HEADER PROTEIN BINDING 27-DEC-17 5Z1N TITLE CRYSTAL STRUCTURE OF C TERMINAL REGION OF G-PROTEIN INTERACTING TITLE 2 PROTEIN 1 (GIP1) FROM DICTYOSTELIUM DISCOIDEUM 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; 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: PE-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 5Z1N 1 REMARK REVDAT 2 21-NOV-18 5Z1N 1 JRNL REVDAT 1 17-OCT-18 5Z1N 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. 1.95 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 10864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 542 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 48.3333 - 3.0943 1.00 2721 138 0.1666 0.2090 REMARK 3 2 3.0943 - 2.4560 1.00 2600 133 0.1962 0.2394 REMARK 3 3 2.4560 - 2.1456 1.00 2545 145 0.1835 0.2367 REMARK 3 4 2.1456 - 1.9494 0.97 2456 126 0.2119 0.2733 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.91 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 : 0.003 1449 REMARK 3 ANGLE : 0.602 1941 REMARK 3 CHIRALITY : 0.040 220 REMARK 3 PLANARITY : 0.005 238 REMARK 3 DIHEDRAL : 10.539 1238 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 5Z1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-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) : 1.000 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.949 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35300 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: PHASER REMARK 200 STARTING MODEL: 3F4M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-20% PEG 20000, 100MM BICINE,, VAPOR REMARK 280 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 16.65900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.31850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.07150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.31850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.65900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.07150 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: 9480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 PRO A 144 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 -97.36 -131.07 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 203 O REMARK 620 2 HOH A 534 O 102.8 REMARK 620 N 1 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 5Z1N A 146 310 UNP Q55BQ2 Q55BQ2_DICDI 146 310 SEQADV 5Z1N GLY A 143 UNP Q55BQ2 EXPRESSION TAG SEQADV 5Z1N PRO A 144 UNP Q55BQ2 EXPRESSION TAG SEQADV 5Z1N 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 *110(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 TYR A 224 1 25 HELIX 5 AA5 LYS A 229 ASP A 232 5 4 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 LEU A 287 1 12 HELIX 9 AA9 GLU A 288 ASP A 291 5 4 HELIX 10 AB1 ASP A 292 ASN A 301 1 10 LINK O ASP A 203 NA NA A 403 1555 1555 2.37 LINK NA NA A 403 O HOH A 534 1555 1555 2.71 SITE 1 AC1 19 PRO A 153 GLU A 155 GLY A 156 LEU A 159 SITE 2 AC1 19 VAL A 163 LEU A 187 LYS A 189 PHE A 191 SITE 3 AC1 19 LEU A 211 PHE A 259 ARG A 260 ASN A 263 SITE 4 AC1 19 PHE A 271 TYR A 303 LEU A 308 ILE A 309 SITE 5 AC1 19 TYR A 310 LHG A 402 HOH A 537 SITE 1 AC2 7 LYS A 185 LYS A 189 LEU A 308 ILE A 309 SITE 2 AC2 7 TYR A 310 PEF A 401 HOH A 537 SITE 1 AC3 5 ASP A 203 LEU A 204 LYS A 206 VAL A 207 SITE 2 AC3 5 HOH A 534 CRYST1 33.318 44.143 96.637 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 0.030014 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022654 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010348 0.00000