL THR ASP SEQRES 5 C 75 MET ALA ASN PHE ALA LEU SER ASP PRO ASN ALA HIS ARG SEQRES 6 C 75 MET ARG ASN PHE LEU ALA ASN ALA PRO GLN SEQRES 1 D 75 GLN LEU VAL PRO TRP ALA ALA ALA SER GLU PHE LYS GLU SEQRES 2 D 75 THR PRO GLU LEU GLU SER ALA VAL ARG ALA MET GLU ALA SEQRES 3 D 75 ALA ALA ASN VAL ASP PRO LEU PHE GLN SER ALA LEU SER SEQRES 4 D 75 VAL PHE MET TRP LEU GLU GLU ASN GLY ILE VAL THR ASP SEQRES 5 D 75 MET ALA ASN PHE ALA LEU SER ASP PRO ASN ALA HIS ARG SEQRES 6 D 75 MET ARG ASN PHE LEU ALA ASN ALA PRO GLN HET EOH C 101 7 HET GOL D 100 14 HETNAM EOH ETHANOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 EOH C2 H6 O FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *224(H2 O) HELIX 1 AA1 LEU A -5 SER A 2 1 8 HELIX 2 AA2 THR A 7 ASP A 24 1 18 HELIX 3 AA3 ASP A 24 ASN A 40 1 17 HELIX 4 AA4 ILE A 42 ASP A 53 1 12 HELIX 5 AA5 ALA A 56 ASN A 65 1 10 HELIX 6 AA6 THR B 7 ASP B 24 1 18 HELIX 7 AA7 ASP B 24 ASN B 40 1 17 HELIX 8 AA8 ILE B 42 ASP B 53 1 12 HELIX 9 AA9 ALA B 56 ALA B 66 1 11 HELIX 10 AB1 THR C 7 ASP C 24 1 18 HELIX 11 AB2 ASP C 24 ASN C 40 1 17 HELIX 12 AB3 ILE C 42 ASP C 53 1 12 HELIX 13 AB4 ALA C 56 ALA C 66 1 11 HELIX 14 AB5 LEU D -5 SER D 2 1 8 HELIX 15 AB6 THR D 7 ASP D 24 1 18 HELIX 16 AB7 ASP D 24 ASN D 40 1 17 HELIX 17 AB8 ILE D 42 ASP D 53 1 12 HELIX 18 AB9 ALA D 56 ASN D 65 1 10 CRYST1 48.670 55.761 52.894 90.00 110.10 90.00 P 1 21 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 0.020547 0.000000 0.007521 0.00000 SCALE2 0.000000 0.017934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020132 0.00000