HEADER RNA BINDING PROTEIN 24-MAY-17 5O3J TITLE CRYSTAL STRUCTURE OF TIA-1 RRM2 IN COMPLEX WITH RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOLYSIN TIA-1 ISOFORM P40; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM2 DOMAIN, UNP RESIDUES 93-170; COMPND 5 SYNONYM: RNA-BINDING PROTEIN TIA-1,T-CELL-RESTRICTED INTRACELLULAR COMPND 6 ANTIGEN-1,TIA-1,P40-TIA-1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(P*UP*UP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TIA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS TIA-1, RNA BINDING PROTEIN, RRM EXPDTA X-RAY DIFFRACTION AUTHOR M.SONNTAG,P.K.A.JAGTAP,J.HENNIG,M.SATTLER REVDAT 4 17-JAN-24 5O3J 1 REMARK REVDAT 3 16-OCT-19 5O3J 1 REMARK REVDAT 2 09-AUG-17 5O3J 1 JRNL REVDAT 1 05-JUL-17 5O3J 0 JRNL AUTH M.SONNTAG,P.K.A.JAGTAP,B.SIMON,M.S.APPAVOU,A.GEERLOF, JRNL AUTH 2 R.STEHLE,F.GABEL,J.HENNIG,M.SATTLER JRNL TITL SEGMENTAL, DOMAIN-SELECTIVE PERDEUTERATION AND SMALL-ANGLE JRNL TITL 2 NEUTRON SCATTERING FOR STRUCTURAL ANALYSIS OF MULTI-DOMAIN JRNL TITL 3 PROTEINS. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 56 9322 2017 JRNL REFN ESSN 1521-3773 JRNL PMID 28636238 JRNL DOI 10.1002/ANIE.201702904 REMARK 2 REMARK 2 RESOLUTION. 2.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 1859 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.312 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 98 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 126 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 6 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 600 REMARK 3 NUCLEIC ACID ATOMS : 43 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.32000 REMARK 3 B22 (A**2) : 2.32000 REMARK 3 B33 (A**2) : -7.52000 REMARK 3 B12 (A**2) : 1.16000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.557 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.526 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.878 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 663 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 551 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 906 ; 0.906 ; 1.834 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1253 ; 0.837 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 79 ; 5.452 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;33.787 ;23.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 79 ;12.793 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;10.869 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 94 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 759 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 176 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 319 ; 1.483 ; 8.832 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 318 ; 1.483 ; 8.838 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 397 ; 2.641 ;13.248 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 398 ; 2.638 ;13.240 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 344 ; 0.920 ; 9.093 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 341 ; 0.911 ; 9.078 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 509 ; 1.701 ;13.634 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 715 ; 3.956 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 714 ; 3.959 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5O3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200005093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1980 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.970 REMARK 200 RESOLUTION RANGE LOW (A) : 35.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.08670 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3BS9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES PH6, 5MM MGSO4, 5% PEG4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.14667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.57333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.86000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.28667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.43333 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 10 OE1 OE2 REMARK 470 ILE A 11 CD1 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 ILE A 16 CD1 REMARK 470 LYS A 17 CG CD CE NZ REMARK 470 ARG A 25 NH1 NH2 REMARK 470 LYS A 33 CD CE NZ REMARK 470 MET A 35 CG SD CE REMARK 470 LYS A 39 CD CE NZ REMARK 470 LYS A 41 CD CE NZ REMARK 470 LYS A 51 CE NZ REMARK 470 C B 3 O5' C5' C4' O4' C3' O3' C2' REMARK 470 C B 3 O2' C1' N1 C2 O2 N3 C4 REMARK 470 C B 3 N4 C5 C6 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 53 -55.33 178.89 REMARK 500 REMARK 500 REMARK: NULL DBREF 5O3J A -2 75 UNP P31483 TIA1_HUMAN 93 170 DBREF 5O3J B 1 3 PDB 5O3J 5O3J 1 3 SEQADV 5O3J GLY A -4 UNP P31483 EXPRESSION TAG SEQADV 5O3J ALA A -3 UNP P31483 EXPRESSION TAG SEQRES 1 A 80 GLY ALA ASN HIS PHE HIS VAL PHE VAL GLY ASP LEU SER SEQRES 2 A 80 PRO GLU ILE THR THR GLU ASP ILE LYS ALA ALA PHE ALA SEQRES 3 A 80 PRO PHE GLY ARG ILE SER ASP ALA ARG VAL VAL LYS ASP SEQRES 4 A 80 MET ALA THR GLY LYS SER LYS GLY TYR GLY PHE VAL SER SEQRES 5 A 80 PHE PHE ASN LYS TRP ASP ALA GLU ASN ALA ILE GLN GLN SEQRES 6 A 80 MET GLY GLY GLN TRP LEU GLY GLY ARG GLN ILE ARG THR SEQRES 7 A 80 ASN TRP SEQRES 1 B 3 U U C HELIX 1 AA1 THR A 12 ALA A 21 1 10 HELIX 2 AA2 ASN A 50 MET A 61 1 12 SHEET 1 AA1 4 ILE A 26 LYS A 33 0 SHEET 2 AA1 4 SER A 40 PHE A 48 -1 O SER A 47 N ASP A 28 SHEET 3 AA1 4 PHE A 0 GLY A 5 -1 N VAL A 4 O GLY A 44 SHEET 4 AA1 4 ARG A 72 ASN A 74 -1 O ASN A 74 N PHE A 3 CRYST1 44.310 44.310 85.720 90.00 90.00 120.00 P 65 6 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 0.022568 0.013030 0.000000 0.00000 SCALE2 0.000000 0.026060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011666 0.00000