HEADER VIRAL PROTEIN 20-OCT-15 5ED7 TITLE CRYSTAL STRUCTURE OF HSV-1 UL21 C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEGUMENT PROTEIN UL21; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 1 (STRAIN 17); SOURCE 3 ORGANISM_COMMON: HHV-1; SOURCE 4 ORGANISM_TAXID: 10299; SOURCE 5 STRAIN: 17; SOURCE 6 GENE: UL21; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.M.METRICK,E.E.HELDWEIN REVDAT 5 06-MAR-24 5ED7 1 REMARK REVDAT 4 04-DEC-19 5ED7 1 REMARK REVDAT 3 20-SEP-17 5ED7 1 JRNL REMARK REVDAT 2 08-JUN-16 5ED7 1 JRNL REVDAT 1 20-APR-16 5ED7 0 JRNL AUTH C.M.METRICK,E.E.HELDWEIN JRNL TITL NOVEL STRUCTURE AND UNEXPECTED RNA-BINDING ABILITY OF THE JRNL TITL 2 C-TERMINAL DOMAIN OF HERPES SIMPLEX VIRUS 1 TEGUMENT PROTEIN JRNL TITL 3 UL21. JRNL REF J.VIROL. V. 90 5759 2016 JRNL REFN ESSN 1098-5514 JRNL PMID 27053559 JRNL DOI 10.1128/JVI.00475-16 REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 7813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 360 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 51.9899 - 3.9226 0.99 2604 121 0.1972 0.2004 REMARK 3 2 3.9226 - 3.1136 1.00 2440 134 0.2381 0.2726 REMARK 3 3 3.1136 - 2.7200 1.00 2409 105 0.2777 0.3221 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 71.09 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 : 0.002 1977 REMARK 3 ANGLE : 0.408 2690 REMARK 3 CHIRALITY : 0.036 303 REMARK 3 PLANARITY : 0.004 351 REMARK 3 DIHEDRAL : 8.555 1181 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): 48.5178 12.2350 74.5435 REMARK 3 T TENSOR REMARK 3 T11: 0.5763 T22: 0.3880 REMARK 3 T33: 0.5255 T12: -0.0131 REMARK 3 T13: -0.0090 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.7569 L22: 2.0587 REMARK 3 L33: 3.4024 L12: -1.7509 REMARK 3 L13: -0.3735 L23: 0.5455 REMARK 3 S TENSOR REMARK 3 S11: -0.2570 S12: -0.1324 S13: 0.0467 REMARK 3 S21: 0.2973 S22: 0.1467 S23: -0.1655 REMARK 3 S31: 0.0572 S32: 0.3141 S33: 0.1266 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 5ED7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000205752. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5-4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7854 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 54.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.92300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM CITRATE, NDSB 256, REMARK 280 SODIUM FLUORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 90.37850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.13650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.13650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.56775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.13650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.13650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.18925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.13650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.13650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 135.56775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.13650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.13650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.18925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.37850 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 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 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 293 -6.34 -140.84 REMARK 500 ARG A 302 44.70 -96.22 REMARK 500 ARG A 359 -136.58 -103.27 REMARK 500 VAL A 485 99.56 -68.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 606 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4U4H RELATED DB: PDB REMARK 900 4U4H IS THE OTHER DOMAIN OF HSV-1 UL21 DBREF 5ED7 A 279 530 UNP P10205 TEG4_HHV11 279 530 SEQRES 1 A 252 PRO PRO GLY PRO THR LEU ARG GLU LEU TRP TRP VAL PHE SEQRES 2 A 252 TYR ALA ALA ASP ARG ALA LEU GLU GLU PRO ARG ALA ASP SEQRES 3 A 252 SER GLY LEU THR ARG GLU GLU VAL ARG ALA VAL ARG GLY SEQRES 4 A 252 PHE ARG GLU GLN ALA TRP LYS LEU PHE GLY SER ALA GLY SEQRES 5 A 252 ALA PRO ARG ALA PHE ILE GLY ALA ALA LEU GLY LEU SER SEQRES 6 A 252 PRO LEU GLN LYS LEU ALA VAL TYR TYR TYR ILE ILE HIS SEQRES 7 A 252 ARG GLU ARG ARG LEU SER PRO PHE PRO ALA LEU VAL ARG SEQRES 8 A 252 LEU VAL GLY ARG TYR THR GLN ARG HIS GLY LEU TYR VAL SEQRES 9 A 252 PRO ARG PRO ASP ASP PRO VAL LEU ALA ASP ALA ILE ASN SEQRES 10 A 252 GLY LEU PHE ARG ASP ALA LEU ALA ALA GLY THR THR ALA SEQRES 11 A 252 GLU GLN LEU LEU MET PHE ASP LEU LEU PRO PRO LYS ASP SEQRES 12 A 252 VAL PRO VAL GLY SER ASP VAL GLN ALA ASP SER THR ALA SEQRES 13 A 252 LEU LEU ARG PHE ILE GLU SER GLN ARG LEU ALA VAL PRO SEQRES 14 A 252 GLY GLY VAL ILE SER PRO GLU HIS VAL ALA TYR LEU GLY SEQRES 15 A 252 ALA PHE LEU SER VAL LEU TYR ALA GLY ARG GLY ARG MET SEQRES 16 A 252 SER ALA ALA THR HIS THR ALA ARG LEU THR GLY VAL THR SEQRES 17 A 252 SER LEU VAL LEU ALA VAL GLY ASP VAL ASP ARG LEU SER SEQRES 18 A 252 ALA PHE ASP ARG GLY ALA ALA GLY ALA ALA SER ARG THR SEQRES 19 A 252 ARG ALA ALA GLY TYR LEU ASP VAL LEU LEU THR VAL ARG SEQRES 20 A 252 LEU ALA ARG SER GLN HET CL A 601 1 HET CL A 602 1 HET CL A 603 1 HET CL A 604 1 HET CL A 605 1 HET CL A 606 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 6(CL 1-) FORMUL 8 HOH *2(H2 O) HELIX 1 AA1 THR A 283 GLU A 299 1 17 HELIX 2 AA2 ARG A 302 LEU A 307 5 6 HELIX 3 AA3 THR A 308 GLY A 327 1 20 HELIX 4 AA4 SER A 343 HIS A 356 1 14 HELIX 5 AA5 PRO A 363 GLY A 379 1 17 HELIX 6 AA6 VAL A 389 MET A 413 1 25 HELIX 7 AA7 SER A 426 GLN A 442 1 17 HELIX 8 AA8 SER A 452 TYR A 467 1 16 HELIX 9 AA9 GLY A 471 GLY A 484 1 14 HELIX 10 AB1 SER A 487 ARG A 497 1 11 HELIX 11 AB2 ARG A 503 GLN A 530 1 28 CISPEP 1 GLY A 281 PRO A 282 0 -1.91 SITE 1 AC1 2 THR A 283 LEU A 284 SITE 1 AC2 1 ARG A 443 SITE 1 AC3 1 LEU A 416 SITE 1 AC4 1 ARG A 472 SITE 1 AC5 1 ARG A 470 CRYST1 54.273 54.273 180.757 90.00 90.00 90.00 P 43 21 2 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 0.018425 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005532 0.00000