HEADER PROTEIN BINDING 23-OCT-15 5EFC TITLE STRUCTURE OF INFLUENZA B LEE PB2 CAP-BINDING DOMAIN BOUND TO GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYMERASE BASIC PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CAP-BINDING DOMAIN; 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 5EFC 1 JRNL REMARK REVDAT 3 13-JAN-16 5EFC 1 JRNL REVDAT 2 25-NOV-15 5EFC 1 JRNL REVDAT 1 18-NOV-15 5EFC 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13739 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 688 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 36.8053 - 3.2484 0.99 2751 125 0.1621 0.1842 REMARK 3 2 3.2484 - 2.5785 1.00 2619 123 0.1809 0.2225 REMARK 3 3 2.5785 - 2.2526 1.00 2581 133 0.1938 0.2542 REMARK 3 4 2.2526 - 2.0467 1.00 2553 155 0.1995 0.2554 REMARK 3 5 2.0467 - 1.9000 1.00 2547 152 0.2409 0.2981 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.37 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 1382 REMARK 3 ANGLE : 1.155 1855 REMARK 3 CHIRALITY : 0.048 193 REMARK 3 PLANARITY : 0.005 237 REMARK 3 DIHEDRAL : 19.389 543 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): 31.8421 39.4215 35.0681 REMARK 3 T TENSOR REMARK 3 T11: 0.0557 T22: 0.0681 REMARK 3 T33: 0.0628 T12: -0.0046 REMARK 3 T13: 0.0028 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.5768 L22: 0.6022 REMARK 3 L33: 0.9104 L12: -0.2456 REMARK 3 L13: -0.1154 L23: 0.1044 REMARK 3 S TENSOR REMARK 3 S11: 0.0063 S12: 0.0285 S13: 0.0169 REMARK 3 S21: -0.0632 S22: -0.0532 S23: -0.0216 REMARK 3 S31: -0.0508 S32: -0.0051 S33: -0.0015 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 5EFC 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_1000214820. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13781 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.71400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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 (%): 39.86 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, HANGING 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 20.25750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.97600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.46500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.97600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.25750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.46500 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: 610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 487 REMARK 465 HIS A 488 REMARK 465 HIS A 489 REMARK 465 HIS A 490 REMARK 465 HIS A 491 REMARK 465 HIS A 492 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 ILE A 420 75.99 -112.65 REMARK 500 ARG A 425 6.01 -61.84 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 698 DISTANCE = 5.95 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EF9 RELATED DB: PDB REMARK 900 RELATED ID: 5EFA RELATED DB: PDB DBREF 5EFC A 320 485 UNP Q9QLL6 PB2_INBLE 320 485 SEQADV 5EFC MET A 319 UNP Q9QLL6 INITIATING METHIONINE SEQADV 5EFC ASP A 486 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EFC HIS A 487 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EFC HIS A 488 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EFC HIS A 489 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EFC HIS A 490 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EFC HIS A 491 UNP Q9QLL6 EXPRESSION TAG SEQADV 5EFC 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 HET GTP A 501 32 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 HOH *98(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 ARG A 443 1 13 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 GLY A 337 -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 ILE A 358 N ASN A 342 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 SITE 1 AC1 11 GLN A 325 PHE A 327 ARG A 334 TRP A 359 SITE 2 AC1 11 GLU A 363 LYS A 378 PHE A 406 TYR A 434 SITE 3 AC1 11 HOH A 603 HOH A 629 HOH A 647 CRYST1 40.515 46.930 87.952 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 0.024682 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011370 0.00000