HEADER RNA BINDING PROTEIN 25-JUN-14 4QPT TITLE STRUCTURAL INVESTIGATION OF HNRNP L COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN L; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-245; COMPND 5 SYNONYM: HNRPL PROTEIN, PROTEIN HNRNPL; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: HNRNPL, FBLIM1, HNRNP-L, HNRPL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA RECOGNITION MOTIF, RRM, RNA, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.BLATTER,F.H.-T.ALLAIN REVDAT 3 28-FEB-24 4QPT 1 REMARK REVDAT 2 04-NOV-15 4QPT 1 JRNL REVDAT 1 20-MAY-15 4QPT 0 JRNL AUTH M.BLATTER,S.DUNIN-HORKAWICZ,I.GRISHINA,C.MARIS,S.THORE, JRNL AUTH 2 T.MAIER,A.BINDEREIF,J.M.BUJNICKI,F.H.ALLAIN JRNL TITL THE SIGNATURE OF THE FIVE-STRANDED VRRM FOLD DEFINED BY JRNL TITL 2 FUNCTIONAL, STRUCTURAL AND COMPUTATIONAL ANALYSIS OF THE JRNL TITL 3 HNRNP L PROTEIN. JRNL REF J.MOL.BIOL. V. 427 3001 2015 JRNL REFN ISSN 0022-2836 JRNL PMID 26051023 JRNL DOI 10.1016/J.JMB.2015.05.020 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 44418 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.350 REMARK 3 FREE R VALUE TEST SET COUNT : 2375 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 31.4300 - 3.4711 0.99 2579 145 0.1443 0.1447 REMARK 3 2 3.4711 - 2.7557 0.99 2538 144 0.1571 0.2023 REMARK 3 3 2.7557 - 2.4075 0.98 2474 144 0.1696 0.2265 REMARK 3 4 2.4075 - 2.1874 0.99 2501 140 0.1615 0.1951 REMARK 3 5 2.1874 - 2.0307 1.00 2475 142 0.1690 0.2185 REMARK 3 6 2.0307 - 1.9109 1.00 2508 143 0.1771 0.1918 REMARK 3 7 1.9109 - 1.8153 0.98 2442 139 0.1947 0.2276 REMARK 3 8 1.8153 - 1.7362 0.98 2454 137 0.2000 0.2425 REMARK 3 9 1.7362 - 1.6694 0.99 2475 138 0.1905 0.2594 REMARK 3 10 1.6694 - 1.6118 0.99 2475 137 0.1906 0.2651 REMARK 3 11 1.6118 - 1.5614 1.00 2499 138 0.1830 0.2649 REMARK 3 12 1.5614 - 1.5168 0.99 2462 139 0.1859 0.2183 REMARK 3 13 1.5168 - 1.4768 0.99 2463 140 0.1862 0.2440 REMARK 3 14 1.4768 - 1.4408 1.00 2511 139 0.1908 0.2483 REMARK 3 15 1.4408 - 1.4081 1.00 2430 148 0.1930 0.2658 REMARK 3 16 1.4081 - 1.3781 0.99 2515 144 0.1928 0.2636 REMARK 3 17 1.3781 - 1.3505 0.91 2242 118 0.1978 0.2317 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.014 1743 REMARK 3 ANGLE : 1.526 2354 REMARK 3 CHIRALITY : 0.103 243 REMARK 3 PLANARITY : 0.011 312 REMARK 3 DIHEDRAL : 13.773 646 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 4QPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086360. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 31.