HEADER TRANSPORT PROTEIN 17-AUG-20 7CT1 TITLE CRYSTAL STRUCTURE OF SNX27 FERM DOMAIN IN COMPLEX WITH A DLF MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUSION PROTEIN SORTING NEXIN-27 AND DLF MOTIF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606, 32630; SOURCE 5 GENE: SNX27, KIAA0488, MY014; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, SNX27, SNX1, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.HU,J.DA,Q.SUN REVDAT 1 25-AUG-21 7CT1 0 JRNL AUTH W.HU,D.JIA,Q.SUN JRNL TITL CRYSTAL STRUCTURE OF SNX27 FERM DOMAIN IN COMPLEX WITH A DLF JRNL TITL 2 MOTIF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 23957 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1183 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.40 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 15.1667 34.7715 36.7214 REMARK 3 T TENSOR REMARK 3 T11: 0.2615 T22: 0.2449 REMARK 3 T33: 0.2441 T12: 0.0353 REMARK 3 T13: 0.0100 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 1.2364 L22: 1.4371 REMARK 3 L33: 0.6484 L12: -0.0311 REMARK 3 L13: -0.0240 L23: -0.0162 REMARK 3 S TENSOR REMARK 3 S11: -0.0624 S12: -0.0736 S13: -0.0774 REMARK 3 S21: 0.1865 S22: 0.0728 S23: -0.0191 REMARK 3 S31: -0.0668 S32: -0.0358 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I/F_MINUS AND I/F_PLUS COLUMNS. REMARK 4 REMARK 4 7CT1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1300018212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-19 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24036 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.947 REMARK 200 RESOLUTION RANGE LOW (A) : 59.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09 M NPS 0.1 M BUFFER SYSTEM 3 PH8.5 REMARK 280 50 % V/V PRECIPITANT MIX 4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 21.59700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.99950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.47050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.99950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.59700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.47050 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 TOTAL BURIED SURFACE AREA: 290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14910 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 273 REMARK 465 GLY A 529 REMARK 465 GLY A 530 REMARK 465 SER A 531 REMARK 465 GLY A 532 REMARK 465 GLY A 533 REMARK 465 SER A 534 REMARK 465 PRO A 535 REMARK 465 ILE A 536 REMARK 465 ASN A 537 REMARK 465 ASN A 538 REMARK 465 GLY A 539 REMARK 465 SER A 540 REMARK 465 LYS A 541 REMARK 465 GLU A 542 REMARK 465 ASN A 543 REMARK 465 GLY A 544 REMARK 465 ILE A 545 REMARK 465 HIS A 546 REMARK 465 GLU A 547 REMARK 465 GLU A 548 REMARK 465 GLN A 549 REMARK 465 ASP A 550 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 ASP A 311 -168.58 -127.61 REMARK 500 VAL A 350 -128.20 59.12 REMARK 500 TYR A 506 40.33 -99.44 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602 