HEADER RNA BINDING PROTEIN 12-AUG-19 6KOR TITLE CRYSTAL STRUCTURE OF THE RRM DOMAIN OF SYNCRIP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN Q; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM DOMAIN; COMPND 5 SYNONYM: HNRNP Q,GLYCINE- AND TYROSINE-RICH RNA-BINDING PROTEIN,GRY- COMPND 6 RBP,NS1-ASSOCIATED PROTEIN 1,SYNAPTOTAGMIN-BINDING,CYTOPLASMIC RNA- COMPND 7 INTERACTING PROTEIN; COMPND 8 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: SYNCRIP, HNRPQ, NSAP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA RECOGNITION MOTIF, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,J.CHAN,W.CHEN,C.JOBICHEN REVDAT 3 22-NOV-23 6KOR 1 REMARK REVDAT 2 04-MAR-20 6KOR 1 JRNL REVDAT 1 22-JAN-20 6KOR 0 JRNL AUTH Y.CHEN,J.CHAN,W.CHEN,J.LI,M.SUN,G.S.KANNAN,Y.K.MOK,Y.A.YUAN, JRNL AUTH 2 C.JOBICHEN JRNL TITL SYNCRIP, A NEW PLAYER IN PRI-LET-7A PROCESSING. JRNL REF RNA V. 26 290 2020 JRNL REFN ESSN 1469-9001 JRNL PMID 31907208 JRNL DOI 10.1261/RNA.072959.119 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 283 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 25.9080 - 3.2774 1.00 2846 149 0.1669 0.2330 REMARK 3 2 3.2774 - 2.6022 1.00 2897 134 0.2180 0.2945 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.24 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 : 0.010 1372 REMARK 3 ANGLE : 1.146 1840 REMARK 3 CHIRALITY : 0.058 198 REMARK 3 PLANARITY : 0.006 239 REMARK 3 DIHEDRAL : 3.555 842 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 6KOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 193.15 REMARK 200 PH : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54187 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.602 REMARK 200 RESOLUTION RANGE LOW (A) : 25.908 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13600 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.04900 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: CRANK2 REMARK 200 STARTING MODEL: 2DGU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NAOH (PH 7.5), 20% PEG REMARK 280 10,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.81700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.91656 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.42967 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 51.81700 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 29.91656 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.42967 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 51.81700 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 29.91656 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.42967 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.83312 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 32.85933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 59.83312 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 32.85933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 59.83312 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 32.85933 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 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 ALA A 5 REMARK 465 PRO A 96 REMARK 465 GLU A 97 REMARK 465 VAL A 98 REMARK 465 GLN A 176 REMARK 465 LYS A 177 REMARK 465 ARG A 178 REMARK 465 LYS A 179 REMARK 465 GLU A 180 REMARK 465 ARG A 181 REMARK 465 LYS A 182 REMARK 465 ALA A 183 REMARK 465 GLN A 184 REMARK 465 ARG A 185 REMARK 465 GLN A 186 REMARK 465 ALA A 187 REMARK 465 ALA A 188 REMARK 465 LYS A 189 REMARK 465 ASN A 190 REMARK 465 GLN A 191 REMARK 465 MET A 192 REMARK 465 TYR A 193 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 62 CD - CE - NZ ANGL. DEV. = -18.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 43 106.87 -54.92 REMARK 500 TRP A 79 50.78 27.83 REMARK 500 PRO A 94 -97.11 -59.51 REMARK 500 ASN A 109 49.94 72.35 REMARK 500 LEU A 135 -150.70 -106.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KOR A 7 193 UNP O60506 HNRPQ_HUMAN 242 428 SEQADV 6KOR GLY A 1 UNP O60506 EXPRESSION TAG SEQADV 6KOR SER A 2 UNP O60506 EXPRESSION TAG SEQADV 6KOR HIS A 3 UNP O60506 EXPRESSION TAG SEQADV 6KOR MET A 4 UNP O60506 EXPRESSION TAG SEQADV 6KOR ALA A 5 UNP O60506 EXPRESSION TAG SEQADV 6KOR SER A 6 UNP O60506 EXPRESSION TAG SEQRES 1 A 193 GLY SER HIS MET ALA SER ASN ASN ARG LEU PHE VAL GLY SEQRES 2 A 193 SER ILE PRO LYS SER LYS THR LYS GLU GLN ILE LEU GLU SEQRES 3 A 193 GLU PHE SER LYS VAL THR GLU GLY LEU THR ASP VAL ILE SEQRES 4 A 193 LEU TYR HIS GLN PRO ASP ASP LYS LYS LYS ASN ARG GLY SEQRES 5 A 193 PHE CYS PHE LEU GLU TYR GLU ASP HIS LYS THR ALA ALA SEQRES 6 A 193 GLN ALA ARG ARG ARG LEU MET SER GLY LYS VAL LYS VAL SEQRES 7 A 193 TRP GLY ASN VAL GLY THR VAL GLU TRP ALA ASP PRO ILE SEQRES 8 A 193 GLU ASP PRO ASP PRO GLU VAL MET ALA LYS VAL LYS VAL SEQRES 9 A 193 LEU PHE VAL ARG ASN LEU ALA ASN THR VAL THR GLU GLU SEQRES 10 A 193 ILE LEU GLU LYS ALA PHE SER GLN PHE GLY LYS LEU GLU SEQRES 11 A 193 ARG VAL LYS LYS LEU LYS ASP TYR ALA PHE ILE HIS PHE SEQRES 12 A 193 ASP GLU ARG ASP GLY ALA VAL LYS ALA MET GLU GLU MET SEQRES 13 A 193 ASN GLY LYS ASP LEU GLU GLY GLU ASN ILE GLU ILE VAL SEQRES 14 A 193 PHE ALA LYS PRO PRO ASP GLN LYS ARG LYS GLU ARG LYS SEQRES 15 A 193 ALA GLN ARG GLN ALA ALA LYS ASN GLN MET TYR FORMUL 2 HOH *46(H2 O) HELIX 1 AA1 THR A 20 THR A 32 1 13 HELIX 2 AA2 ASP A 60 SER A 73 1 14 HELIX 3 AA3 VAL A 78 VAL A 82 5 5 HELIX 4 AA4 THR A 115 GLN A 125 1 11 HELIX 5 AA5 GLU A 145 ASN A 157 1 13 SHEET 1 AA1 4 LEU A 35 ILE A 39 0 SHEET 2 AA1 4 CYS A 54 TYR A 58 -1 O GLU A 57 N THR A 36 SHEET 3 AA1 4 ARG A 9 VAL A 12 -1 N LEU A 10 O LEU A 56 SHEET 4 AA1 4 VAL A 85 TRP A 87 -1 O GLU A 86 N PHE A 11 SHEET 1 AA2 4 LEU A 129 LYS A 134 0 SHEET 2 AA2 4 TYR A 138 PHE A 143 -1 O HIS A 142 N GLU A 130 SHEET 3 AA2 4 VAL A 104 ARG A 108 -1 N VAL A 107 O ALA A 139 SHEET 4 AA2 4 GLU A 167 PHE A 170 -1 O VAL A 169 N PHE A 106 SHEET 1 AA3 2 ASP A 160 LEU A 161 0 SHEET 2 AA3 2 GLU A 164 ASN A 165 -1 O GLU A 164 N LEU A 161 CRYST1 103.634 103.634 49.289 90.00 90.00 120.00 H 3 9 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 0.009649 0.005571 0.000000 0.00000 SCALE2 0.000000 0.011142 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020289 0.00000