HEADER RAN-BINDING PROTEIN 22-APR-16 5JI7 TITLE THE CRYSTAL STRUCTURE OF IUS-SPRY DOMAIN FROM RANBPM/9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAN-BINDING PROTEIN 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IUS-SPRY DOMAIN, UNP RESIDUES 108-350; COMPND 5 SYNONYM: RANBP9,BPM-L,BPM90,RAN-BINDING PROTEIN M,RANBPM,RANBP7; COMPND 6 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: RANBP9, RANBPM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BETA SANDWICH, RAN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.K.HONG,K.-H.KIM,E.E.KIM REVDAT 2 20-MAR-24 5JI7 1 JRNL REMARK REVDAT 1 09-NOV-16 5JI7 0 JRNL AUTH S.K.HONG,K.H.KIM,E.J.SONG,E.E.KIM JRNL TITL STRUCTURAL BASIS FOR THE INTERACTION BETWEEN THE IUS-SPRY JRNL TITL 2 DOMAIN OF RANBPM AND DDX-4 IN GERM CELL DEVELOPMENT. JRNL REF J.MOL.BIOL. V. 428 4330 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27622290 JRNL DOI 10.1016/J.JMB.2016.09.004 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.710 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 36.4286 - 3.6459 0.99 2118 153 0.1725 0.1958 REMARK 3 2 3.6459 - 2.8943 1.00 2044 146 0.1706 0.1914 REMARK 3 3 2.8943 - 2.5285 1.00 2004 145 0.1757 0.1880 REMARK 3 4 2.5285 - 2.2974 1.00 2006 144 0.1659 0.2118 REMARK 3 5 2.2974 - 2.1327 1.00 1993 143 0.1625 0.1733 REMARK 3 6 2.1327 - 2.0070 1.00 1971 142 0.1587 0.2041 REMARK 3 7 2.0070 - 1.9065 1.00 1986 143 0.1548 0.1935 REMARK 3 8 1.9065 - 1.8235 1.00 1982 143 0.1442 0.1705 REMARK 3 9 1.8235 - 1.7533 1.00 1965 141 0.1419 0.1792 REMARK 3 10 1.7533 - 1.6928 1.00 1953 141 0.1464 0.1755 REMARK 3 11 1.6928 - 1.6399 1.00 1950 140 0.1485 0.1788 REMARK 3 12 1.6399 - 1.5930 1.00 1971 141 0.1589 0.1886 REMARK 3 13 1.5930 - 1.5511 1.00 1954 141 0.1597 0.1926 REMARK 3 14 1.5511 - 1.5132 0.99 1904 137 0.1769 0.2037 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 35.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.970 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) : 0.57740 REMARK 3 B22 (A**2) : -0.07850 REMARK 3 B33 (A**2) : -0.49900 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 : 0.007 1608 REMARK 3 ANGLE : 1.251 2186 REMARK 3 CHIRALITY : 0.089 222 REMARK 3 PLANARITY : 0.005 289 REMARK 3 DIHEDRAL : 13.875 581 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 5JI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220647. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-09; 10-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PAL/PLS; PAL/PLS REMARK 200 BEAMLINE : 5C (4A); 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000; 0.97928, 0.97951, REMARK 200 0.97160 REMARK 200 MONOCHROMATOR : MIRRORS; MIRRORS REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 44.8250 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.15400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.68 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-CACODYLATE, PH 6.5, 6% PEG REMARK 280 4000, 0.2M KCL, 0.02M MGCL2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 21.34850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.88300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.33300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.88300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.34850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.33300 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 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 LEU A 108 REMARK 465 ALA A 109 REMARK 465 ALA A 110 REMARK 465 GLY A 111 REMARK 465 PRO