DBREF 7CT1 A 273 526 UNP Q96L92 SNX27_HUMAN 273 526 DBREF 7CT1 A 527 558 PDB 7CT1 7CT1 527 558 SEQRES 1 A 286 SER ASP VAL GLU LEU ARG VAL ALA LEU PRO ASP GLY THR SEQRES 2 A 286 THR VAL THR VAL ARG VAL LYS LYS ASN SER THR THR ASP SEQRES 3 A 286 GLN VAL TYR GLN ALA ILE ALA ALA LYS VAL GLY MET ASP SEQRES 4 A 286 SER THR THR VAL ASN TYR PHE ALA LEU PHE GLU VAL ILE SEQRES 5 A 286 SER HIS SER PHE VAL ARG LYS LEU ALA PRO ASN GLU PHE SEQRES 6 A 286 PRO HIS LYS LEU TYR ILE GLN ASN TYR THR SER ALA VAL SEQRES 7 A 286 PRO GLY THR CYS LEU THR ILE ARG LYS TRP LEU PHE THR SEQRES 8 A 286 THR GLU GLU GLU ILE LEU LEU ASN ASP ASN ASP LEU ALA SEQRES 9 A 286 VAL THR TYR PHE PHE HIS GLN ALA VAL ASP ASP VAL LYS SEQRES 10 A 286 LYS GLY TYR ILE LYS ALA GLU GLU LYS SER TYR GLN LEU SEQRES 11 A 286 GLN LYS LEU TYR GLU GLN ARG LYS MET VAL MET TYR LEU SEQRES 12 A 286 ASN MET LEU ARG THR CYS GLU GLY TYR ASN GLU ILE ILE SEQRES 13 A 286 PHE PRO HIS CYS ALA CYS ASP SER ARG ARG LYS GLY HIS SEQRES 14 A 286 VAL ILE THR ALA ILE SER ILE THR HIS PHE LYS LEU HIS SEQRES 15 A 286 ALA CYS THR GLU GLU GLY GLN LEU GLU ASN GLN VAL ILE SEQRES 16 A 286 ALA PHE GLU TRP ASP GLU MET GLN ARG TRP ASP THR ASP SEQRES 17 A 286 GLU GLU GLY MET ALA PHE CYS PHE GLU TYR ALA ARG GLY SEQRES 18 A 286 GLU LYS LYS PRO ARG TRP VAL LYS ILE PHE THR PRO TYR SEQRES 19 A 286 PHE ASN TYR MET HIS GLU CYS PHE GLU ARG VAL PHE CYS SEQRES 20 A 286 GLU LEU LYS TRP ARG LYS GLU GLU TYR GLY GLY SER GLY SEQRES 21 A 286 GLY SER PRO ILE ASN ASN GLY SER LYS GLU ASN GLY ILE SEQRES 22 A 286 HIS GLU GLU GLN ASP GLN GLU PRO GLN ASP LEU PHE ALA HET GOL A 601 6 HET GOL A 602 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *153(H2 O) HELIX 1 AA1 THR A 296 GLY A 309 1 14 HELIX 2 AA2 THR A 314 ASN A 316 5 3 HELIX 3 AA3 PHE A 337 ASN A 345 1 9 HELIX 4 AA4 ASN A 345 VAL A 350 1 6 HELIX 5 AA5 THR A 363 LEU A 369 1 7 HELIX 6 AA6 ASN A 373 LYS A 390 1 18 HELIX 7 AA7 LYS A 398 GLN A 408 1 11 HELIX 8 AA8 LYS A 410 ARG A 419 1 10 HELIX 9 AA9 GLU A 470 ASP A 472 5 3 HELIX 10 AB1 TYR A 506 TYR A 528 1 23 SHEET 1 AA1 2 VAL A 275 ALA A 280 0 SHEET 2 AA1 2 THR A 286 VAL A 291 -1 O VAL A 287 N VAL A 279 SHEET 1 AA2 3 PHE A 328 LYS A 331 0 SHEET 2 AA2 3 PHE A 318 SER A 325 -1 N GLU A 322 O ARG A 330 SHEET 3 AA2 3 LEU A 355 LYS A 359 -1 O THR A 356 N PHE A 321 SHEET 1 AA3 4 ILE A 427 ILE A 428 0 SHEET 2 AA3 4 HIS A 441 ILE A 446 -1 O ILE A 446 N ILE A 427 SHEET 3 AA3 4 PHE A 451 CYS A 456 -1 O LYS A 452 N ALA A 445 SHEET 4 AA3 4 LEU A 462 PHE A 469 -1 O PHE A 469 N PHE A 451 SHEET 1 AA4 3 MET A 474 ASP A 480 0 SHEET 2 AA4 3 ALA A 485 TYR A 490 -1 O GLU A 489 N GLN A 475 SHEET 3 AA4 3 ARG A 498 ILE A 502 -1 O ILE A 502 N PHE A 486 SITE 1 AC1 2 GLU A 276 ILE A 368 SITE 1 AC2 6 TYR A 317 GLN A 403 GLU A 407 ARG A 516 SITE 2 AC2 6 CYS A 519 TRP A 523 CRYST1 43.194 72.941 103.999 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 0.023151 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009615 0.00000