HEADER LIPID BINDING PROTEIN 08-APR-18 5ZN9 TITLE CRYSTAL STRUCTURE OF PX DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-27; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PX-DOMAIN; COMPND 5 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: SNX27, KIAA0488, MY014; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PX, LIPID, VESICLE, RETROMER, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,Z.ZHU,F.LI,S.LIAO,C.XU REVDAT 2 22-NOV-23 5ZN9 1 REMARK REVDAT 1 10-APR-19 5ZN9 0 JRNL AUTH Y.LI,Z.ZHU,F.LI,S.LIAO,C.XU JRNL TITL CRYSTAL STRUCTURE OF PX DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 21983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1987 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 49.1858 - 4.2783 0.99 1557 154 0.1935 0.2337 REMARK 3 2 4.2783 - 3.3961 0.99 1491 144 0.1815 0.1964 REMARK 3 3 3.3961 - 2.9669 0.99 1460 148 0.1905 0.1833 REMARK 3 4 2.9669 - 2.6956 0.99 1450 143 0.1964 0.2271 REMARK 3 5 2.6956 - 2.5024 0.99 1426 144 0.1968 0.2365 REMARK 3 6 2.5024 - 2.3549 0.98 1453 145 0.1949 0.2166 REMARK 3 7 2.3549 - 2.2370 0.99 1403 146 0.1778 0.2315 REMARK 3 8 2.2370 - 2.1396 0.98 1425 141 0.1915 0.2136 REMARK 3 9 2.1396 - 2.0572 0.99 1419 138 0.1826 0.2152 REMARK 3 10 2.0572 - 1.9862 0.99 1383 141 0.1786 0.2257 REMARK 3 11 1.9862 - 1.9241 0.97 1421 138 0.1781 0.2513 REMARK 3 12 1.9241 - 1.8691 0.97 1403 139 0.1965 0.2261 REMARK 3 13 1.8691 - 1.8199 0.98 1382 141 0.1896 0.2389 REMARK 3 14 1.8199 - 1.7755 0.93 1323 125 0.1977 0.2248 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.130 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 1735 REMARK 3 ANGLE : 0.824 2346 REMARK 3 CHIRALITY : 0.048 244 REMARK 3 PLANARITY : 0.006 304 REMARK 3 DIHEDRAL : 14.543 1047 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 5ZN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300007359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL18U 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21984 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.776 REMARK 200 RESOLUTION RANGE LOW (A) : 49.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3LUI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M LISO4; 0.1M TRIS; PH 8.5; 25% REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 49.16700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.91600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.85350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.91600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.16700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.85350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6260 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 350 REMARK 350 BIOMOLECULE: 2 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: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ASP A 165 REMARK 465 TYR A 166 REMARK 465 THR A 167 REMARK 465 GLU A 168 REMARK 465 LYS A 169 REMARK 465 GLN A 170 REMARK 465 GLU A 183 REMARK 465 GLN A 184 REMARK 465 ASN A 185 REMARK 465 GLY A 186 REMARK 465 GLU A 187 REMARK 465 ASP B 165 REMARK 465 TYR B 166 