HEADER PROTEIN BINDING 30-NOV-22 8HLO TITLE CRYSTAL STRUCTURE OF ASAP1-SH3 AND MICAL1-PRM COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARF-GAP WITH SH3 DOMAIN, ANK REPEAT AND PH DOMAIN- COMPND 3 CONTAINING PROTEIN 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SH3 DOMAIN; COMPND 6 SYNONYM: 130 KDA PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-DEPENDENT ARF1 COMPND 7 GTPASE-ACTIVATING PROTEIN,ADP-RIBOSYLATION FACTOR-DIRECTED GTPASE- COMPND 8 ACTIVATING PROTEIN 1,ARF GTPASE-ACTIVATING PROTEIN 1,DEVELOPMENT AND COMPND 9 DIFFERENTIATION-ENHANCING FACTOR 1,DEF-1,DIFFERENTIATION-ENHANCING COMPND 10 FACTOR 1,PIP2-DEPENDENT ARF1 GAP; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: PROLINE RICH MOTIF FROM MICAL1; COMPND 14 CHAIN: C; COMPND 15 SYNONYM: MOLECULE INTERACTING WITH CASL PROTEIN 1,MICAL-1,NEDD9- COMPND 16 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ASAP1, DDEF1, KIAA1249, SHAG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: MICAL1, MICAL, NICAL; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SH3, PROLINE-RICH MOTIF, HIGH-AFFINITY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR F.NIU,Z.WEI,C.YU REVDAT 1 22-FEB-23 8HLO 0 JRNL AUTH X.JIA,L.LIN,S.XU,L.LI,Z.WEI,C.YU,F.NIU JRNL TITL CRYSTAL STRUCTURE OF THE SH3 DOMAIN OF ASAP1 IN COMPLEX WITH JRNL TITL 2 THE PROLINE RICH MOTIF (PRM) OF MICAL1 REVEALS A UNIQUE JRNL TITL 3 SH3/PRM INTERACTION MODE. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 36674928 JRNL DOI 10.3390/IJMS24021414 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.JIA,L.LIN,S.XU,L.LI,Z.WEI,C.YU,F.NIU REMARK 1 TITL CRYSTAL STRUCTURE OF THE SH3 DOMAIN OF ASAP1 IN COMPLEX WITH REMARK 1 TITL 2 THE PROLINE RICH MOTIF (PRM) OF MICAL1 REVEALS A UNIQUE REMARK 1 TITL 3 SH3/PRM INTERACTION MODE. REMARK 1 REF INT J MOL SCI V. 24 2023 REMARK 1 REFN ESSN 1422-0067 REMARK 1 PMID 36674928 REMARK 1 DOI 10.1101/GR.1239303 REMARK 2 REMARK 2 RESOLUTION. 1.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.9 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 21440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.114 REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.142 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.280 REMARK 3 FREE R VALUE TEST SET COUNT : 1989 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 39.1280 - 2.8141 1.00 1550 154 0.1124 0.1463 REMARK 3 2 2.8141 - 2.2337 1.00 1514 163 0.1194 0.1314 REMARK 3 3 2.2337 - 1.9513 1.00 1512 161 0.0983 0.1268 REMARK 3 4 1.9513 - 1.7729 1.00 1515 153 0.1057 0.1407 REMARK 3 5 1.7729 - 1.6458 1.00 1523 153 0.1107 0.1492 REMARK 3 6 1.6458 - 1.5488 1.00 1508 156 0.1065 0.1358 REMARK 3 7 1.5488 - 1.4712 1.00 1516 158 0.1048 0.1540 REMARK 3 8 1.4712 - 1.4072 1.00 1480 154 0.1061 0.1468 REMARK 3 9 1.4072 - 1.3530 1.00 1524 156 0.1067 0.1357 REMARK 3 10 1.3530 - 1.3063 0.99 1490 149 0.1159 0.1646 REMARK 3 11 1.3063 - 1.2655 0.93 1416 143 0.1213 0.1641 REMARK 3 12 1.2655 - 1.2293 0.82 1244 128 0.1305 0.1762 REMARK 3 13 1.2293 - 1.1969 0.66 994 98 0.1379 0.1568 REMARK 3 14 1.1969 - 1.1680 0.44 665 63 0.1576 0.2163 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.460 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 : 0.008 683 REMARK 3 ANGLE : 1.317 935 REMARK 3 CHIRALITY : 0.071 95 REMARK 3 PLANARITY : 0.008 128 REMARK 3 DIHEDRAL : 14.607 267 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 8HLO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21440 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.168 REMARK 200 RESOLUTION RANGE LOW (A) : 39.128 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, 1.4M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, PH 7.4, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,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 39.59400 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 19.79700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.59400 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 19.79700 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 A1325 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1330 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1365 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1394 LIES ON A SPECIAL POSITION. 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 ASP A1119 -165.66 -163.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1397 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A1398 DISTANCE = 6.52 ANGSTROMS DBREF 8HLO A 1087 1147 UNP Q9QWY8 ASAP1_MOUSE 1087 1147 DBREF 8HLO C 828 836 UNP Q8TDZ2 MICA1_HUMAN 828 836 SEQADV 8HLO GLY A 1081 UNP Q9QWY8 EXPRESSION TAG SEQADV 8HLO PRO A 1082 UNP Q9QWY8 EXPRESSION TAG SEQADV 8HLO GLY A 1083 UNP Q9QWY8 EXPRESSION TAG SEQADV 8HLO SER A 1084 UNP Q9QWY8 EXPRESSION TAG SEQADV 8HLO GLU A 1085 UNP Q9QWY8 EXPRESSION TAG SEQADV 8HLO PHE A 1086 UNP Q9QWY8 EXPRESSION TAG SEQADV 8HLO GLY C 824 UNP Q8TDZ2 EXPRESSION TAG SEQADV 8HLO PRO C 825 UNP Q8TDZ2 EXPRESSION TAG SEQADV 8HLO GLY C 826 UNP Q8TDZ2 EXPRESSION TAG SEQADV 8HLO SER C 827 UNP Q8TDZ2 EXPRESSION TAG SEQRES 1 A 67 GLY PRO GLY SER GLU PHE VAL ARG ARG VAL LYS THR ILE SEQRES 2 A 67 TYR ASP CYS GLN ALA ASP ASN ASP ASP GLU LEU THR PHE SEQRES 3 A 67 ILE GLU GLY GLU VAL ILE ILE VAL THR GLY GLU GLU ASP SEQRES 4 A 67 GLN GLU TRP TRP ILE GLY HIS ILE GLU GLY GLN PRO GLU SEQRES 5 A 67 ARG LYS GLY VAL PHE PRO VAL SER PHE VAL HIS ILE LEU SEQRES 6 A 67 SER ASP SEQRES 1 C 13 GLY PRO GLY SER GLU PRO PRO PRO LYS PRO PRO ARG SER HET SO4 A1201 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *114(H2 O) SHEET 1 AA1 5 GLN A1130 PRO A1138 0 SHEET 2 AA1 5 TRP A1122 ILE A1127 -1 N TRP A1123 O PHE A1137 SHEET 3 AA1 5 VAL A1111 GLU A1117 -1 N ILE A1113 O HIS A1126 SHEET 4 AA1 5 ARG A1089 THR A1092 -1 N VAL A1090 O ILE A1112 SHEET 5 AA1 5 VAL A1142 LEU A1145 -1 O LEU A1145 N ARG A1089 CRYST1 45.181 45.181 59.391 90.00 90.00 120.00 P 62 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 0.022133 0.012779 0.000000 0.00000 SCALE2 0.000000 0.025557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016838 0.00000