HEADER SPLICING 08-FEB-12 4DNN TITLE CRYSTAL STRUCTURE OF THE QUAKING QUA1 HOMODIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN QUAKING; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 14-67 DOMAIN; COMPND 5 SYNONYM: MQKI, QKI; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: QK, QK1, QKA1, QKI, QUAKING; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET22B KEYWDS HELIX-TURN-HELIX, HYDROPHOBIC HOMODIMER INTERFACE, PERPENDICULAR KEYWDS 2 STACKING OF PROTOMERS, DEVELOPMENTAL PROTEIN, RNA-BINDING, SPLICING, KEYWDS 3 TRANSLATION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR C.BEUCK,S.QU,J.R.WILLIAMSON REVDAT 2 17-OCT-12 4DNN 1 JRNL REVDAT 1 12-SEP-12 4DNN 0 JRNL AUTH C.BEUCK,S.QU,W.S.FAGG,M.ARES,J.R.WILLIAMSON JRNL TITL STRUCTURAL ANALYSIS OF THE QUAKING HOMODIMERIZATION JRNL TITL 2 INTERFACE. JRNL REF J.MOL.BIOL. V. 423 766 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22982292 JRNL DOI 10.1016/J.JMB.2012.08.027 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7067 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) : 0.216 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.470 REMARK 3 FREE R VALUE TEST SET COUNT : 316 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 2.6456 - 2.1000 1.00 3313 149 0.2203 0.2466 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 38.55 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30790 REMARK 3 B22 (A**2) : 1.77130 REMARK 3 B33 (A**2) : -2.07920 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 871 REMARK 3 ANGLE : 1.102 1172 REMARK 3 CHIRALITY : 0.068 129 REMARK 3 PLANARITY : 0.006 152 REMARK 3 DIHEDRAL : 12.149 352 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain A REMARK 3 ORIGIN FOR THE GROUP (A): 30.7069 15.4666 28.6974 REMARK 3 T TENSOR REMARK 3 T11: 0.2694 T22: 0.2129 REMARK 3 T33: 0.1941 T12: -0.0091 REMARK 3 T13: 0.0603 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 2.1253 L22: 3.5838 REMARK 3 L33: 4.8439 L12: -0.5391 REMARK 3 L13: -0.3449 L23: 1.7306 REMARK 3 S TENSOR REMARK 3 S11: -0.2739 S12: 0.2427 S13: -0.1446 REMARK 3 S21: -0.3544 S22: 0.0521 S23: 0.1211 REMARK 3 S31: 0.3929 S32: 0.1007 S33: 0.1296 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain B REMARK 3 ORIGIN FOR THE GROUP (A): 23.9365 22.6899 41.9519 REMARK 3 T TENSOR REMARK 3 T11: 0.1158 T22: 0.1131 REMARK 3 T33: 0.1657 T12: 0.0052 REMARK 3 T13: -0.0076 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 4.0255 L22: 2.6626 REMARK 3 L33: 5.2299 L12: -0.1022 REMARK 3 L13: -1.4051 L23: 1.3103 REMARK 3 S TENSOR REMARK 3 S11: -0.1310 S12: 0.0228 S13: -0.0544 REMARK 3 S21: -0.0469 S22: 0.0982 S23: -0.0132 REMARK 3 S31: 0.3117 S32: 0.2522 S33: 0.0045 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 4DNN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-12. REMARK 100 THE RCSB ID CODE IS RCSB070554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791358, 0.9184018, 0.979569 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL, ASYMMETRIC REMARK 200 CUT 4.965 DEGS REMARK 200 OPTICS : RH COATED FLAT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7046 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03600 REMARK 200 FOR THE DATA SET : 35.