HEADER SIGNALING PROTEIN 22-MAY-21 7MYX TITLE CRYSTAL STRUCTURE OF THE PH DOMAIN (R86A) OF AKT1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAC-ALPHA SERINE/THREONINE-PROTEIN KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PH DOMAIN, UNP RESIDUES 1-121; COMPND 5 SYNONYM: PROTEIN KINASE B,PKB,PROTEIN KINASE B ALPHA,PKB ALPHA,PROTO- COMPND 6 ONCOGENE C-AKT,RAC-PK-ALPHA; COMPND 7 EC: 2.7.11.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AKT1, PKB, RAC; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA AFF. FRUGIPERDA 1 BOLD-2017; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2449148 KEYWDS KINASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.BAE,E.PARK,P.A.COLE,M.J.ECK REVDAT 2 18-OCT-23 7MYX 1 REMARK REVDAT 1 09-NOV-22 7MYX 0 JRNL AUTH H.BAE,T.VIENNET,E.PARK,N.CHU,A.SALGUERO,M.J.ECK,H.ARTHANARI, JRNL AUTH 2 P.A.COLE JRNL TITL PH DOMAIN-MEDIATED AUTOINHIBITION AND ONCOGENIC ACTIVATION JRNL TITL 2 OF AKT. JRNL REF ELIFE V. 11 2022 JRNL REFN ESSN 2050-084X JRNL PMID 35968932 JRNL DOI 10.7554/ELIFE.80148 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122+SVN 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 20603 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.640 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 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 36.9600 - 3.3500 0.96 1366 147 0.1699 0.2054 REMARK 3 2 3.3500 - 2.6600 0.98 1362 135 0.1749 0.2081 REMARK 3 3 2.6600 - 2.3200 0.98 1356 150 0.1842 0.2086 REMARK 3 4 2.3200 - 2.1100 0.98 1333 144 0.1703 0.1875 REMARK 3 5 2.1100 - 1.9600 0.99 1360 141 0.1696 0.2088 REMARK 3 6 1.9600 - 1.8400 0.98 1332 137 0.1708 0.1818 REMARK 3 7 1.8400 - 1.7500 0.98 1339 146 0.1859 0.2020 REMARK 3 8 1.7500 - 1.6700 0.99 1358 146 0.1768 0.1991 REMARK 3 9 1.6700 - 1.6100 0.97 1320 135 0.1880 0.2330 REMARK 3 10 1.6100 - 1.5500 0.97 1328 147 0.1678 0.1841 REMARK 3 11 1.5500 - 1.5100 0.97 1289 138 0.1707 0.2532 REMARK 3 12 1.5100 - 1.4600 0.96 1296 138 0.1791 0.2062 REMARK 3 13 1.4600 - 1.4200 0.96 1307 143 0.1921 0.1781 REMARK 3 14 1.4200 - 1.3900 0.94 1271 139 0.2029 0.2383 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) : 0.125 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.494 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.77 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 : 0.006 981 REMARK 3 ANGLE : 0.791 1328 REMARK 3 CHIRALITY : 0.085 143 REMARK 3 PLANARITY : 0.007 170 REMARK 3 DIHEDRAL : 14.162 373 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 7MYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-20 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 1.19.1_4122+SVN REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 36.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04086 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.11150 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: 1UNP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.28 M SODIUM CITRATE, 0.1 M HEPES PH REMARK 280 7.5, 0.01 M PRASEODYMIUM(III) ACETATE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.39300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.81350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.39300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.81350 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLN A 43 REMARK 465 ASP A 44 REMARK 465 VAL A 45 REMARK 465 ASP A 46 REMARK 465 GLN A 47 REMARK 465 ARG A 48 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 TRP A 80 CZ2 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 ASN A 54 107.50 -160.74 REMARK 500 TRP A 80 -115.52 53.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 7MYX A 1 121 UNP P31749 AKT1_HUMAN 1 121 SEQADV 7MYX ALA A 86 UNP P31749 ARG 86 ENGINEERED MUTATION SEQRES 1 A 121 MET SER ASP VAL ALA ILE VAL LYS GLU GLY TRP LEU HIS SEQRES 2 A 121 LYS ARG GLY GLU TYR ILE LYS THR TRP ARG PRO ARG TYR SEQRES 3 A 121 PHE LEU LEU LYS ASN ASP GLY THR PHE ILE GLY TYR LYS SEQRES 4 A 121 GLU ARG PRO GLN ASP VAL ASP GLN ARG GLU ALA PRO LEU SEQRES 5 A 121 ASN ASN PHE SER VAL ALA GLN CYS GLN LEU MET LYS THR SEQRES 6 A 121 GLU ARG PRO ARG PRO ASN THR PHE ILE ILE ARG CYS LEU SEQRES 7 A 121 GLN TRP THR THR VAL ILE GLU ALA THR PHE HIS VAL GLU SEQRES 8 A 121 THR PRO GLU GLU ARG GLU GLU TRP THR THR ALA ILE GLN SEQRES 9 A 121 THR VAL ALA ASP GLY LEU LYS LYS GLN GLU GLU GLU GLU SEQRES 10 A 121 MET ASP PHE ARG FORMUL 2 HOH *111(H2 O) HELIX 1 AA1 THR A 92 ASP A 119 1 28 SHEET 1 AA1 7 ASN A 53 SER A 56 0 SHEET 2 AA1 7 THR A 34 TYR A 38 -1 N GLY A 37 O ASN A 53 SHEET 3 AA1 7 TRP A 22 LYS A 30 -1 N TYR A 26 O TYR A 38 SHEET 4 AA1 7 ILE A 6 ARG A 15 -1 N VAL A 7 O LEU A 29 SHEET 5 AA1 7 THR A 82 HIS A 89 -1 O THR A 87 N ARG A 15 SHEET 6 AA1 7 THR A 72 GLN A 79 -1 N PHE A 73 O PHE A 88 SHEET 7 AA1 7 GLN A 61 THR A 65 -1 N GLN A 61 O ARG A 76 CISPEP 1 ARG A 67 PRO A 68 0 -0.68 CRYST1 84.786 33.627 42.352 90.00 119.33 90.00 C 1 2 1 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 0.011794 0.000000 0.006628 0.00000 SCALE2 0.000000 0.029738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027084 0.00000