HEADER VIRAL PROTEIN 19-DEC-25 9ZRA TITLE CRYSTAL STRUCTURE OF MACRODOMAIN FROM CHIKUNGUNYA VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYPROTEIN P1234; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MACRODOMAIN, RESIDUES 1334-1493; COMPND 5 SYNONYM: NON-STRUCTURAL POLYPROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHIKUNGUNYA VIRUS; SOURCE 3 ORGANISM_TAXID: 37124; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MACRO DOMAIN, CHIKUNGUNYA VIRUS, ALPHA VIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,M.ENDRE,L.STOLS,Y.KIM,A.JOACHIMIAK REVDAT 1 12-AUG-26 9ZRA 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 39416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 2019 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 41.0300 - 3.1300 1.00 2909 150 0.1274 0.1386 REMARK 3 2 3.1300 - 2.4800 1.00 2906 125 0.1483 0.1844 REMARK 3 3 2.4800 - 2.1700 1.00 2844 166 0.1494 0.1917 REMARK 3 4 2.1700 - 1.9700 1.00 2832 198 0.1521 0.1975 REMARK 3 5 1.9700 - 1.8300 1.00 2860 151 0.1545 0.1703 REMARK 3 6 1.8300 - 1.7200 1.00 2856 165 0.1603 0.1898 REMARK 3 7 1.7200 - 1.6400 1.00 2873 143 0.1753 0.2068 REMARK 3 8 1.6400 - 1.5600 1.00 2855 149 0.1759 0.2248 REMARK 3 9 1.5600 - 1.5000 1.00 2851 155 0.1927 0.2251 REMARK 3 10 1.5000 - 1.4500 1.00 2833 172 0.1968 0.2363 REMARK 3 11 1.4500 - 1.4100 1.00 2909 117 0.2132 0.2798 REMARK 3 12 1.4100 - 1.3700 0.99 2816 146 0.2365 0.2632 REMARK 3 13 1.3700 - 1.3300 0.73 2088 118 0.2543 0.2772 REMARK 3 14 1.3300 - 1.3000 0.34 965 64 0.2219 0.2189 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.910 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 1350 REMARK 3 ANGLE : 0.753 1830 REMARK 3 CHIRALITY : 0.069 200 REMARK 3 PLANARITY : 0.007 241 REMARK 3 DIHEDRAL : 12.094 511 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 9ZRA 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_1000303499. 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 : 7.5 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42057 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 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 (%): 49.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PEG 8000 ETHYLENE GLYCOL, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 51.93850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.96925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.90775 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 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 O HOH A 514 O HOH A 520 2.03 REMARK 500 O GLY A 27 O HOH A 301 2.11 REMARK 500 O HOH A 360 O HOH A 415 2.15 REMARK 500 O HOH A 427 O HOH A 468 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 1 64.90 -150.11 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 525 DISTANCE = 6.19 ANGSTROMS DBREF 9ZRA A 1 160 UNP D0U7D9 D0U7D9_CHIKV 1334 1493 SEQADV 9ZRA SER A -2 UNP D0U7D9 EXPRESSION TAG SEQADV 9ZRA ASN A -1 UNP D0U7D9 EXPRESSION TAG SEQADV 9ZRA ALA A 0 UNP D0U7D9 EXPRESSION TAG SEQRES 1 A 163 SER ASN ALA ALA PRO SER TYR ARG VAL LYS ARG MET ASP SEQRES 2 A 163 ILE ALA LYS ASN ASP GLU GLU CYS VAL VAL ASN ALA ALA SEQRES 3 A 163 ASN PRO ARG GLY LEU PRO GLY ASP GLY VAL CYS LYS ALA SEQRES 4 A 163 VAL TYR LYS LYS TRP PRO GLU SER PHE LYS ASN SER ALA SEQRES 5 A 163 THR PRO VAL GLY THR ALA LYS THR VAL MET CYS GLY THR SEQRES 6 A 163 TYR PRO VAL ILE HIS ALA VAL GLY PRO ASN PHE SER ASN SEQRES 7 A 163 TYR SER GLU SER GLU GLY ASP ARG GLU LEU ALA ALA ALA SEQRES 8 A 163 TYR ARG GLU VAL ALA LYS GLU VAL THR ARG LEU GLY VAL SEQRES 9 A 163 ASN SER VAL ALA ILE PRO LEU LEU SER THR GLY VAL TYR SEQRES 10 A 163 SER GLY GLY LYS ASP ARG LEU THR GLN SER LEU ASN HIS SEQRES 11 A 163 LEU PHE THR ALA MET ASP SER THR ASP ALA ASP VAL VAL SEQRES 12 A 163 ILE TYR CYS ARG ASP LYS GLU TRP GLU LYS LYS ILE SER SEQRES 13 A 163 GLU ALA ILE GLN MET ARG THR HET GOL A 201 12 HET EDO A 202 4 HET EDO A 203 4 HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *225(H2 O) HELIX 1 AA1 ASP A 10 ASN A 14 5 5 HELIX 2 AA2 ASP A 31 TRP A 41 1 11 HELIX 3 AA3 PRO A 42 LYS A 46 5 5 HELIX 4 AA4 SER A 77 GLY A 100 1 24 HELIX 5 AA5 GLY A 112 GLY A 116 5 5 HELIX 6 AA6 ARG A 120 ASP A 133 1 14 HELIX 7 AA7 ASP A 145 ARG A 159 1 15 SHEET 1 AA1 3 TYR A 4 ARG A 8 0 SHEET 2 AA1 3 ASP A 138 CYS A 143 1 O ILE A 141 N ARG A 5 SHEET 3 AA1 3 SER A 103 PRO A 107 1 N VAL A 104 O VAL A 140 SHEET 1 AA2 3 VAL A 19 ALA A 22 0 SHEET 2 AA2 3 TYR A 63 ALA A 68 1 O ILE A 66 N VAL A 19 SHEET 3 AA2 3 ALA A 55 CYS A 60 -1 N LYS A 56 O HIS A 67 CRYST1 41.031 41.031 103.877 90.00 90.00 90.00 P 41 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 0.024372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024372 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009627 0.00000 CONECT 1306 1308 1310 CONECT 1307 1309 1311 CONECT 1308 1306 CONECT 1309 1307 CONECT 1310 1306 1312 1314 CONECT 1311 1307 1313 1315 CONECT 1312 1310 CONECT 1313 1311 CONECT 1314 1310 1316 CONECT 1315 1311 1317 CONECT 1316 1314 CONECT 1317 1315 CONECT 1318 1319 1320 CONECT 1319 1318 CONECT 1320 1318 1321 CONECT 1321 1320 CONECT 1322 1323 1324 CONECT 1323 1322 CONECT 1324 1322 1325 CONECT 1325 1324 MASTER 252 0 3 7 6 0 0 6 1479 1 20 13 END