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28800 REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHENIX (PHENIX.AUTOSOL) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, CALCIUM ACETATE, REMARK 280 PEG 600, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 16.99150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.40700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.01200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.40700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.99150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.01200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 ASN A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 THR A 65 REMARK 465 GLU A 66 REMARK 465 LYS A 67 REMARK 465 GLY B 63 REMARK 465 SER B 64 REMARK 465 THR B 65 REMARK 465 GLU B 66 REMARK 465 LYS B 67 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 ASP A 59 20.59 -75.85 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 CA B 101 DBREF 4DNN A 14 67 UNP Q9QYS9 QKI_MOUSE 14 67 DBREF 4DNN B 14 67 UNP Q9QYS9 QKI_MOUSE 14 67 SEQADV 4DNN GLY A -2 UNP Q9QYS9 EXPRESSION TAG SEQADV 4DNN SER A -1 UNP Q9QYS9 EXPRESSION TAG SEQADV 4DNN SER A 35 UNP Q9QYS9 CYS 35 ENGINEERED MUTATION SEQADV 4DNN GLY B -2 UNP Q9QYS9 EXPRESSION TAG SEQADV 4DNN SER B -1 UNP Q9QYS9 EXPRESSION TAG SEQADV 4DNN SER B 35 UNP Q9QYS9 CYS 35 ENGINEERED MUTATION SEQRES 1 A 56 GLY SER THR PRO ASP TYR LEU MSE GLN LEU MSE ASN ASP SEQRES 2 A 56 LYS LYS LEU MSE SER SER LEU PRO ASN PHE SER GLY ILE SEQRES 3 A 56 PHE ASN HIS LEU GLU ARG LEU LEU ASP GLU GLU ILE SER SEQRES 4 A 56 ARG VAL ARG LYS ASP MSE TYR ASN ASP THR LEU ASN GLY SEQRES 5 A 56 SER THR GLU LYS SEQRES 1 B 56 GLY SER THR PRO ASP TYR LEU MSE GLN LEU MSE ASN ASP SEQRES 2 B 56 LYS LYS LEU MSE SER SER LEU PRO ASN PHE SER GLY ILE SEQRES 3 B 56 PHE ASN HIS LEU GLU ARG LEU LEU ASP GLU GLU ILE SER SEQRES 4 B 56 ARG VAL ARG LYS ASP MSE TYR ASN ASP THR LEU ASN GLY SEQRES 5 B 56 SER THR GLU LYS MODRES 4DNN MSE A 19 MET SELENOMETHIONINE MODRES 4DNN MSE A 22 MET SELENOMETHIONINE MODRES 4DNN MSE A 28 MET SELENOMETHIONINE MODRES 4DNN MSE A 56 MET SELENOMETHIONINE MODRES 4DNN MSE B 19 MET SELENOMETHIONINE MODRES 4DNN MSE B 22 MET SELENOMETHIONINE MODRES 4DNN MSE B 28 MET SELENOMETHIONINE MODRES 4DNN MSE B 56 MET SELENOMETHIONINE HET MSE A 19 8 HET MSE A 22 13 HET MSE A 28 13 HET MSE A 56 8 HET MSE B 19 8 HET MSE B 22 8 HET MSE B 28 13 HET MSE B 56 8 HET CA B 101 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 CA CA 2+ FORMUL 4 HOH *44(H2 O) HELIX 1 1 THR A 14 LEU A 31 1 18 HELIX 2 2 LEU A 31 GLY A 36 1 6 HELIX 3 3 HIS A 40 ASP A 59 1 20 HELIX 4 4 PRO B 15 LEU B 31 1 17 HELIX 5 5 LEU B 31 GLY B 36 1 6 HELIX 6 6 HIS B 40 ASP B 59 1 20 LINK C LEU A 18 N MSE A 19 1555 1555 1.34 LINK C MSE A 19 N GLN A 20 1555 1555 1.33 LINK C LEU A 21 N MSE A 22 1555 1555 1.33 LINK C MSE A 22 N ASN A 23 1555 1555 1.33 LINK C LEU A 27 N MSE A 28 1555 1555 1.33 LINK C MSE A 28 N SER A 29 1555 1555 1.33 LINK C ASP A 55 N MSE A 56 1555 1555 1.33 LINK C MSE A 56 N TYR A 57 1555 1555 1.33 LINK C LEU B 18 N MSE B 19 1555 1555 1.33 LINK C MSE B 19 N GLN B 20 1555 1555 1.33 LINK C LEU B 21 N MSE B 22 1555 1555 1.33 LINK C MSE B 22 N ASN B 23 1555 1555 1.33 LINK C LEU B 27 N MSE B 28 1555 1555 1.33 LINK C MSE B 28 N SER B 29 1555 1555 1.34 LINK C ASP B 55 N MSE B 56 1555 1555 1.33 LINK C MSE B 56 N TYR B 57 1555 1555 1.33 CISPEP 1 SER B -1 THR B 14 0 3.56 SITE 1 AC1 3 LYS B 25 GLU B 42 ASP B 46 CRYST1 33.983 36.024 92.814 90.00 90.00 90.00 P 21 21 21 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 0.029426 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010774 0.00000