HEADER VIRAL PROTEIN 19-DEC-25 9ZRC TITLE CRYSTAL STRUCTURE OF MACRODOMAIN FROM EASTERN EQUINE ENCEPHALITIS TITLE 2 VIRUS I COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYPROTEIN P1234; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-STRUCTURAL POLYPROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EASTERN EQUINE ENCEPHALITIS VIRUS; SOURCE 3 ORGANISM_TAXID: 11021; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MACRO DOMAIN, EASTERN EQUINE ENCEPHALITIS VIRUS, ALPHA VIRUS, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,M.ENDRE,L.STOLS,Y.KIM,A.JOACHIMIAK REVDAT 1 12-AUG-26 9ZRC 0 JRNL AUTH C.CHANG,M.ENDRE,L.STOLS,Y.KIM,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF MACRODOMAIN FROM CHIKUNGUNYA VIRUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 33259 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1654 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 38.8500 - 2.8600 1.00 3053 182 0.1545 0.1771 REMARK 3 2 2.8600 - 2.2700 1.00 2927 169 0.1588 0.1681 REMARK 3 3 2.2700 - 1.9900 1.00 2919 137 0.1372 0.1559 REMARK 3 4 1.9900 - 1.8000 1.00 2886 162 0.1358 0.1713 REMARK 3 5 1.8000 - 1.6800 1.00 2865 147 0.1289 0.1683 REMARK 3 6 1.6800 - 1.5800 1.00 2890 132 0.1216 0.1687 REMARK 3 7 1.5800 - 1.5000 1.00 2831 140 0.1151 0.1726 REMARK 3 8 1.5000 - 1.4300 1.00 2898 132 0.1320 0.1732 REMARK 3 9 1.4300 - 1.3800 0.99 2811 161 0.1474 0.1954 REMARK 3 10 1.3800 - 1.3300 0.85 2370 142 0.1503 0.2017 REMARK 3 11 1.3300 - 1.2900 0.66 1876 100 0.1515 0.1871 REMARK 3 12 1.2900 - 1.2500 0.45 1279 50 0.1586 0.1921 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.420 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 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 : 0.005 1398 REMARK 3 ANGLE : 0.725 1915 REMARK 3 CHIRALITY : 0.076 205 REMARK 3 PLANARITY : 0.004 261 REMARK 3 DIHEDRAL : 11.368 541 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 9ZRC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1000303510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33929 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS , PEG 3350, PH 5.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 20.22500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.45300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.86350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.45300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.86350 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 SER A -2 REMARK 465 ASN A -1 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 OD1 ASP A 137 O HOH A 301 2.06 REMARK 500 OD2 ASP A 137 O HOH A 302 2.19 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 469 DISTANCE = 7.15 ANGSTROMS DBREF 9ZRC A 1 155 UNP Q66580 Q66580_EEEV 1327 1481 SEQADV 9ZRC SER A -2 UNP Q66580 EXPRESSION TAG SEQADV 9ZRC ASN A -1 UNP Q66580 EXPRESSION TAG SEQADV 9ZRC ALA A 0 UNP Q66580 EXPRESSION TAG SEQRES 1 A 158 SER ASN ALA ALA PRO ALA TYR ARG VAL VAL ARG GLY ASP SEQRES 2 A 158 ILE THR LYS SER ASN ASP GLU VAL ILE VAL ASN ALA ALA SEQRES 3 A 158 ASN ASN LYS GLY GLN PRO GLY GLY GLY VAL CYS GLY ALA SEQRES 4 A 158 LEU TYR ARG LYS TRP PRO GLY ALA PHE ASP LYS GLN PRO SEQRES 5 A 158 VAL ALA THR GLY LYS ALA HIS LEU VAL LYS HIS SER PRO SEQRES 6 A 158 ASN VAL ILE HIS ALA VAL GLY PRO ASN PHE SER ARG LEU SEQRES 7 A 158 SER GLU ASN GLU GLY ASP GLN LYS LEU SER GLU VAL TYR SEQRES 8 A 158 MET ASP ILE ALA ARG ILE ILE ASN ASN GLU ARG PHE THR SEQRES 9 A 158 LYS VAL SER ILE PRO LEU LEU SER THR GLY ILE TYR ALA SEQRES 10 A 158 GLY GLY LYS ASP ARG VAL MET GLN SER LEU ASN HIS LEU SEQRES 11 A 158 PHE THR ALA MET ASP THR THR ASP ALA ASP ILE THR ILE SEQRES 12 A 158 TYR CYS LEU ASP LYS GLN TRP GLU SER ARG ILE LYS GLU SEQRES 13 A 158 ALA ILE HET BTB A 201 14 HET CL A 202 1 HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETNAM CL CHLORIDE ION HETSYN BTB BIS-TRIS BUFFER FORMUL 2 BTB C8 H19 N O5 FORMUL 3 CL CL 1- FORMUL 4 HOH *169(H2 O) HELIX 1 AA1 ASP A 10 SER A 14 5 5 HELIX 2 AA2 GLY A 31 TRP A 41 1 11 HELIX 3 AA3 PRO A 42 PHE A 45 5 4 HELIX 4 AA4 SER A 76 ARG A 99 1 24 HELIX 5 AA5 GLY A 111 GLY A 115 5 5 HELIX 6 AA6 ARG A 119 ASP A 132 1 14 HELIX 7 AA7 ASP A 144 ILE A 155 1 12 SHEET 1 AA1 6 TYR A 4 ARG A 8 0 SHEET 2 AA1 6 ASP A 137 CYS A 142 1 O ILE A 140 N ARG A 5 SHEET 3 AA1 6 LYS A 102 PRO A 106 1 N VAL A 103 O THR A 139 SHEET 4 AA1 6 VAL A 18 ALA A 22 1 N VAL A 20 O SER A 104 SHEET 5 AA1 6 ASN A 63 ALA A 67 1 O ILE A 65 N ASN A 21 SHEET 6 AA1 6 ALA A 55 VAL A 58 -1 N HIS A 56 O HIS A 66 CISPEP 1 ALA A 1 PRO A 2 0 2.20 CISPEP 2 SER A 61 PRO A 62 0 2.70 CRYST1 40.450 47.727 66.906 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 0.024722 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014946 0.00000 CONECT 1348 1349 1350 CONECT 1349 1348 CONECT 1350 1348 1351 1353 1355 CONECT 1351 1350 1352 CONECT 1352 1351 CONECT 1353 1350 1354 CONECT 1354 1353 CONECT 1355 1350 1356 1359 CONECT 1356 1355 1357 CONECT 1357 1356 1358 CONECT 1358 1357 CONECT 1359 1355 1360 CONECT 1360 1359 1361 CONECT 1361 1360 MASTER 231 0 2 7 6 0 0 6 1386 1 14 13 END