A 112 REMARK 465 GLY A 113 REMARK 465 PRO A 114 REMARK 465 ALA A 115 REMARK 465 GLY A 116 REMARK 465 GLY A 117 REMARK 465 ALA A 118 REMARK 465 PRO A 119 REMARK 465 THR A 120 REMARK 465 PRO A 121 REMARK 465 ALA A 122 REMARK 465 LEU A 123 REMARK 465 VAL A 124 REMARK 465 ALA A 125 REMARK 465 GLY A 126 REMARK 465 SER A 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 131 REMARK 465 PRO A 132 REMARK 465 PHE A 133 REMARK 465 PRO A 134 REMARK 465 HIS A 135 REMARK 465 GLY A 136 REMARK 465 ASP A 137 REMARK 465 SER A 138 REMARK 465 ALA A 139 REMARK 465 LEU A 140 REMARK 465 ASN A 141 REMARK 465 GLU A 142 REMARK 465 GLN A 143 REMARK 465 GLU A 144 REMARK 465 LYS A 145 REMARK 465 GLU A 146 REMARK 465 ARG A 346 REMARK 465 THR A 347 REMARK 465 LYS A 348 REMARK 465 ILE A 349 REMARK 465 GLN A 350 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 TYR A 271 -64.90 -143.80 REMARK 500 GLN A 319 -23.22 -145.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JI9 RELATED DB: PDB REMARK 900 RELATED ID: 5JIA RELATED DB: PDB REMARK 900 RELATED ID: 5JIU RELATED DB: PDB DBREF 5JI7 A 108 350 UNP Q96S59 RANB9_HUMAN 108 350 SEQRES 1 A 243 LEU ALA ALA GLY PRO GLY PRO ALA GLY GLY ALA PRO THR SEQRES 2 A 243 PRO ALA LEU VAL ALA GLY SER SER ALA ALA ALA PRO PHE SEQRES 3 A 243 PRO HIS GLY ASP SER ALA LEU ASN GLU GLN GLU LYS GLU SEQRES 4 A 243 LEU GLN ARG ARG LEU LYS ARG LEU TYR PRO ALA VAL ASP SEQRES 5 A 243 GLU GLN GLU THR PRO LEU PRO ARG SER TRP SER PRO LYS SEQRES 6 A 243 ASP LYS PHE SER TYR ILE GLY LEU SER GLN ASN ASN LEU SEQRES 7 A 243 ARG VAL HIS TYR LYS GLY HIS GLY LYS THR PRO LYS ASP SEQRES 8 A 243 ALA ALA SER VAL ARG ALA THR HIS PRO ILE PRO ALA ALA SEQRES 9 A 243 CYS GLY ILE TYR TYR PHE GLU VAL LYS ILE VAL SER LYS SEQRES 10 A 243 GLY ARG ASP GLY TYR MET GLY ILE GLY LEU SER ALA GLN SEQRES 11 A 243 GLY VAL ASN MET ASN ARG LEU PRO GLY TRP ASP LYS HIS SEQRES 12 A 243 SER TYR GLY TYR HIS GLY ASP ASP GLY HIS SER PHE CYS SEQRES 13 A 243 SER SER GLY THR GLY GLN PRO TYR GLY PRO THR PHE THR SEQRES 14 A 243 THR GLY ASP VAL ILE GLY CYS CYS VAL ASN LEU ILE ASN SEQRES 15 A 243 ASN THR CYS PHE TYR THR LYS ASN GLY HIS SER LEU GLY SEQRES 16 A 243 ILE ALA PHE THR ASP LEU PRO PRO ASN LEU TYR PRO THR SEQRES 17 A 243 VAL GLY LEU GLN THR PRO GLY GLU VAL VAL ASP ALA ASN SEQRES 18 A 243 PHE GLY GLN HIS PRO PHE VAL PHE ASP ILE GLU ASP TYR SEQRES 19 A 243 MET ARG GLU TRP ARG THR LYS ILE GLN FORMUL 2 HOH *221(H2 O) HELIX 1 AA1 ARG A 149 TYR A 155 1 7 HELIX 2 AA2 THR A 195 ALA A 199 5 5 HELIX 3 AA3 PRO A 209 CYS A 212 5 4 HELIX 4 AA4 ASP A 337 GLU A 344 1 8 SHEET 1 AA1 7 TRP A 169 LYS A 174 0 SHEET 2 AA1 7 ALA A 200 ALA A 204 -1 O ARG A 203 N SER A 170 SHEET 3 AA1 7 TYR A 313 LEU A 318 -1 O LEU A 318 N ALA A 200 SHEET 4 AA1 7 GLY A 231 SER A 235 -1 N SER A 235 O TYR A 313 SHEET 5 AA1 7 SER A 251 HIS A 255 -1 O TYR A 252 N LEU A 234 SHEET 6 AA1 7 HIS A 260 CYS A 263 -1 O PHE A 262 N GLY A 253 SHEET 7 AA1 7 GLN A 269 PRO A 270 -1 O GLN A 269 N SER A 261 SHEET 1 AA2 7 ILE A 178 SER A 181 0 SHEET 2 AA2 7 ARG A 186 TYR A 189 -1 O HIS A 188 N GLY A 179 SHEET 3 AA2 7 GLU A 323 ASN A 328 -1 O VAL A 325 N VAL A 187 SHEET 4 AA2 7 ILE A 214 LYS A 224 -1 N GLU A 218 O ASN A 328 SHEET 5 AA2 7 VAL A 280 ASN A 286 -1 O ILE A 281 N VAL A 219 SHEET 6 AA2 7 THR A 291 LYS A 296 -1 O PHE A 293 N CYS A 284 SHEET 7 AA2 7 HIS A 299 PHE A 305 -1 O LEU A 301 N TYR A 294 CRYST1 42.697 62.666 69.766 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 0.023421 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014334 0.00000