HEADER PROTEIN TRANSPORT 06-NOV-15 5EMA TITLE CRYSTAL STRUCTURE OF THE SNX27 PDZ DOMAIN BOUND TO THE PHOSPHORYLATED TITLE 2 C-TERMINAL LRRC3B PDZ BINDING MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-27; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN (UNP RESIDUES 39-133); COMPND 5 SYNONYM: MAP-RESPONSIVE GENE PROTEIN,METHAMPHETAMINE-RESPONSIVE COMPND 6 TRANSCRIPT 1 PROTEIN,PDZ-PROTEIN MRT1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ASP-ASP-ILE-SEP-THR-VAL-VAL; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SNX27, MRT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS ENDOSOME, PDZ DOMAIN, SORTING NEXIN, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.M.COLLINS,T.CLAIRFEUILLE REVDAT 7 13-NOV-24 5EMA 1 REMARK REVDAT 6 27-SEP-23 5EMA 1 REMARK REVDAT 5 08-JAN-20 5EMA 1 REMARK REVDAT 4 27-SEP-17 5EMA 1 REMARK REVDAT 3 19-OCT-16 5EMA 1 JRNL REVDAT 2 21-SEP-16 5EMA 1 JRNL REVDAT 1 07-SEP-16 5EMA 0 JRNL AUTH T.CLAIRFEUILLE,C.MAS,A.S.CHAN,Z.YANG,M.TELLO-LAFOZ, JRNL AUTH 2 M.CHANDRA,J.WIDAGDO,M.C.KERR,B.PAUL,I.MERIDA,R.D.TEASDALE, JRNL AUTH 3 N.J.PAVLOS,V.ANGGONO,B.M.COLLINS JRNL TITL A MOLECULAR CODE FOR ENDOSOMAL RECYCLING OF PHOSPHORYLATED JRNL TITL 2 CARGOS BY THE SNX27-RETROMER COMPLEX. JRNL REF NAT.STRUCT.MOL.BIOL. V. 23 921 2016 JRNL REFN ESSN 1545-9985 JRNL PMID 27595347 JRNL DOI 10.1038/NSMB.3290 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 23811 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 36.7357 - 3.1713 0.93 1630 149 0.1717 0.1742 REMARK 3 2 3.1713 - 2.5173 0.99 1638 151 0.1673 0.1878 REMARK 3 3 2.5173 - 2.1991 0.99 1608 147 0.1439 0.1516 REMARK 3 4 2.1991 - 1.9981 0.98 1596 146 0.1384 0.1788 REMARK 3 5 1.9981 - 1.8549 0.98 1570 145 0.1464 0.1506 REMARK 3 6 1.8549 - 1.7455 0.97 1594 146 0.1554 0.1754 REMARK 3 7 1.7455 - 1.6581 0.97 1559 143 0.1552 0.1798 REMARK 3 8 1.6581 - 1.5859 0.97 1555 142 0.1554 0.1845 REMARK 3 9 1.5859 - 1.5249 0.97 1533 140 0.1600 0.1663 REMARK 3 10 1.5249 - 1.4723 0.97 1556 144 0.1692 0.2181 REMARK 3 11 1.4723 - 1.4262 0.96 1517 138 0.1796 0.2116 REMARK 3 12 1.4262 - 1.3854 0.96 1529 140 0.1949 0.2164 REMARK 3 13 1.3854 - 1.3490 0.95 1504 139 0.1886 0.2418 REMARK 3 14 1.3490 - 1.3161 0.89 1422 130 0.2377 0.2532 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.800 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 : 0.010 803 REMARK 3 ANGLE : 1.431 1088 REMARK 3 CHIRALITY : 0.078 127 REMARK 3 PLANARITY : 0.005 145 REMARK 3 DIHEDRAL : 13.506 303 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 5EMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215160. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 0.95370 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23850 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 48.