PDB Short entry for 1UNP HEADER TRANSFERASE 12-SEP-03 1UNP TITLE CRYSTAL STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF PKB ALPHA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAC-ALPHA SERINE/THREONINE KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-121; COMPND 5 SYNONYM: RAC-PK-ALPHA, PROTEIN KINASE B, PKB, C-AKT; COMPND 6 EC: 2.7.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX4T-1 KEYWDS PLECKSTRIN HOMOLOGY DOMAIN, TRANSFERASE, PHOSPHOINOSITIDE, PKB, AKT EXPDTA X-RAY DIFFRACTION AUTHOR C.C.MILBURN,M.DEAK,S.M.KELLY,N.C.PRICE,D.R.ALESSI,D.M.F.VAN AALTEN REVDAT 5 13-DEC-23 1UNP 1 REMARK REVDAT 4 28-FEB-18 1UNP 1 SOURCE AUTHOR JRNL REVDAT 3 01-SEP-09 1UNP 1 REMARK DBREF REVDAT 2 24-FEB-09 1UNP 1 VERSN REVDAT 1 16-SEP-04 1UNP 0 JRNL AUTH C.C.MILBURN,M.DEAK,S.M.KELLY,N.C.PRICE,D.R.ALESSI, JRNL AUTH 2 D.M.VAN AALTEN JRNL TITL BINDING OF PHOSPHATIDYLINOSITOL 3,4,5-TRISPHOSPHATE TO THE JRNL TITL 2 PLECKSTRIN HOMOLOGY DOMAIN OF PROTEIN KINASE B INDUCES A JRNL TITL 3 CONFORMATIONAL CHANGE. JRNL REF BIOCHEM. J. V. 375 531 2003 JRNL REFN ESSN 1470-8728 JRNL PMID 12964941 JRNL DOI 10.1042/BJ20031229 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.C.THOMAS,M.DEAK,D.R.ALESSI,M.F.VAN AALTEN REMARK 1 TITL HIGH-RESOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN REMARK 1 TITL 2 OF PROTEIN KINASE B/AKT BOUND TO PHOSPHATIDYLINOSITOL REMARK 1 TITL 3 (3,4,5)-TRISPHOSPHATE REMARK 1 REF CURR.BIOL. V. 12 1256 2002 REMARK 1 REFN ISSN 0960-9822 REMARK 1 PMID 12176338 REMARK 1 DOI 10.1016/S0960-9822(02)00972-7 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 873989.270 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 12394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 601 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1941 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 90 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1009 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.37000 REMARK 3 B22 (A**2) : 6.40000 REMARK 3 B33 (A**2) : -4.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.590 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.590 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.100 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 59.31 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PROTEIN_BREAK.TOP REMARK 3 TOPOLOGY FILE 3 : PROTEIN.LINK REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1290013509. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12409 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1H10 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG 4000, 0.25 M SODIUM ACETATE, REMARK 280 0.1 M TRIS PH 8.5 3.3 % POLYPROPYLENE GLYCOL 400, PH 8.50 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 42.03200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.90150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.03200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.90150 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: PQS 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 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 NH2 ARG A 76 NH2 ARG A 76 2555 1.95 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 20 25.78 -65.92 REMARK 500 PRO A 42 151.14 -44.30 REMARK 500 TRP A 80 -107.96 69.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H10 RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF REMARK 900 PROTEIN KINASE B/AKT BOUND TO INS(1,3,4,5)-TETRAKISPHOPHATE REMARK 900 RELATED ID: 1UNQ RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN REMARK 900 OF PROTEIN KINASE B/AKT BOUND TO INS(1,3,4,5)- TETRAKISPHOPHATE REMARK 900 RELATED ID: 1UNR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PH DOMAIN OF PKB ALPHA IN COMPLEX WITH A REMARK 900 SULFATE MOLECULE DBREF 1UNP A 1 121 UNP P31749 AKT1_HUMAN 1 121 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 ARG 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 *132(H2 O) HELIX 1 1 THR A 92 ASP A 119 1 28 SHEET 1 AA 7 ASN A 53 SER A 56 0 SHEET 2 AA 7 THR A 34 TYR A 38 -1 O PHE A 35 N PHE A 55 SHEET 3 AA 7 TRP A 22 LYS A 30 -1 O TYR A 26 N TYR A 38 SHEET 4 AA 7 ILE A 6 ARG A 15 -1 N VAL A 7 O LEU A 29 SHEET 5 AA 7 THR A 82 HIS A 89 -1 O THR A 87 N ARG A 15 SHEET 6 AA 7 THR A 72 GLN A 79 -1 O PHE A 73 N PHE A 88 SHEET 7 AA 7 GLN A 61 THR A 65 -1 O GLN A 61 N ARG A 76 SSBOND 1 CYS A 60 CYS A 77 1555 1555 2.03 CISPEP 1 ARG A 67 PRO A 68 0 -0.17 CRYST1 84.064 33.803 42.071 90.00 119.48 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 0.011896 0.000000 0.006725 0.00000 SCALE2 0.000000 0.029583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027304 0.00000