HEADER SIGNALING PROTEIN 21-DEC-16 5MR1 TITLE CRYSTAL STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF INTERACTOR TITLE 2 PROTEIN FOR CYTOHESIN EXCHANGE FACTORS 1 (IPCEF1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERACTOR PROTEIN FOR CYTOHESIN EXCHANGE FACTORS 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOINOSITIDE-BINDING PROTEIN PIP3-E; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: FIRST TWO RESIDUES REMAIN AFTER CLEAVAGE OF COMPND 7 PURIFICAITON TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IPCEF1, KIAA0403; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS CYTOHESIN, SCAFFOLD PROTEIN, PLECKSTRIN HOMOLOGY, PIP3E, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.NEWMAN,H.AITKENHEAD,D.WANG,N.BURGESS-BROWN,E.WILLIAMS,F.VON AUTHOR 2 DELFT,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,O.GILEADI REVDAT 6 17-JAN-24 5MR1 1 REMARK REVDAT 5 18-NOV-20 5MR1 1 KEYWDS REVDAT 4 24-JAN-18 5MR1 1 SOURCE REVDAT 3 13-DEC-17 5MR1 1 AUTHOR JRNL REVDAT 2 23-AUG-17 5MR1 1 REMARK REVDAT 1 11-JAN-17 5MR1 0 JRNL AUTH J.A.NEWMAN,H.AITKENHEAD,D.WANG,N.BURGESS-BROWN,E.WILLIAMS, JRNL AUTH 2 F.VON DELFT,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,O.GILEADI JRNL TITL CRYSTAL STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF JRNL TITL 2 INTERACTOR PROTEIN FOR CYTOHESIN EXCHANGE FACTORS 1 (IPCEF1) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 35897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1739 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 27.9687 - 2.7452 1.00 3103 160 0.1789 0.2102 REMARK 3 2 2.7452 - 2.1792 0.99 2954 167 0.1707 0.1691 REMARK 3 3 2.1792 - 1.9038 0.99 2916 135 0.1438 0.1567 REMARK 3 4 1.9038 - 1.7297 0.98 2902 134 0.1373 0.1429 REMARK 3 5 1.7297 - 1.6058 0.98 2874 125 0.1299 0.1593 REMARK 3 6 1.6058 - 1.5111 0.98 2839 133 0.1293 0.1576 REMARK 3 7 1.5111 - 1.4354 0.97 2813 148 0.1450 0.1844 REMARK 3 8 1.4354 - 1.3730 0.96 2798 143 0.1544 0.1857 REMARK 3 9 1.3730 - 1.3201 0.96 2777 143 0.1774 0.2081 REMARK 3 10 1.3201 - 1.2746 0.96 2745 159 0.2059 0.2248 REMARK 3 11 1.2746 - 1.2347 0.95 2741 150 0.2401 0.2553 REMARK 3 12 1.2347 - 1.1994 0.92 2696 142 0.2741 0.2975 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.13 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 : 0.011 907 REMARK 3 ANGLE : 1.091 1233 REMARK 3 CHIRALITY : 0.097 122 REMARK 3 PLANARITY : 0.007 158 REMARK 3 DIHEDRAL : 13.897 327 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 5MR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35945 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 1.59300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 1UPQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 25% PEG 3350, REMARK 280 0.1 M BIS TRIS PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K 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 21.98700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.51350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.80600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.51350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.98700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.80600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 SER A 40 REMARK 465 MET A 41 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 LYS A 52 CD CE NZ REMARK 470 LYS A 54 CE NZ REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LYS A 70 CD CE NZ REMARK 470 GLU A 83 CG CD OE1 OE2 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 292 O HOH A 293 1.89 REMARK 500 O HOH A 294 O HOH A 300 1.95 REMARK 500 O HOH A 247 O HOH A 266 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 249 O HOH A 293 4455 2.01 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 LYS A 54 -2.11 73.06 REMARK 500 ASP A 93 -0.54 74.38 REMARK 500 ILE A 115 -80.19 -120.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 5MR1 A 42 142 UNP Q8WWN9 ICEF1_HUMAN 42 142 SEQADV 5MR1 SER A 40 UNP Q8WWN9 EXPRESSION TAG SEQADV 5MR1 MET A 41 UNP Q8WWN9 EXPRESSION TAG SEQRES 1 A 103 SER MET ALA ASP CYS GLN GLY TRP LEU TYR LYS LYS LYS SEQRES 2 A 103 GLU LYS GLY SER PHE LEU SER ASN LYS TRP LYS LYS PHE SEQRES 3 A 103 TRP VAL ILE LEU LYS GLY SER SER LEU TYR TRP TYR SER SEQRES 4 A 103 ASN GLN MET ALA GLU LYS ALA ASP GLY PHE VAL ASN LEU SEQRES 5 A 103 PRO ASP PHE THR VAL GLU ARG ALA SER GLU CYS LYS LYS SEQRES 6 A 103 LYS HIS ALA PHE LYS ILE SER HIS PRO GLN ILE LYS THR SEQRES 7 A 103 PHE TYR PHE ALA ALA GLU ASN VAL GLN GLU MET ASN VAL SEQRES 8 A 103 TRP LEU ASN LYS LEU GLY SER ALA VAL ILE HIS GLN FORMUL 2 HOH *114(H2 O) HELIX 1 AA1 ASN A 124 VAL A 139 1 16 SHEET 1 AA1 7 GLY A 87 ASN A 90 0 SHEET 2 AA1 7 SER A 73 TYR A 77 -1 N LEU A 74 O VAL A 89 SHEET 3 AA1 7 LYS A 63 LYS A 70 -1 N TRP A 66 O TYR A 77 SHEET 4 AA1 7 CYS A 44 LYS A 50 -1 N GLY A 46 O VAL A 67 SHEET 5 AA1 7 THR A 117 ALA A 121 -1 O ALA A 121 N TYR A 49 SHEET 6 AA1 7 ALA A 107 SER A 111 -1 N ILE A 110 O PHE A 118 SHEET 7 AA1 7 THR A 95 ARG A 98 -1 N GLU A 97 O LYS A 109 CRYST1 43.974 49.612 53.027 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 0.022741 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020156 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018858 0.00000