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 REMARK 200 R SYM FOR SHELL (I) : 0.61300 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% MPD, 0.1M SODIUM CHLORIDE, 0.04M REMARK 280 SODIUM PHOSPHATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 18.98500 REMARK 290 SMTRY3 2 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 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 GLN A 460 33.37 72.72 REMARK 500 GLN A 460 32.68 72.72 REMARK 500 GLN A 494 66.11 -114.08 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 PO4 A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MQL RELATED DB: PDB REMARK 900 RELATED ID: 2MQM RELATED DB: PDB REMARK 900 RELATED ID: 2MQO RELATED DB: PDB DBREF 4QPT A 372 586 UNP Q5U1Y5 Q5U1Y5_RAT 31 245 SEQRES 1 A 215 TYR GLY PRO HIS ALA ASP SER PRO VAL LEU MET VAL TYR SEQRES 2 A 215 GLY LEU ASP GLN SER LYS MET ASN CYS ASP ARG VAL PHE SEQRES 3 A 215 ASN VAL PHE CYS LEU TYR GLY ASN VAL GLU LYS VAL LYS SEQRES 4 A 215 PHE MET LYS SER LYS PRO GLY ALA ALA MET VAL GLU MET SEQRES 5 A 215 ALA ASP GLY TYR ALA VAL ASP ARG ALA ILE THR HIS LEU SEQRES 6 A 215 ASN ASN ASN PHE MET PHE GLY GLN LYS MET ASN VAL CYS SEQRES 7 A 215 VAL SER LYS GLN PRO ALA ILE MET PRO GLY GLN SER TYR SEQRES 8 A 215 GLY LEU GLU ASP GLY SER CYS SER TYR LYS ASP PHE SER SEQRES 9 A 215 GLU SER ARG ASN ASN ARG PHE SER THR PRO GLU GLN ALA SEQRES 10 A 215 ALA LYS ASN ARG ILE GLN HIS PRO SER ASN VAL LEU HIS SEQRES 11 A 215 PHE PHE ASN ALA PRO LEU GLU VAL THR GLU GLU ASN PHE SEQRES 12 A 215 PHE GLU ILE CYS ASP GLU LEU GLY VAL LYS ARG PRO THR SEQRES 13 A 215 SER VAL LYS VAL PHE SER GLY LYS SER GLU ARG SER SER SEQRES 14 A 215 SER GLY LEU LEU GLU TRP ASP SER LYS SER ASP ALA LEU SEQRES 15 A 215 GLU THR LEU GLY PHE LEU ASN HIS TYR GLN MET LYS ASN SEQRES 16 A 215 PRO ASN GLY PRO TYR PRO TYR THR LEU LYS LEU CYS PHE SEQRES 17 A 215 SER THR ALA GLN HIS ALA SER HET PO4 A 601 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *273(H2 O) HELIX 1 1 ASN A 392 CYS A 401 1 10 HELIX 2 2 ASP A 425 ASN A 437 1 13 HELIX 3 3 THR A 484 ALA A 489 1 6 HELIX 4 4 THR A 510 GLY A 522 1 13 HELIX 5 5 SER A 548 ASN A 560 1 13 SHEET 1 A 5 ASN A 447 VAL A 450 0 SHEET 2 A 5 VAL A 380 TYR A 384 -1 N MET A 382 O CYS A 449 SHEET 3 A 5 ALA A 419 MET A 423 -1 O VAL A 421 N LEU A 381 SHEET 4 A 5 VAL A 406 PHE A 411 -1 N GLU A 407 O GLU A 422 SHEET 5 A 5 TYR A 471 ASP A 473 -1 O LYS A 472 N VAL A 409 SHEET 1 B 2 PHE A 440 MET A 441 0 SHEET 2 B 2 GLN A 444 LYS A 445 -1 O GLN A 444 N MET A 441 SHEET 1 C 4 SER A 528 VAL A 531 0 SHEET 2 C 4 SER A 540 GLU A 545 -1 O GLU A 545 N SER A 528 SHEET 3 C 4 VAL A 499 ALA A 505 -1 N LEU A 500 O LEU A 544 SHEET 4 C 4 LYS A 576 PHE A 579 -1 O CYS A 578 N HIS A 501 SHEET 1 D 2 GLN A 563 MET A 564 0 SHEET 2 D 2 TYR A 573 THR A 574 -1 O TYR A 573 N MET A 564 SITE 1 AC1 3 HIS A 501 SER A 580 THR A 581 CRYST1 48.480 37.970 58.040 90.00 105.35 90.00 P 1 21 1 2 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 0.020627 0.000000 0.005664 0.00000 SCALE2 0.000000 0.026337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017867 0.00000