HEADER RNA BINDING PROTEIN 07-JUN-18 6GQE TITLE X-RAY STRUCTURE OF KH1-2 DOMAIN OF IMP3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR 2 MRNA-BINDING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IMP-3,IGF-II MRNA-BINDING PROTEIN 3,KH DOMAIN-CONTAINING COMPND 5 PROTEIN OVEREXPRESSED IN CANCER,HKOC,VICKZ FAMILY MEMBER 3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IGF2BP3, IMP3, KOC1, VICKZ3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MULTIDOMAIN-RNA BINDING PROTEIN, INSULIN-LIKE GROWTH FACTOR 2, MRNA KEYWDS 2 BINDING PROTEIN 3 (IMP3), MRNA-PROTEIN INTERACTIONS, RNA BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.JANOWSKI,A.SCHLUNDT,M.SATTLER,D.NIESSING REVDAT 5 17-JAN-24 6GQE 1 REMARK REVDAT 4 14-AUG-19 6GQE 1 REMARK REVDAT 3 05-JUN-19 6GQE 1 JRNL REVDAT 2 22-MAY-19 6GQE 1 COMPND SOURCE DBREF SEQADV REVDAT 1 24-APR-19 6GQE 0 JRNL AUTH T.SCHNEIDER,L.H.HUNG,M.AZIZ,A.WILMEN,S.THAUM,J.WAGNER, JRNL AUTH 2 R.JANOWSKI,S.MULLER,S.SCHREINER,P.FRIEDHOFF,S.HUTTELMAIER, JRNL AUTH 3 D.NIESSING,M.SATTLER,A.SCHLUNDT,A.BINDEREIF JRNL TITL COMBINATORIAL RECOGNITION OF CLUSTERED RNA ELEMENTS BY THE JRNL TITL 2 MULTIDOMAIN RNA-BINDING PROTEIN IMP3. JRNL REF NAT COMMUN V. 10 2266 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31118463 JRNL DOI 10.1038/S41467-019-09769-8 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6518 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.500 REMARK 3 FREE R VALUE TEST SET COUNT : 848 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 452 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.99000 REMARK 3 B22 (A**2) : -2.14000 REMARK 3 B33 (A**2) : 6.13000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.519 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.293 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.322 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.983 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1301 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1272 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1753 ; 1.251 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2978 ; 0.899 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 164 ; 5.753 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;40.448 ;25.818 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 264 ;14.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;14.547 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 210 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1399 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 216 ; 0.002 ; 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): 655 ; 1.746 ; 3.877 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 654 ; 1.747 ; 3.876 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 817 ; 2.881 ; 5.801 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 818 ; 2.880 ; 5.803 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 646 ; 1.613 ; 4.144 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 647 ; 1.612 ; 4.146 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 936 ; 2.735 ; 6.136 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1399 ; 4.617 ;46.915 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1400 ; 4.615 ;46.937 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 6GQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-18 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 : 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) : 1.000009 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7366 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: 2ANN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M MAGNESIUM ACETATE, 0.05 M REMARK 280 SODIUM CACODYLATE PH 6.5, 30% W/V POLYETHYLENE GLYCOL 4,000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 18.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.43500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.43500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.04500 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: 9580 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 GLY A 188 REMARK 465 ALA A 189 REMARK 465 MET A 190 REMARK 465 ALA A 237 REMARK 465 GLY A 238 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 ALA A 191 N CA CB DBREF 6GQE A 192 355 UNP O00425 IF2B3_HUMAN 192 355 SEQADV 6GQE GLY A 188 UNP O00425 EXPRESSION TAG SEQADV 6GQE ALA A 189 UNP O00425 EXPRESSION TAG SEQADV 6GQE MET A 190 UNP O00425 EXPRESSION TAG SEQADV 6GQE ALA A 191 UNP O00425 EXPRESSION TAG SEQADV 6GQE ASP A 294 UNP O00425 LYS 294 ENGINEERED MUTATION SEQADV 6GQE ASP A 295 UNP O00425 GLU 295 ENGINEERED MUTATION SEQRES 1 A 168 GLY ALA MET ALA LYS PRO CYS ASP LEU PRO LEU ARG LEU SEQRES 2 A 168 LEU VAL PRO THR GLN PHE VAL GLY ALA ILE ILE GLY LYS SEQRES 3 A 168 GLU GLY ALA THR ILE ARG ASN ILE THR LYS GLN THR GLN SEQRES 4 A 168 SER LYS ILE ASP VAL HIS ARG LYS GLU ASN ALA GLY ALA SEQRES 5 A 168 ALA GLU LYS SER ILE THR ILE LEU SER THR PRO GLU GLY SEQRES 6 A 168 THR SER ALA ALA CYS LYS SER ILE LEU GLU ILE MET HIS SEQRES 7 A 168 LYS GLU ALA GLN ASP ILE LYS PHE THR GLU GLU ILE PRO SEQRES 8 A 168 LEU LYS ILE LEU ALA HIS ASN ASN PHE VAL GLY ARG LEU SEQRES 9 A 168 ILE GLY ASP ASP GLY ARG ASN LEU LYS LYS ILE GLU GLN SEQRES 10 A 168 ASP THR ASP THR LYS ILE THR ILE SER PRO LEU GLN GLU SEQRES 11 A 168 LEU THR LEU TYR ASN PRO GLU ARG THR ILE THR VAL LYS SEQRES 12 A 168 GLY ASN VAL GLU THR CYS ALA LYS ALA GLU GLU GLU ILE SEQRES 13 A 168 MET LYS LYS ILE ARG GLU SER TYR GLU ASN ASP ILE FORMUL 2 HOH *16(H2 O) HELIX 1 AA1 PHE A 206 GLY A 212 1 7 HELIX 2 AA2 GLY A 215 GLN A 226 1 12 HELIX 3 AA3 THR A 249 ILE A 271 1 23 HELIX 4 AA4 VAL A 288 ASP A 307 1 20 HELIX 5 AA5 PRO A 314 LEU A 318 5 5 HELIX 6 AA6 ASN A 332 GLU A 352 1 21 SHEET 1 AA1 6 LYS A 228 ARG A 233 0 SHEET 2 AA1 6 GLU A 241 LEU A 247 -1 O SER A 243 N HIS A 232 SHEET 3 AA1 6 LEU A 198 PRO A 203 -1 N LEU A 198 O ILE A 246 SHEET 4 AA1 6 LEU A 279 HIS A 284 -1 O LEU A 282 N ARG A 199 SHEET 5 AA1 6 GLU A 324 LYS A 330 -1 O VAL A 329 N LEU A 279 SHEET 6 AA1 6 LYS A 309 ILE A 312 -1 N LYS A 309 O LYS A 330 CISPEP 1 LYS A 192 PRO A 193 0 -10.20 CRYST1 36.200 58.090 60.870 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 0.027624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016428 0.00000