HEADER PROTEIN BINDING 05-JAN-18 5Z39 TITLE CRYSTAL STRUCTURE OF C TERMINAL REGION OF G-PROTEIN INTERACTING TITLE 2 PROTEIN 1 (GIP1) FROM DICTYOSTELIUM DISCOIDEUM FORM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-PROTEIN INTERACTING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN, UNP RESIDUES 146-310; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 44689; SOURCE 5 GENE: DDB0216772; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SUMOSTAR KEYWDS ALPHA HELIX, LIPID BINDING, G-PROTEIN BINDING, SOCIAL AMOEBAE, KEYWDS 2 CHEMOTAXIS, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.MIYAGAWA,H.KOTEISHI,Y.KAMIMURA,Y.MIYANAGA,K.TAKESHITA,A.NAKAGAWA, AUTHOR 2 M.UEDA REVDAT 3 22-NOV-23 5Z39 1 REMARK REVDAT 2 28-NOV-18 5Z39 1 JRNL REVDAT 1 17-OCT-18 5Z39 0 JRNL AUTH T.MIYAGAWA,H.KOTEISHI,Y.KAMIMURA,Y.MIYANAGA,K.TAKESHITA, JRNL AUTH 2 A.NAKAGAWA,M.UEDA JRNL TITL STRUCTURAL BASIS OF GIP1 FOR CYTOSOLIC SEQUESTRATION OF G JRNL TITL 2 PROTEIN IN WIDE-RANGE CHEMOTAXIS JRNL REF NAT COMMUN V. 9 4635 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30401901 JRNL DOI 10.1038/S41467-018-07035-X REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4242 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 425 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 40.0898 - 3.9510 1.00 1324 149 0.2011 0.2371 REMARK 3 2 3.9510 - 3.1364 1.00 1260 139 0.2400 0.3132 REMARK 3 3 3.1364 - 2.7400 1.00 1233 137 0.2487 0.2953 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.28 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 : 0.002 1430 REMARK 3 ANGLE : 0.454 1913 REMARK 3 CHIRALITY : 0.036 218 REMARK 3 PLANARITY : 0.003 234 REMARK 3 DIHEDRAL : 10.163 1231 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 5Z39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006322. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0-9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.700 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4277 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740 REMARK 200 RESOLUTION RANGE LOW (A) : 43.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 0.61100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 5Z1N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-20% PEG 20000, 100 MM BICINE,, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 16.73400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.84050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.80900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.84050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.73400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.80900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 143 REMARK 465 TYR A 310 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 145 CG CD1 CD2 REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 ARG A 169 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LYS A 229 CG CD CE NZ 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 171 -108.75 -99.98 REMARK 500 GLU A 288 49.22 -96.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 LHG A 402 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEF A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LHG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 DBREF 5Z39 A 146 310 UNP Q55BQ2 Q55BQ2_DICDI 146 310 SEQADV 5Z39 GLY A 143 UNP Q55BQ2 EXPRESSION TAG SEQADV 5Z39 PRO A 144 UNP Q55BQ2 EXPRESSION TAG SEQADV 5Z39 LEU A 145 UNP Q55BQ2 EXPRESSION TAG SEQRES 1 A 168 GLY PRO LEU SER GLY LEU LYS LYS LEU ILE PRO GLU GLU SEQRES 2 A 168 GLY ARG GLU LEU ILE GLY SER VAL LYS LYS ILE ILE LYS SEQRES 3 A 168 ARG VAL SER ASN GLU GLU LYS ALA ASN GLU MET GLU LYS SEQRES 4 A 168 ASN ILE LEU LYS ILE LEU ILE LYS VAL PHE PHE TYR ILE SEQRES 5 A 168 ASP SER LYS ALA ILE GLN ILE GLY ASP LEU ALA LYS VAL SEQRES 6 A 168 ASP ARG ALA LEU ARG ASP GLY PHE ASN HIS LEU ASP ARG SEQRES 7 A 168 ALA PHE ARG TYR TYR GLY VAL LYS LYS ALA ALA ASP LEU SEQRES 8 A 168 VAL VAL ILE LEU GLU LYS ALA SER THR ALA LEU LYS GLU SEQRES 9 A 168 ALA GLU GLN GLU THR VAL THR LEU LEU THR PRO PHE PHE SEQRES 10 A 168 ARG PRO HIS ASN ILE GLN LEU ILE ARG ASN THR PHE ALA SEQRES 11 A 168 PHE LEU GLY SER LEU ASP PHE PHE THR LYS VAL TRP ASP SEQRES 12 A 168 ASP LEU GLU ILE GLU ASP ASP LEU PHE LEU LEU ILE SER SEQRES 13 A 168 ALA LEU ASN LYS TYR THR GLN ILE GLU LEU ILE TYR HET PEF A 401 47 HET LHG A 402 5 HET NA A 403 1 HETNAM PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE HETNAM LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE HETNAM NA SODIUM ION HETSYN PEF 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL FORMUL 2 PEF C37 H74 N O8 P FORMUL 3 LHG C38 H75 O10 P FORMUL 4 NA NA 1+ FORMUL 5 HOH *7(H2 O) HELIX 1 AA1 LEU A 145 LEU A 151 1 7 HELIX 2 AA2 PRO A 153 SER A 171 1 19 HELIX 3 AA3 ASN A 172 SER A 196 1 25 HELIX 4 AA4 GLN A 200 ASP A 203 5 4 HELIX 5 AA5 LEU A 204 TYR A 224 1 21 HELIX 6 AA6 LEU A 233 THR A 256 1 24 HELIX 7 AA7 ARG A 260 GLY A 275 1 16 HELIX 8 AA8 SER A 276 ASP A 286 1 11 HELIX 9 AA9 ILE A 289 THR A 304 1 16 LINK O GLU A 288 NA NA A 403 1555 1555 2.88 SITE 1 AC1 19 PRO A 153 GLU A 155 LEU A 159 VAL A 163 SITE 2 AC1 19 ILE A 186 LEU A 187 LYS A 189 PHE A 191 SITE 3 AC1 19 PHE A 215 ARG A 260 ASN A 263 PHE A 271 SITE 4 AC1 19 LEU A 274 PHE A 279 PHE A 280 LEU A 296 SITE 5 AC1 19 TYR A 303 LEU A 308 LHG A 402 SITE 1 AC2 2 LEU A 308 PEF A 401 SITE 1 AC3 4 GLU A 288 ILE A 289 ASP A 291 ASP A 292 CRYST1 33.468 43.618 101.681 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 0.029879 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009835 0.00000