HEADER STRUCTURAL PROTEIN 09-SEP-22 8GTX TITLE CRYSTAL STRUCTURE OF HUMAN SPINDLIN1-HBX COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPINDLIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OVARIAN CANCER-RELATED PROTEIN,SPINDLIN1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HBX; COMPND 8 CHAIN: B; COMPND 9 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: SPIN1, OCR, SPIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS TUDOR DOMAIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.LI,W.LIU REVDAT 1 13-SEP-23 8GTX 0 JRNL AUTH W.LIU,H.T.LI JRNL TITL CRYSTAL STRUCTURE OF HUMAN SPINDLIN1-HBX COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 28688 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 : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1396 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 46.8500 - 3.8700 0.99 2904 154 0.1539 0.1744 REMARK 3 2 3.8700 - 3.0700 1.00 2774 148 0.1515 0.1793 REMARK 3 3 3.0700 - 2.6800 1.00 2748 125 0.1702 0.2044 REMARK 3 4 2.6800 - 2.4400 1.00 2740 152 0.1702 0.2192 REMARK 3 5 2.4400 - 2.2600 1.00 2717 145 0.1718 0.2189 REMARK 3 6 2.2600 - 2.1300 1.00 2712 136 0.1544 0.1747 REMARK 3 7 2.1300 - 2.0200 1.00 2711 135 0.1585 0.1756 REMARK 3 8 2.0200 - 1.9300 1.00 2713 126 0.1722 0.2274 REMARK 3 9 1.9300 - 1.8600 1.00 2674 135 0.1854 0.2565 REMARK 3 10 1.8600 - 1.8000 0.96 2599 140 0.2067 0.2606 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.84 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8GTX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300032081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.57700 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: MOLREP REMARK 200 STARTING MODEL: 4MZG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16%(W/V) PEG 8000, 0.04M POTASSIUM REMARK 280 PHOSPHATE DIBASIC, 20% (V/V) GLYCEROL, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 23.89400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.84750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.54800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.84750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.89400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.54800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 ASP A 195 REMARK 465 SER A 196 REMARK 465 ASN A 197 REMARK 465 ASP A 198 REMARK 465 SER A 199 REMARK 465 PRO A 200 REMARK 465 PRO A 201 REMARK 465 ALA A 202 REMARK 465 GLU A 203 REMARK 465 ARG A 204 REMARK 465 GLU A 205 REMARK 465 PRO A 206 REMARK 465 GLY A 207 REMARK 465 GLU A 208 REMARK 465 VAL A 209 REMARK 465 VAL A 210 REMARK 465 ASP A 211 REMARK 465 SER A 262 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 SER A 49 -121.49 58.65 REMARK 500 ASN A 83 86.42 -151.37 REMARK 500 ASP A 116 87.53 -151.13 REMARK 500 THR A 143 -160.82 -127.66 REMARK 500 VAL A 161 -62.34 68.