HEADER PROTEIN BINDING 23-OCT-15 5EF9 TITLE STRUCTURE OF INFLUENZA B LEE PB2 CAP-BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYMERASE BASIC PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CAP-BINDING DOMAIN, UNP RESIDUES 320-485; COMPND 5 SYNONYM: RNA-DIRECTED RNA POLYMERASE SUBUNIT P3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA B VIRUS; SOURCE 3 ORGANISM_TAXID: 518987; SOURCE 4 STRAIN: B/LEE/1940; SOURCE 5 GENE: PB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTRCHIS2B KEYWDS CAP-BINDING DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR X.MA,S.SHIA REVDAT 4 06-MAR-24 5EF9 1 JRNL REMARK REVDAT 3 13-JAN-16 5EF9 1 JRNL REVDAT 2 25-NOV-15 5EF9 1 JRNL REVDAT 1 18-NOV-15 5EF9 0 JRNL AUTH L.XIE,C.WARTCHOW,S.SHIA,K.UEHARA,M.STEFFEK,R.WARNE,J.SUTTON, JRNL AUTH 2 G.T.MUIRU,V.H.LEONARD,D.E.BUSSIERE,X.MA JRNL TITL MOLECULAR BASIS OF MRNA CAP RECOGNITION BY INFLUENZA B JRNL TITL 2 POLYMERASE PB2 SUBUNIT. JRNL REF J.BIOL.CHEM. V. 291 363 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26559973 JRNL DOI 10.1074/JBC.M115.693051 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 986 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 43.8531 - 3.2516 1.00 2757 142 0.1651 0.2216 REMARK 3 2 3.2516 - 2.5810 1.00 2626 132 0.1792 0.2335 REMARK 3 3 2.5810 - 2.2547 1.00 2582 149 0.1753 0.2127 REMARK 3 4 2.2547 - 2.0486 1.00 2552 143 0.1670 0.2037 REMARK 3 5 2.0486 - 1.9018 1.00 2584 137 0.1850 0.2224 REMARK 3 6 1.9018 - 1.7896 1.00 2530 140 0.2095 0.2483 REMARK 3 7 1.7896 - 1.7000 1.00 2551 143 0.2416 0.2913 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.27 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 : 0.007 1403 REMARK 3 ANGLE : 1.098 1876 REMARK 3 CHIRALITY : 0.047 194 REMARK 3 PLANARITY : 0.004 246 REMARK 3 DIHEDRAL : 14.268 544 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): 31.9096 40.4289 34.9363 REMARK 3 T TENSOR REMARK 3 T11: 0.0672 T22: 0.0687 REMARK 3 T33: 0.0690 T12: 0.0016 REMARK 3 T13: -0.0017 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.4243 L22: 0.1787 REMARK 3 L33: 0.4386 L12: 0.0335 REMARK 3 L13: -0.0396 L23: 0.0016 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: 0.0073 S13: 0.0500 REMARK 3 S21: -0.0473 S22: -0.0150 S23: -0.0005 REMARK 3 S31: -0.0055 S32: -0.0085 S33: -0.2964 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 5EF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214816. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-13 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19223 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 87.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.94000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 42% PEG400, 0.1 M HEPES PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 20.42850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.83850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.43800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.83850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.42850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.43800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 MET A 319 REMARK 465 LYS A 320 REMARK 465 ILE A 321 REMARK 465 ARG A 322 REMARK 465 GLN A 323 REMARK 465 HIS A 492 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 GLU A 461 O HOH A 501 2.08 REMARK 500 O HOH A 502 O HOH A 503 2.12 REMARK 500 O HOH A 576 O HOH A 637 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 527 O HOH A 533 4566 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EFA RELATED DB: PDB REMARK 900 RELATED ID: 5EFC RELATED DB: PDB DBREF 5EF9 A 320 485 UNP Q9QLL6 PB2_INBLE 320 485 SEQADV 5EF9 MET A 319 UNP Q9QLL6 INITIATING METHIONINE SEQADV 5EF9 ASP A 486 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EF9 HIS A 487 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EF9 HIS A 488 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EF9 HIS A 489 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EF9 HIS A 490 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EF9 HIS A 491 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EF9 HIS A 492 UNP Q9QLL6 EXPRESSION TAG SEQRES 1 A 174 MET LYS ILE ARG GLN ARG GLN ARG PHE GLY ARG LEU GLU SEQRES 2 A 174 LEU LYS ARG ILE SER GLY ARG GLY PHE LYS ASN ASP GLU SEQRES 3 A 174 GLU ILE LEU ILE GLY ASN GLY THR ILE GLN LYS ILE GLY SEQRES 4 A 174 ILE TRP ASP GLY GLU GLU GLU PHE HIS VAL ARG CYS GLY SEQRES 5 A 174 GLU CYS ARG GLY ILE LEU LYS LYS SER GLN MET ARG MET SEQRES 6 A 174 GLU LYS LEU LEU ILE ASN SER ALA LYS LYS GLU ASP MET SEQRES 7 A 174 LYS ASP LEU ILE ILE LEU CYS MET VAL PHE SER GLN ASP SEQRES 8 A 174 THR ARG MET PHE GLN GLY VAL ARG GLY GLU ILE ASN PHE SEQRES 9 A 174 LEU ASN ARG ALA GLY GLN LEU LEU SER PRO MET TYR GLN SEQRES 10 A 174 LEU GLN ARG TYR PHE LEU ASN ARG SER ASN ASP LEU PHE SEQRES 11 A 174 ASP GLN TRP GLY TYR GLU GLU SER PRO LYS ALA SER GLU SEQRES 12 A 174 LEU HIS GLY ILE ASN GLU LEU MET ASN ALA SER ASP TYR SEQRES 13 A 174 THR LEU LYS GLY VAL VAL VAL THR LYS ASN VAL ASP HIS SEQRES 14 A 174 HIS HIS HIS HIS HIS FORMUL 2 HOH *155(H2 O) HELIX 1 AA1 LYS A 392 SER A 407 1 16 HELIX 2 AA2 ASP A 409 GLY A 415 1 7 HELIX 3 AA3 SER A 431 ASN A 442 1 12 HELIX 4 AA4 ARG A 443 GLY A 452 1 10 SHEET 1 AA1 8 GLN A 325 PHE A 327 0 SHEET 2 AA1 8 LEU A 330 SER A 336 -1 O LEU A 330 N PHE A 327 SHEET 3 AA1 8 GLU A 363 CYS A 369 -1 O GLU A 364 N ILE A 335 SHEET 4 AA1 8 CYS A 372 SER A 379 -1 O GLY A 374 N VAL A 367 SHEET 5 AA1 8 ARG A 382 ASN A 389 -1 O LYS A 385 N LYS A 377 SHEET 6 AA1 8 VAL A 479 THR A 482 1 O VAL A 480 N LEU A 386 SHEET 7 AA1 8 LEU A 462 ILE A 465 -1 N HIS A 463 O VAL A 481 SHEET 8 AA1 8 ALA A 471 SER A 472 -1 O SER A 472 N GLY A 464 SHEET 1 AA2 2 PHE A 340 LEU A 347 0 SHEET 2 AA2 2 ILE A 353 ASP A 360 -1 O ASP A 360 N PHE A 340 SHEET 1 AA3 2 TYR A 453 GLU A 455 0 SHEET 2 AA3 2 TYR A 474 LEU A 476 -1 O THR A 475 N GLU A 454 CRYST1 40.857 46.876 87.677 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 0.024476 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011405 0.00000