HEADER SIGNALING PROTEIN/INHIBITOR 22-DEC-22 8HU2 TITLE RATTUS SYNTENIN-1 PDZ DOMAIN WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTENIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 SYNONYM: SYNDECAN-BINDING PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SDCBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS INHIBITOR, COMPLEX, SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.HEO,J.LEE,J.H.YUN,W.LEE REVDAT 1 17-JAN-24 8HU2 0 JRNL AUTH Y.HEO,J.LEE,J.H.YUN,W.LEE JRNL TITL CRYSTAL STRUCTURE OF STNPDZ WITH INHIBITOR AT 1.60 ANGSTROMS JRNL TITL 2 RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28703 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2018 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 47.0900 - 3.8500 0.99 2023 155 0.1987 0.2338 REMARK 3 2 3.8500 - 3.0600 1.00 1941 143 0.1881 0.2213 REMARK 3 3 3.0600 - 2.6700 1.00 1925 149 0.2063 0.2438 REMARK 3 4 2.6700 - 2.4300 1.00 1902 143 0.1999 0.2176 REMARK 3 5 2.4300 - 2.2500 1.00 1932 147 0.1984 0.2360 REMARK 3 6 2.2500 - 2.1200 1.00 1892 145 0.1908 0.2270 REMARK 3 7 2.1200 - 2.0100 1.00 1899 144 0.1789 0.2290 REMARK 3 8 2.0100 - 1.9300 1.00 1857 142 0.1852 0.2273 REMARK 3 9 1.9300 - 1.8500 1.00 1901 141 0.1956 0.2299 REMARK 3 10 1.8500 - 1.7900 1.00 1881 142 0.2055 0.2478 REMARK 3 11 1.7900 - 1.7300 1.00 1898 139 0.2121 0.2253 REMARK 3 12 1.7300 - 1.6800 1.00 1889 143 0.2298 0.2651 REMARK 3 13 1.6800 - 1.6400 1.00 1891 144 0.2681 0.2708 REMARK 3 14 1.6400 - 1.6000 0.99 1854 141 0.2910 0.3029 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) : 0.182 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.389 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.01 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 : 0.005 1271 REMARK 3 ANGLE : 0.772 1713 REMARK 3 CHIRALITY : 0.059 200 REMARK 3 PLANARITY : 0.004 218 REMARK 3 DIHEDRAL : 7.604 755 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 8HU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300034235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-22 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 : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 47.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.60 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.2000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.930 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: 5G1E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM PHOSPHATE MONOBASIC, 0.8 REMARK 280 M POTASSIUM PHOSPHATE DIBASIC, 0.1 M CAPS/SODIUM HYDROXIDE (PH REMARK 280 10.5), 0.2 M LITHIUM SULFATE, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 24.35733 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 48.71467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.71467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.35733 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 571 LIES ON A SPECIAL POSITION. 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 112 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 123 CG CD OE1 NE2 REMARK 480 LYS A 126 CD CE NZ REMARK 480 ARG A 130 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 178 CB CG CD CE NZ REMARK 480 PHE A 184 CG CD1 CD2 CE1 CE2 CZ REMARK 480 LYS A 219 CE NZ 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 A 509 O HOH A 515 2.17 REMARK 500 O HOH A 402 O HOH A 558 2.17 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 ARG A 195 77.77 9.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HU2 A 113 274 UNP Q9JI92 SDCB1_RAT 113 274 SEQADV 8HU2 GLY A 112 UNP Q9JI92 EXPRESSION TAG SEQRES 1 A 163 GLY GLY ILE ARG GLU VAL ILE LEU CYS LYS ASP GLN ASP SEQRES 2 A 163 GLY LYS ILE GLY LEU ARG LEU LYS SER VAL ASP ASN GLY SEQRES 3 A 163 ILE PHE VAL GLN LEU VAL GLN ALA ASN SER PRO ALA SER SEQRES 4 A 163 LEU VAL GLY LEU ARG PHE GLY ASP GLN VAL LEU GLN ILE SEQRES 5 A 163 ASN GLY GLU ASN CYS ALA GLY TRP SER SER ASP LYS ALA SEQRES 6 A 163 HIS LYS VAL LEU LYS GLN ALA PHE GLY GLU LYS ILE THR SEQRES 7 A 163 MET THR ILE ARG ASP ARG PRO PHE GLU ARG THR VAL THR SEQRES 8 A 163 MET HIS LYS ASP SER SER GLY HIS VAL GLY PHE ILE PHE SEQRES 9 A 163 LYS SER GLY LYS ILE THR SER ILE VAL LYS ASP SER SER SEQRES 10 A 163 ALA ALA ARG ASN GLY LEU LEU THR ASP HIS HIS ILE CYS SEQRES 11 A 163 GLU ILE ASN GLY GLN ASN VAL ILE GLY LEU LYS ASP ALA SEQRES 12 A 163 GLN ILE ALA ASP ILE LEU SER THR ALA GLY THR VAL VAL SEQRES 13 A 163 THR ILE THR ILE MET PRO ALA HET M8R A 301 30 HETNAM M8R (2~{S})-2-(9~{H}-FLUOREN-9-YLMETHOXYCARBONYLAMINO)-3- HETNAM 2 M8R (4-OXIDANYLIDENE-5~{H}-PYRIMIDIN-2-YL)PROPANOIC ACID FORMUL 2 M8R C22 H19 N3 O5 FORMUL 3 HOH *178(H2 O) HELIX 1 AA1 SER A 147 VAL A 152 1 6 HELIX 2 AA2 SER A 172 ALA A 183 1 12 HELIX 3 AA3 SER A 227 ASN A 232 1 6 HELIX 4 AA4 LYS A 252 ALA A 263 1 12 SHEET 1 AA1 4 ILE A 114 CYS A 120 0 SHEET 2 AA1 4 LYS A 187 ARG A 193 -1 O ILE A 192 N ARG A 115 SHEET 3 AA1 4 GLN A 159 ILE A 163 -1 N GLN A 159 O ARG A 193 SHEET 4 AA1 4 GLU A 166 ASN A 167 -1 O GLU A 166 N ILE A 163 SHEET 1 AA2 2 LEU A 129 VAL A 134 0 SHEET 2 AA2 2 GLY A 137 VAL A 143 -1 O GLN A 141 N ARG A 130 SHEET 1 AA3 5 ARG A 199 HIS A 204 0 SHEET 2 AA3 5 VAL A 266 PRO A 273 -1 O ILE A 271 N ARG A 199 SHEET 3 AA3 5 HIS A 238 ILE A 243 -1 N HIS A 239 O MET A 272 SHEET 4 AA3 5 LYS A 219 ILE A 223 -1 N ILE A 220 O HIS A 238 SHEET 5 AA3 5 PHE A 213 LYS A 216 -1 N ILE A 214 O THR A 221 SHEET 1 AA4 4 ARG A 199 HIS A 204 0 SHEET 2 AA4 4 VAL A 266 PRO A 273 -1 O ILE A 271 N ARG A 199 SHEET 3 AA4 4 HIS A 238 ILE A 243 -1 N HIS A 239 O MET A 272 SHEET 4 AA4 4 GLN A 246 ASN A 247 -1 O GLN A 246 N ILE A 243 CRYST1 71.098 71.098 73.072 90.00 90.00 120.00 P 31 2 1 6 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 0.014065 0.008120 0.000000 0.00000 SCALE2 0.000000 0.016241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013685 0.00000