HEADER RNA BINDING PROTEIN 03-MAY-18 6DBP TITLE RNA-RECOGNITION MOTIF 1 OF HUMAN MSI2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN MUSASHI HOMOLOG 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MUSASHI-2; COMPND 5 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: MSI2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: DE3 KEYWDS MUSASHI2 RNA RECOGNITION MOTIF, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.GOLDGUR,M.G.KHARAS,G.MINUESA REVDAT 4 04-OCT-23 6DBP 1 REMARK REVDAT 3 04-DEC-19 6DBP 1 REMARK REVDAT 2 03-JUL-19 6DBP 1 JRNL REVDAT 1 08-MAY-19 6DBP 0 JRNL AUTH G.MINUESA,S.K.ALBANESE,W.XIE,Y.KAZANSKY,D.WORROLL,A.CHOW, JRNL AUTH 2 A.SCHURER,S.M.PARK,C.Z.ROTSIDES,J.TAGGART,A.RIZZI,L.N.NADEN, JRNL AUTH 3 T.CHOU,S.GOURKANTI,D.CAPPEL,M.C.PASSARELLI,L.FAIRCHILD, JRNL AUTH 4 C.ADURA,J.F.GLICKMAN,J.SCHULMAN,C.FAMULARE,M.PATEL,J.K.EIBL, JRNL AUTH 5 G.M.ROSS,S.BHATTACHARYA,D.S.TAN,C.S.LESLIE,T.BEUMING, JRNL AUTH 6 D.J.PATEL,Y.GOLDGUR,J.D.CHODERA,M.G.KHARAS JRNL TITL SMALL-MOLECULE TARGETING OF MUSASHI RNA-BINDING ACTIVITY IN JRNL TITL 2 ACUTE MYELOID LEUKEMIA. JRNL REF NAT COMMUN V. 10 2691 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31217428 JRNL DOI 10.1038/S41467-019-10523-3 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 16762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1665 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 28.6920 - 3.6680 0.98 1386 148 0.1640 0.1816 REMARK 3 2 3.6680 - 2.9123 0.98 1359 151 0.1747 0.1956 REMARK 3 3 2.9123 - 2.5444 0.99 1334 157 0.1875 0.2316 REMARK 3 4 2.5444 - 2.3119 0.98 1379 139 0.1805 0.2411 REMARK 3 5 2.3119 - 2.1462 0.99 1347 151 0.1643 0.2174 REMARK 3 6 2.1462 - 2.0197 0.98 1329 162 0.1681 0.1988 REMARK 3 7 2.0197 - 1.9186 0.98 1362 144 0.1726 0.2093 REMARK 3 8 1.9186 - 1.8351 0.99 1367 147 0.1793 0.2330 REMARK 3 9 1.8351 - 1.7645 0.96 1303 147 0.1849 0.2169 REMARK 3 10 1.7645 - 1.7036 0.85 1168 123 0.1880 0.2342 REMARK 3 11 1.7036 - 1.6503 0.70 967 105 0.1888 0.2932 REMARK 3 12 1.6503 - 1.6032 0.59 796 91 0.1914 0.2357 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.100 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) : 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 : 0.007 1363 REMARK 3 ANGLE : 0.863 1831 REMARK 3 CHIRALITY : 0.060 188 REMARK 3 PLANARITY : 0.007 239 REMARK 3 DIHEDRAL : 3.342 831 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 6DBP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16779 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1UAW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL, 150 MM NACL, 1 MM REMARK 280 EDTA, 1MM DTT, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.20650 REMARK 290 SMTRY3 2 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: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 PRO