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GTX A 50 262 UNP Q9Y657 SPIN1_HUMAN 50 262 DBREF 8GTX B 1 20 PDB 8GTX 8GTX 1 20 SEQADV 8GTX GLY A 45 UNP Q9Y657 EXPRESSION TAG SEQADV 8GTX PRO A 46 UNP Q9Y657 EXPRESSION TAG SEQADV 8GTX LEU A 47 UNP Q9Y657 EXPRESSION TAG SEQADV 8GTX GLY A 48 UNP Q9Y657 EXPRESSION TAG SEQADV 8GTX SER A 49 UNP Q9Y657 EXPRESSION TAG SEQRES 1 A 218 GLY PRO LEU GLY SER ARG ARG ASN ILE VAL GLY CYS ARG SEQRES 2 A 218 ILE GLN HIS GLY TRP LYS GLU GLY ASN GLY PRO VAL THR SEQRES 3 A 218 GLN TRP LYS GLY THR VAL LEU ASP GLN VAL PRO VAL ASN SEQRES 4 A 218 PRO SER LEU TYR LEU ILE LYS TYR ASP GLY PHE ASP CYS SEQRES 5 A 218 VAL TYR GLY LEU GLU LEU ASN LYS ASP GLU ARG VAL SER SEQRES 6 A 218 ALA LEU GLU VAL LEU PRO ASP ARG VAL ALA THR SER ARG SEQRES 7 A 218 ILE SER ASP ALA HIS LEU ALA ASP THR MET ILE GLY LYS SEQRES 8 A 218 ALA VAL GLU HIS MET PHE GLU THR GLU ASP GLY SER LYS SEQRES 9 A 218 ASP GLU TRP ARG GLY MET VAL LEU ALA ARG ALA PRO VAL SEQRES 10 A 218 MET ASN THR TRP PHE TYR ILE THR TYR GLU LYS ASP PRO SEQRES 11 A 218 VAL LEU TYR MET TYR GLN LEU LEU ASP ASP TYR LYS GLU SEQRES 12 A 218 GLY ASP LEU ARG ILE MET PRO ASP SER ASN ASP SER PRO SEQRES 13 A 218 PRO ALA GLU ARG GLU PRO GLY GLU VAL VAL ASP SER LEU SEQRES 14 A 218 VAL GLY LYS GLN VAL GLU TYR ALA LYS GLU ASP GLY SER SEQRES 15 A 218 LYS ARG THR GLY MET VAL ILE HIS GLN VAL GLU ALA LYS SEQRES 16 A 218 PRO SER VAL TYR PHE ILE LYS PHE ASP ASP ASP PHE HIS SEQRES 17 A 218 ILE TYR VAL TYR ASP LEU VAL LYS THR SER SEQRES 1 B 20 ALA ALA ARG MET CYS CYS LYS LEU ASP PRO ALA ARG ASP SEQRES 2 B 20 VAL LEU CYS LEU ARG PRO ILE HET GOL A 301 6 HET GOL A 302 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *302(H2 O) HELIX 1 AA1 GLY A 48 ASN A 52 5 5 HELIX 2 AA2 ASP A 125 ILE A 133 1 9 HELIX 3 AA3 GLN A 180 GLU A 187 1 8 SHEET 1 AA1 5 TYR A 98 LEU A 100 0 SHEET 2 AA1 5 ASN A 83 TYR A 91 -1 N ILE A 89 O TYR A 98 SHEET 3 AA1 5 THR A 70 VAL A 80 -1 N LEU A 77 O LEU A 88 SHEET 4 AA1 5 CYS A 56 TRP A 62 -1 N HIS A 60 O TRP A 72 SHEET 5 AA1 5 VAL A 108 ARG A 117 -1 O GLU A 112 N GLN A 59 SHEET 1 AA2 5 TYR A 177 TYR A 179 0 SHEET 2 AA2 5 PHE A 166 TYR A 170 -1 N ILE A 168 O TYR A 177 SHEET 3 AA2 5 LYS A 148 ARG A 158 -1 N LEU A 156 O TYR A 167 SHEET 4 AA2 5 ALA A 136 GLU A 142 -1 N PHE A 141 O ASP A 149 SHEET 5 AA2 5 LEU A 190 ILE A 192 -1 O ARG A 191 N GLU A 138 SHEET 1 AA3 7 GLN A 217 ALA A 221 0 SHEET 2 AA3 7 LYS A 227 GLN A 235 -1 O GLY A 230 N VAL A 218 SHEET 3 AA3 7 VAL A 242 PHE A 247 -1 O LYS A 246 N MET A 231 SHEET 4 AA3 7 TYR A 254 LYS A 260 -1 O TYR A 254 N ILE A 245 SHEET 5 AA3 7 ARG B 3 ASP B 9 1 O MET B 4 N VAL A 259 SHEET 6 AA3 7 VAL B 14 ARG B 18 -1 O VAL B 14 N ASP B 9 SHEET 7 AA3 7 GLN A 217 ALA A 221 1 N GLU A 219 O LEU B 17 CRYST1 47.788 67.096 93.695 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 0.020926 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010673 0.00000