REMARK 465 THR B 167 REMARK 465 GLU B 168 REMARK 465 LYS B 169 REMARK 465 GLN B 170 REMARK 465 ALA B 171 REMARK 465 SER B 274 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 LYS A 188 CG CD CE NZ REMARK 470 LYS A 231 CE NZ REMARK 470 GLU A 269 CG CD OE1 OE2 REMARK 470 ARG B 178 CZ NH1 NH2 REMARK 470 LYS B 180 CG CD CE NZ REMARK 470 LYS B 188 CE NZ REMARK 470 ARG B 259 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 273 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 443 O HOH B 464 2.11 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 LEU A 271 49.68 -85.34 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 301 DBREF 5ZN9 A 165 274 UNP Q96L92 SNX27_HUMAN 156 265 DBREF 5ZN9 B 165 274 UNP Q96L92 SNX27_HUMAN 156 265 SEQRES 1 A 110 ASP TYR THR GLU LYS GLN ALA VAL PRO ILE SER VAL PRO SEQRES 2 A 110 ARG TYR LYS HIS VAL GLU GLN ASN GLY GLU LYS PHE VAL SEQRES 3 A 110 VAL TYR ASN VAL TYR MET ALA GLY ARG GLN LEU CYS SER SEQRES 4 A 110 LYS ARG TYR ARG GLU PHE ALA ILE LEU HIS GLN ASN LEU SEQRES 5 A 110 LYS ARG GLU PHE ALA ASN PHE THR PHE PRO ARG LEU PRO SEQRES 6 A 110 GLY LYS TRP PRO PHE SER LEU SER GLU GLN GLN LEU ASP SEQRES 7 A 110 ALA ARG ARG ARG GLY LEU GLU GLU TYR LEU GLU LYS VAL SEQRES 8 A 110 CYS SER ILE ARG VAL ILE GLY GLU SER ASP ILE MET GLN SEQRES 9 A 110 GLU PHE LEU SER GLU SER SEQRES 1 B 110 ASP TYR THR GLU LYS GLN ALA VAL PRO ILE SER VAL PRO SEQRES 2 B 110 ARG TYR LYS HIS VAL GLU GLN ASN GLY GLU LYS PHE VAL SEQRES 3 B 110 VAL TYR ASN VAL TYR MET ALA GLY ARG GLN LEU CYS SER SEQRES 4 B 110 LYS ARG TYR ARG GLU PHE ALA ILE LEU HIS GLN ASN LEU SEQRES 5 B 110 LYS ARG GLU PHE ALA ASN PHE THR PHE PRO ARG LEU PRO SEQRES 6 B 110 GLY LYS TRP PRO PHE SER LEU SER GLU GLN GLN LEU ASP SEQRES 7 B 110 ALA ARG ARG ARG GLY LEU GLU GLU TYR LEU GLU LYS VAL SEQRES 8 B 110 CYS SER ILE ARG VAL ILE GLY GLU SER ASP ILE MET GLN SEQRES 9 B 110 GLU PHE LEU SER GLU SER HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 B 301 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *147(H2 O) HELIX 1 AA1 TYR A 206 PHE A 220 1 15 HELIX 2 AA2 SER A 237 SER A 257 1 21 HELIX 3 AA3 ILE A 258 GLU A 263 1 6 HELIX 4 AA4 SER A 264 LEU A 271 1 8 HELIX 5 AA5 TYR B 206 PHE B 220 1 15 HELIX 6 AA6 SER B 237 SER B 257 1 21 HELIX 7 AA7 ILE B 258 GLU B 263 1 6 HELIX 8 AA8 SER B 264 LEU B 271 1 8 SHEET 1 AA1 3 ILE A 174 HIS A 181 0 SHEET 2 AA1 3 VAL A 190 MET A 196 -1 O TYR A 195 N SER A 175 SHEET 3 AA1 3 ARG A 199 ARG A 205 -1 O LEU A 201 N VAL A 194 SHEET 1 AA2 3 ILE B 174 GLN B 184 0 SHEET 2 AA2 3 GLU B 187 MET B 196 -1 O PHE B 189 N VAL B 182 SHEET 3 AA2 3 ARG B 199 ARG B 205 -1 O LEU B 201 N VAL B 194 SITE 1 AC1 8 ARG A 205 TYR A 206 ARG A 207 HOH A 404 SITE 2 AC1 8 HOH A 415 HOH A 430 HOH A 432 HOH A 446 SITE 1 AC2 6 ARG A 178 LYS A 180 PRO A 229 GLY A 230 SITE 2 AC2 6 HOH A 410 HOH A 440 SITE 1 AC3 6 ARG B 205 TYR B 206 ARG B 207 HOH B 406 SITE 2 AC3 6 HOH B 407 HOH B 410 CRYST1 98.334 47.707 47.832 90.00 90.00 90.00 P 21 21 21 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 0.010169 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020907 0.00000