B 83 REMARK 465 LYS B 84 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 161 O HOH B 163 1.94 REMARK 500 N MET A 1 O HOH A 101 2.01 REMARK 500 O HOH A 128 O HOH A 163 2.06 REMARK 500 NH1 ARG A 42 O HOH A 102 2.13 REMARK 500 O HOH A 159 O HOH B 159 2.14 REMARK 500 NH2 ARG B 79 O HOH B 101 2.15 REMARK 500 OD1 ASP B 15 O HOH B 102 2.18 REMARK 500 O HOH B 126 O HOH B 136 2.18 REMARK 500 O MET A 1 O HOH A 103 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 168 O HOH B 165 2645 1.98 REMARK 500 O HOH B 124 O HOH B 162 1455 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 6DBP A 2 84 UNP Q96DH6 MSI2H_HUMAN 22 104 DBREF 6DBP B 2 84 UNP Q96DH6 MSI2H_HUMAN 22 104 SEQADV 6DBP MET A 1 UNP Q96DH6 INITIATING METHIONINE SEQADV 6DBP MET B 1 UNP Q96DH6 INITIATING METHIONINE SEQRES 1 A 84 MET LYS MET PHE ILE GLY GLY LEU SER TRP GLN THR SER SEQRES 2 A 84 PRO ASP SER LEU ARG ASP TYR PHE SER LYS PHE GLY GLU SEQRES 3 A 84 ILE ARG GLU CYS MET VAL MET ARG ASP PRO THR THR LYS SEQRES 4 A 84 ARG SER ARG GLY PHE GLY PHE VAL THR PHE ALA ASP PRO SEQRES 5 A 84 ALA SER VAL ASP LYS VAL LEU GLY GLN PRO HIS HIS GLU SEQRES 6 A 84 LEU ASP SER LYS THR ILE ASP PRO LYS VAL ALA PHE PRO SEQRES 7 A 84 ARG ARG ALA GLN PRO LYS SEQRES 1 B 84 MET LYS MET PHE ILE GLY GLY LEU SER TRP GLN THR SER SEQRES 2 B 84 PRO ASP SER LEU ARG ASP TYR PHE SER LYS PHE GLY GLU SEQRES 3 B 84 ILE ARG GLU CYS MET VAL MET ARG ASP PRO THR THR LYS SEQRES 4 B 84 ARG SER ARG GLY PHE GLY PHE VAL THR PHE ALA ASP PRO SEQRES 5 B 84 ALA SER VAL ASP LYS VAL LEU GLY GLN PRO HIS HIS GLU SEQRES 6 B 84 LEU ASP SER LYS THR ILE ASP PRO LYS VAL ALA PHE PRO SEQRES 7 B 84 ARG ARG ALA GLN PRO LYS FORMUL 3 HOH *140(H2 O) HELIX 1 AA1 SER A 13 SER A 22 1 10 HELIX 2 AA2 LYS A 23 GLY A 25 5 3 HELIX 3 AA3 ASP A 51 GLN A 61 1 11 HELIX 4 AA4 SER B 13 SER B 22 1 10 HELIX 5 AA5 LYS B 23 GLY B 25 5 3 HELIX 6 AA6 ASP B 51 GLN B 61 1 11 SHEET 1 AA1 5 LYS A 74 ALA A 76 0 SHEET 2 AA1 5 LYS A 2 SER A 9 -1 N PHE A 4 O LYS A 74 SHEET 3 AA1 5 ARG A 42 PHE A 49 -1 O GLY A 45 N ILE A 5 SHEET 4 AA1 5 ILE A 27 ARG A 34 -1 N GLU A 29 O THR A 48 SHEET 5 AA1 5 ARG B 79 ARG B 80 -1 O ARG B 79 N VAL A 32 SHEET 1 AA2 2 HIS A 64 LEU A 66 0 SHEET 2 AA2 2 LYS A 69 ILE A 71 -1 O LYS A 69 N LEU A 66 SHEET 1 AA3 5 ARG A 79 ARG A 80 0 SHEET 2 AA3 5 ILE B 27 ARG B 34 -1 O VAL B 32 N ARG A 79 SHEET 3 AA3 5 ARG B 42 PHE B 49 -1 O THR B 48 N GLU B 29 SHEET 4 AA3 5 LYS B 2 SER B 9 -1 N MET B 3 O VAL B 47 SHEET 5 AA3 5 LYS B 74 ALA B 76 -1 O ALA B 76 N LYS B 2 SHEET 1 AA4 2 GLU B 65 LEU B 66 0 SHEET 2 AA4 2 LYS B 69 THR B 70 -1 O LYS B 69 N LEU B 66 CRYST1 30.317 64.413 38.387 90.00 108.87 90.00 P 1 21 1 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 0.032985 0.000000 0.011275 0.00000 SCALE2 0.000000 0.015525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027530 0.00000