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: 4Z8J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULPHATE AND 0.1 M SODIUM REMARK 280 ACETATE (PH 4.6), VAPOR DIFFUSION, 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 18.58550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.11450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.11450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.58550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.24500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 35 REMARK 465 SER A 36 REMARK 465 HIS A 37 REMARK 465 GLY A 38 REMARK 465 GLY A 39 REMARK 465 PRO B 0 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 HZ1 LYS A 97 O HOH A 301 1.54 REMARK 500 O HOH A 356 O HOH A 387 1.94 REMARK 500 NZ LYS A 97 O HOH A 301 1.98 REMARK 500 O HOH A 381 O HOH A 386 2.05 REMARK 500 O HOH A 365 O HOH A 424 2.07 REMARK 500 O HOH A 315 O HOH A 381 2.08 REMARK 500 ND2 ASN A 108 O HOH A 302 2.13 REMARK 500 O HOH A 400 O HOH A 433 2.18 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 126 -16.06 -143.11 REMARK 500 LYS A 126 -16.06 -149.92 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Z8J RELATED DB: PDB REMARK 900 RELATED ID: 5ELQ RELATED DB: PDB REMARK 900 RELATED ID: 5EM9 RELATED DB: PDB REMARK 900 RELATED ID: 5EMB RELATED DB: PDB DBREF 5EMA A 41 135 UNP Q8K4V4 SNX27_RAT 39 133 DBREF 5EMA B 0 7 PDB 5EMA 5EMA 0 7 SEQADV 5EMA GLY A 35 UNP Q8K4V4 EXPRESSION TAG SEQADV 5EMA SER A 36 UNP Q8K4V4 EXPRESSION TAG SEQADV 5EMA HIS A 37 UNP Q8K4V4 EXPRESSION TAG SEQADV 5EMA GLY A 38 UNP Q8K4V4 EXPRESSION TAG SEQADV 5EMA GLY A 39 UNP Q8K4V4 EXPRESSION TAG SEQADV 5EMA SER A 40 UNP Q8K4V4 EXPRESSION TAG SEQRES 1 A 101 GLY SER HIS GLY GLY SER PRO ARG VAL VAL ARG ILE VAL SEQRES 2 A 101 LYS SER GLU SER GLY TYR GLY PHE ASN VAL ARG GLY GLN SEQRES 3 A 101 VAL SER GLU GLY GLY GLN LEU ARG SER ILE ASN GLY GLU SEQRES 4 A 101 LEU TYR ALA PRO LEU GLN HIS VAL SER ALA VAL LEU PRO SEQRES 5 A 101 GLY GLY ALA ALA ASP ARG ALA GLY VAL ARG LYS GLY ASP SEQRES 6 A 101 ARG ILE LEU GLU VAL ASN GLY VAL ASN VAL GLU GLY ALA SEQRES 7 A 101 THR HIS LYS GLN VAL VAL ASP LEU ILE ARG ALA GLY GLU SEQRES 8 A 101 LYS GLU LEU ILE LEU THR VAL LEU SER VAL SEQRES 1 B 8 PRO ASP ASP ILE SEP THR VAL VAL HET SEP B 4 13 HET GOL A 201 13 HETNAM SEP PHOSPHOSERINE HETNAM GOL GLYCEROL HETSYN SEP PHOSPHONOSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *150(H2 O) HELIX 1 AA1 GLY A 88 GLY A 94 1 7 HELIX 2 AA2 THR A 113 ARG A 122 1 10 SHEET 1 AA1 4 ARG A 42 VAL A 47 0 SHEET 2 AA1 4 GLU A 127 LEU A 133 -1 O LEU A 128 N ILE A 46 SHEET 3 AA1 4 ARG A 100 VAL A 104 -1 N LEU A 102 O THR A 131 SHEET 4 AA1 4 VAL A 107 ASN A 108 -1 O VAL A 107 N VAL A 104 SHEET 1 AA2 3 HIS A 80 VAL A 84 0 SHEET 2 AA2 3 PHE A 55 GLY A 59 -1 N ARG A 58 O HIS A 80 SHEET 3 AA2 3 ILE B 3 VAL B 6 -1 O ILE B 3 N GLY A 59 SHEET 1 AA3 2 ARG A 68 ILE A 70 0 SHEET 2 AA3 2 GLU A 73 TYR A 75 -1 O GLU A 73 N ILE A 70 LINK C ILE B 3 N SEP B 4 1555 1555 1.32 LINK C SEP B 4 N THR B 5 1555 1555 1.33 SITE 1 AC1 7 ASN A 56 LEU A 74 ALA A 83 ASN A 105 SITE 2 AC1 7 GLU A 127 HOH A 310 HOH A 313 CRYST1 37.171 48.490 56.229 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 0.026903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017784 0.00000