HEADER TRANSFERASE 12-AUG-18 6EDX TITLE CRYSTAL STRUCTURE OF SGK3 PX DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE SGK3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOKINE-INDEPENDENT SURVIVAL KINASE,SERUM/GLUCOCORTICOID- COMPND 5 REGULATED KINASE 3,SERUM/GLUCOCORTICOID-REGULATED KINASE-LIKE; COMPND 6 EC: 2.7.11.1; 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 GENE: SGK3, CISK, SGKL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PX DOMAIN, ENDOSOME, TRAFFICKING, SORTING NEXIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.CHANDRA,B.M.COLLINS REVDAT 4 11-OCT-23 6EDX 1 REMARK REVDAT 3 01-JAN-20 6EDX 1 REMARK REVDAT 2 17-APR-19 6EDX 1 JRNL REVDAT 1 05-SEP-18 6EDX 0 JRNL AUTH M.CHANDRA,Y.K.CHIN,C.MAS,J.R.FEATHERS,B.PAUL,S.DATTA, JRNL AUTH 2 K.E.CHEN,X.JIA,Z.YANG,S.J.NORWOOD,B.MOHANTY,A.BUGARCIC, JRNL AUTH 3 R.D.TEASDALE,W.M.HENNE,M.MOBLI,B.M.COLLINS JRNL TITL CLASSIFICATION OF THE HUMAN PHOX HOMOLOGY (PX) DOMAINS BASED JRNL TITL 2 ON THEIR PHOSPHOINOSITIDE BINDING SPECIFICITIES. JRNL REF NAT COMMUN V. 10 1528 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 30948714 JRNL DOI 10.1038/S41467-019-09355-Y REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9533 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130 REMARK 3 FREE R VALUE TEST SET COUNT : 966 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 26.2850 - 3.8432 0.90 1256 143 0.1337 0.1683 REMARK 3 2 3.8432 - 3.0520 0.90 1223 140 0.1684 0.2274 REMARK 3 3 3.0520 - 2.6666 0.90 1208 136 0.2145 0.2226 REMARK 3 4 2.6666 - 2.4230 0.90 1225 137 0.2372 0.2361 REMARK 3 5 2.4230 - 2.2494 0.90 1213 134 0.2333 0.2579 REMARK 3 6 2.2494 - 2.1169 0.90 1231 136 0.2552 0.2466 REMARK 3 7 2.1169 - 2.0109 0.89 1193 140 0.2477 0.2626 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.600 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 : 0.008 988 REMARK 3 ANGLE : 0.980 1328 REMARK 3 CHIRALITY : 0.044 134 REMARK 3 PLANARITY : 0.006 172 REMARK 3 DIHEDRAL : 15.963 381 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 6EDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 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 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9533 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.009 REMARK 200 RESOLUTION RANGE LOW (A) : 42.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.100 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: 1XTE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 2M SODIUM REMARK 280 MALONATE (PH 5.0), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.16950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.16950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.98150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.16950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.16950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.98150 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 37.16950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 37.16950 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.98150 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 37.16950 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 37.16950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.98150 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 GLU A 5 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 GLN A 83 CG CD OE1 NE2 REMARK 470 GLU A 90 CG CD OE1 OE2 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 GLU A 20 -159.05 -119.25 REMARK 500 HIS A 118 36.67 -89.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 DBREF 6EDX A 4 119 UNP Q96BR1 SGK3_HUMAN 10 125 SEQADV 6EDX GLY A 2 UNP Q96BR1 EXPRESSION TAG SEQADV 6EDX SER A 3 UNP Q96BR1 EXPRESSION TAG SEQRES 1 A 118 GLY SER LYS GLU SER CYS PRO SER VAL SER ILE PRO SER SEQRES 2 A 118 SER ASP GLU HIS ARG GLU LYS LYS LYS ARG PHE THR VAL SEQRES 3 A 118 TYR LYS VAL LEU VAL SER VAL GLY ARG SER GLU TRP PHE SEQRES 4 A 118 VAL PHE ARG ARG TYR ALA GLU PHE ASP LYS LEU TYR ASN SEQRES 5 A 118 THR LEU LYS LYS GLN PHE PRO ALA MET ALA LEU LYS ILE SEQRES 6 A 118 PRO ALA LYS ARG ILE PHE GLY ASP ASN PHE ASP PRO ASP SEQRES 7 A 118 PHE ILE LYS GLN ARG ARG ALA GLY LEU ASN GLU PHE ILE SEQRES 8 A 118 GLN ASN LEU VAL ARG TYR PRO GLU LEU TYR ASN HIS PRO SEQRES 9 A 118 ASP VAL ARG ALA PHE LEU GLN MET ASP SER PRO LYS HIS SEQRES 10 A 118 GLN HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *21(H2 O) HELIX 1 AA1 ARG A 44 PHE A 59 1 16 HELIX 2 AA2 PRO A 60 ALA A 63 5 4 HELIX 3 AA3 ASP A 77 VAL A 96 1 20 HELIX 4 AA4 TYR A 98 ASN A 103 1 6 HELIX 5 AA5 HIS A 104 LEU A 111 1 8 HELIX 6 AA6 SER A 115 GLN A 119 5 5 SHEET 1 AA1 3 SER A 9 GLU A 20 0 SHEET 2 AA1 3 LYS A 23 VAL A 34 -1 O VAL A 27 N ASP A 16 SHEET 3 AA1 3 SER A 37 ARG A 43 -1 O VAL A 41 N VAL A 30 SITE 1 AC1 7 SER A 15 PRO A 78 ILE A 81 LYS A 82 SITE 2 AC1 7 ARG A 85 HOH A 302 HOH A 312 CRYST1 74.339 74.339 51.963 90.00 90.00 90.00 I 4 8 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 0.013452 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019244 0.00000