HEADER VIRAL PROTEIN 02-JAN-22 7TDQ TITLE CRYSTAL STRUCTURE OF KSHV KICGAS/ORF52 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEGUMENT PROTEIN ORF52; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 8 STRAIN GK18; SOURCE 3 ORGANISM_TAXID: 868565; SOURCE 4 STRAIN: ISOLATE GK18; SOURCE 5 GENE: ORF52; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: E. COLI KEYWDS TEGUMENT PROTEIN; OLIGOMERIZATION; DNA-BINDING, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.YIN,Y.TIAN,D.BHOWMIK,F.ZHU REVDAT 3 15-NOV-23 7TDQ 1 REMARK REVDAT 2 18-OCT-23 7TDQ 1 REMARK REVDAT 1 02-NOV-22 7TDQ 0 JRNL AUTH D.BHOWMIK,Y.TIAN,B.WANG,F.ZHU,Q.YIN JRNL TITL STRUCTURAL BASIS OF HIGHER ORDER OLIGOMERIZATION OF KSHV JRNL TITL 2 INHIBITOR OF CGAS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 85119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35939686 JRNL DOI 10.1073/PNAS.2200285119 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 14384 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1442 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 49.7700 - 5.3800 0.99 1301 146 0.1896 0.2221 REMARK 3 2 5.3800 - 4.2700 1.00 1314 142 0.1893 0.1868 REMARK 3 3 4.2700 - 3.7300 0.99 1295 145 0.1885 0.2584 REMARK 3 4 3.7300 - 3.3900 1.00 1306 143 0.2237 0.2869 REMARK 3 5 3.3900 - 3.1500 1.00 1292 149 0.2697 0.3060 REMARK 3 6 3.1500 - 2.9600 1.00 1291 141 0.2748 0.3181 REMARK 3 7 2.9600 - 2.8200 1.00 1318 149 0.2936 0.3409 REMARK 3 8 2.8200 - 2.6900 0.99 1300 148 0.2937 0.3406 REMARK 3 9 2.6900 - 2.5900 0.98 1282 144 0.3231 0.3587 REMARK 3 10 2.5900 - 2.5000 0.95 1243 135 0.3130 0.3835 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.379 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.27 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 : 0.002 1286 REMARK 3 ANGLE : 0.505 1732 REMARK 3 CHIRALITY : 0.032 220 REMARK 3 PLANARITY : 0.003 222 REMARK 3 DIHEDRAL : 17.676 500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.6371 45.0484 56.2487 REMARK 3 T TENSOR REMARK 3 T11: 0.4499 T22: 0.3711 REMARK 3 T33: 0.4475 T12: -0.0239 REMARK 3 T13: 0.0167 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.1099 L22: -0.2481 REMARK 3 L33: 3.1753 L12: -0.1375 REMARK 3 L13: -0.6968 L23: 0.2193 REMARK 3 S TENSOR REMARK 3 S11: -0.0608 S12: -0.0677 S13: -0.1077 REMARK 3 S21: -0.0867 S22: -0.0611 S23: -0.0332 REMARK 3 S31: 0.0749 S32: 0.0758 S33: 0.1559 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 7TDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000255669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 80 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 : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15886 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : 0.10200 REMARK 200 FOR THE DATA SET : 19.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.59500 REMARK 200 R SYM FOR SHELL (I) : 0.49700 REMARK 200 FOR SHELL : 1.320 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2OA5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICROL OF PROTEIN (10 MG/ML) + 1 REMARK 280 MICROL OF RESERVOIR SOLUTION OF 9% (V/V) PEG3350, 100MM NA- REMARK 280 CITRATE PH 4.5 + 0.2MICROL OF THE DETERGENT ADDITIVE N-OCTYL-N,N- REMARK 280 