HEADER LIPID BINDING PROTEIN 08-AUG-18 6ECM TITLE CRYSTAL STRUCTURE OF SNX15 PX DOMAIN IN DOMAIN SWAPPED CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-15; COMPND 3 CHAIN: A; COMPND 4 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: SNX15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PX DOMAIN, ENDOSOME, TRAFFICKING, SORTING NEXIN, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.CHANDRA,B.M.COLLINS REVDAT 4 11-OCT-23 6ECM 1 REMARK REVDAT 3 01-JAN-20 6ECM 1 REMARK REVDAT 2 17-APR-19 6ECM 1 JRNL REVDAT 1 22-AUG-18 6ECM 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. 2.35 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 5569 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 560 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 45.6593 - 3.7346 1.00 1354 151 0.2233 0.2635 REMARK 3 2 3.7346 - 2.9644 0.99 1239 138 0.2624 0.3364 REMARK 3 3 2.9644 - 2.5897 0.99 1219 137 0.2924 0.3970 REMARK 3 4 2.5897 - 2.3530 0.97 1197 134 0.2940 0.3636 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.430 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 : 0.006 853 REMARK 3 ANGLE : 1.036 1147 REMARK 3 CHIRALITY : 0.038 120 REMARK 3 PLANARITY : 0.005 145 REMARK 3 DIHEDRAL : 15.001 318 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 6ECM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236083. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.9796 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5645 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 26.20 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 24.60 REMARK 200 R MERGE FOR SHELL (I) : 1.07400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 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: 4IKD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS (PH 8.5) 200 MM LISO4, 24% REMARK 280 PEG4000, 10% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 41.79000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.24900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.24900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.68500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.24900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.24900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.89500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.24900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.24900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 62.68500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.24900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.24900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.89500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.79000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 54.49800 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 54.49800 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 41.79000 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 -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ARG A 3 REMARK 465 GLN A 4 REMARK 465 ALA A 5 REMARK 465 LYS A 6 REMARK 465 ASP A 7 REMARK 465 ASP A 8 REMARK 465 LYS A 37 REMARK 465 LYS A 38 REMARK 465 ASP A 39 REMARK 465 PRO A 40 REMARK 465 GLU A 41 REMARK 465 ASP A 42 REMARK 465 PRO A 77 REMARK 465 ALA A 78 REMARK 465 PHE A 79 REMARK 465 PRO A 80 REMARK 465 ARG A 81 REMARK 465 ALA A 82 REMARK 465 GLN A 83 REMARK 465 VAL A 84 REMARK 465 PHE A 85 REMARK 465 GLY A 86 REMARK 465 ARG A 87 REMARK 465 PHE A 88 REMARK 465 GLU A 89 REMARK 465 GLY A 126 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 PHE A 76 CG CD1 CD2 CE1 CE2 CZ 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 LEU A 10 91.60 151.88 REMARK 500 ARG A 124 -70.42 -61.36 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 SO4 A 201 DBREF 6ECM A 1 126 UNP Q9NRS6 SNX15_HUMAN 1 126 SEQADV 6ECM GLY A -1 UNP Q9NRS6 EXPRESSION TAG SEQADV 6ECM SER A 0 UNP Q9NRS6 EXPRESSION TAG SEQRES 1 A 128 GLY SER MET SER ARG GLN ALA LYS ASP ASP PHE LEU ARG SEQRES 2 A 128 HIS TYR THR VAL SER ASP PRO ARG THR HIS PRO LYS GLY SEQRES 3 A 128 TYR THR GLU TYR LYS VAL THR ALA GLN PHE ILE SER LYS SEQRES 4 A 128 LYS ASP PRO GLU ASP VAL LYS GLU VAL VAL VAL TRP LYS SEQRES 5 A 128 ARG TYR SER ASP PHE ARG LYS LEU HIS GLY ASP LEU ALA SEQRES 6 A 128 TYR THR HIS ARG ASN LEU PHE ARG ARG LEU GLU GLU PHE SEQRES 7 A 128 PRO ALA PHE PRO ARG ALA GLN VAL PHE GLY ARG PHE GLU SEQRES 8 A 128 ALA SER VAL ILE GLU GLU ARG ARG LYS GLY ALA GLU ASP SEQRES 9 A 128 LEU LEU ARG PHE THR VAL HIS ILE PRO ALA LEU ASN ASN SEQRES 10 A 128 SER PRO GLN LEU LYS GLU PHE PHE ARG GLY GLY HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *9(H2 O) HELIX 1 AA1 ARG A 51 GLU A 74 1 24 HELIX 2 AA2 SER A 91 PHE A 106 1 16 HELIX 3 AA3 ILE A 110 ASN A 115 1 6 HELIX 4 AA4 SER A 116 PHE A 122 1 7 SHEET 1 AA1 3 ARG A 11 THR A 20 0 SHEET 2 AA1 3 THR A 26 PHE A 34 -1 O LYS A 29 N SER A 16 SHEET 3 AA1 3 LYS A 44 LYS A 50 -1 O VAL A 48 N VAL A 30 SITE 1 AC1 4 ARG A 51 TYR A 52 SER A 53 ARG A 96 CRYST1 54.498 54.498 83.580 90.00 90.00 90.00 P 43 21 2 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 0.018349 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011965 0.00000