DIMETHYL-3-AMMONIO-1-PROPANESULFONATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.66600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.34150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.21050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.66600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.34150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.21050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.66600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.34150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.21050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.66600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 29.34150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.21050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 125 LIES ON A SPECIAL POSITION. 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 8 REMARK 465 LYS A 9 REMARK 465 LYS A 10 REMARK 465 SER B 8 REMARK 465 LYS B 9 REMARK 465 LYS B 10 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 VAL A 82 -44.59 -137.48 REMARK 500 LEU A 94 73.45 -104.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 7TDQ A 9 95 UNP Q2HR80 ORF52_HHV8P 9 95 DBREF 7TDQ B 9 95 UNP Q2HR80 ORF52_HHV8P 9 95 SEQADV 7TDQ SER A 8 UNP Q2HR80 EXPRESSION TAG SEQADV 7TDQ MSE A 62 UNP Q2HR80 LEU 62 ENGINEERED MUTATION SEQADV 7TDQ SER B 8 UNP Q2HR80 EXPRESSION TAG SEQADV 7TDQ MSE B 62 UNP Q2HR80 LEU 62 ENGINEERED MUTATION SEQRES 1 A 88 SER LYS LYS ASP LEU THR MSE GLU ASP LEU THR ALA LYS SEQRES 2 A 88 ILE SER GLN LEU THR VAL GLU ASN ARG GLU LEU ARG LYS SEQRES 3 A 88 ALA LEU GLY SER THR ALA ASP PRO ARG ASP ARG PRO LEU SEQRES 4 A 88 THR ALA THR GLU LYS GLU ALA GLN LEU THR ALA THR VAL SEQRES 5 A 88 GLY ALA MSE SER ALA ALA ALA ALA LYS LYS ILE GLU ALA SEQRES 6 A 88 ARG VAL ARG THR ILE PHE SER LYS VAL VAL THR GLN LYS SEQRES 7 A 88 GLN VAL ASP ASP ALA LEU LYS GLY LEU SER SEQRES 1 B 88 SER LYS LYS ASP LEU THR MSE GLU ASP LEU THR ALA LYS SEQRES 2 B 88 ILE SER GLN LEU THR VAL GLU ASN ARG GLU LEU ARG LYS SEQRES 3 B 88 ALA LEU GLY SER THR ALA ASP PRO ARG ASP ARG PRO LEU SEQRES 4 B 88 THR ALA THR GLU LYS GLU ALA GLN LEU THR ALA THR VAL SEQRES 5 B 88 GLY ALA MSE SER ALA ALA ALA ALA LYS LYS ILE GLU ALA SEQRES 6 B 88 ARG VAL ARG THR ILE PHE SER LYS VAL VAL THR GLN LYS SEQRES 7 B 88 GLN VAL ASP ASP ALA LEU LYS GLY LEU SER MODRES 7TDQ MSE A 14 MET MODIFIED RESIDUE MODRES 7TDQ MSE B 14 MET MODIFIED RESIDUE HET MSE A 14 8 HET MSE A 62 8 HET MSE B 14 8 HET MSE B 62 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *46(H2 O) HELIX 1 AA1 THR A 13 SER A 37 1 25 HELIX 2 AA2 ASP A 40 ARG A 44 5 5 HELIX 3 AA3 THR A 47 SER A 79 1 33 HELIX 4 AA4 THR A 83 LEU A 94 1 12 HELIX 5 AA5 LEU B 12 GLY B 36 1 25 HELIX 6 AA6 ASP B 40 ARG B 44 5 5 HELIX 7 AA7 THR B 47 SER B 79 1 33 HELIX 8 AA8 THR B 83 SER B 95 1 13 LINK C THR A 13 N MSE A 14 1555 1555 1.33 LINK C MSE A 14 N GLU A 15 1555 1555 1.34 LINK C ALA A 61 N MSE A 62 1555 1555 1.33 LINK C MSE A 62 N SER A 63 1555 1555 1.34 LINK C THR B 13 N MSE B 14 1555 1555 1.33 LINK C MSE B 14 N GLU B 15 1555 1555 1.33 LINK C ALA B 61 N MSE B 62 1555 1555 1.33 LINK C MSE B 62 N SER B 63 1555 1555 1.34 CRYST1 53.332 58.683 138.421 90.00 90.00 90.00 I 2 2 2 16 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 0.018750 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007224 0.00000