PDB Short entry for 4Z8J HEADER PROTEIN TRANSPORT 09-APR-15 4Z8J TITLE CRYSTAL STRUCTURE OF THE SNX27 PDZ DOMAIN BOUND TO THE C-TERMINAL PTHR TITLE 2 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: C-TERMINAL PDZ BINDING MOTIF FROM PARATHYROID HORMONE COMPND 10 RECEPTOR (PTHR); COMPND 11 CHAIN: B; COMPND 12 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 PDZ DOMAIN, SNX27, PTHR, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.CLAIRFEUILLE,N.PAVLOS,B.M.COLLINS REVDAT 2 27-SEP-23 4Z8J 1 REMARK REVDAT 1 24-FEB-16 4Z8J 0 JRNL AUTH T.CLAIRFEUILLE,R.D.TEASDALE,B.M.COLLINS,N.PAVLOS JRNL TITL ROLE OF SNX27-RETROMER IN PTHR TRAFFICKING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.95 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 63961 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3238 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 14.8526 - 2.6965 0.94 2698 134 0.1728 0.1482 REMARK 3 2 2.6965 - 2.1424 1.00 2753 126 0.1417 0.1238 REMARK 3 3 2.1424 - 1.8722 1.00 2661 156 0.1307 0.1499 REMARK 3 4 1.8722 - 1.7013 1.00 2730 108 0.1318 0.1363 REMARK 3 5 1.7013 - 1.5795 1.00 2662 140 0.1242 0.1333 REMARK 3 6 1.5795 - 1.4864 1.00 2643 156 0.1229 0.1375 REMARK 3 7 1.4864 - 1.4121 1.00 2654 150 0.1230 0.1459 REMARK 3 8 1.4121 - 1.3506 1.00 2645 130 0.1202 0.1294 REMARK 3 9 1.3506 - 1.2987 1.00 2658 129 0.1219 0.1452 REMARK 3 10 1.2987 - 1.2539 1.00 2616 148 0.1220 0.1207 REMARK 3 11 1.2539 - 1.2147 1.00 2623 149 0.1279 0.1451 REMARK 3 12 1.2147 - 1.1800 1.00 2632 149 0.1221 0.1322 REMARK 3 13 1.1800 - 1.1489 1.00 2632 134 0.1162 0.1248 REMARK 3 14 1.1489 - 1.1209 1.00 2613 134 0.1241 0.1453 REMARK 3 15 1.1209 - 1.0954 1.00 2621 151 0.1268 0.1453 REMARK 3 16 1.0954 - 1.0721 1.00 2619 142 0.1506 0.1681 REMARK 3 17 1.0721 - 1.0507 1.00 2618 130 0.1649 0.2072 REMARK 3 18 1.0507 - 1.0309 1.00 2586 157 0.1620 0.1578 REMARK 3 19 1.0309 - 1.0125 1.00 2629 144 0.1656 0.1695 REMARK 3 20 1.0125 - 0.9953 1.00 2592 166 0.1916 0.1895 REMARK 3 21 0.9953 - 0.9792 1.00 2610 148 0.2038 0.1997 REMARK 3 22 0.9792 - 0.9642 1.00 2647 120 0.2331 0.2464 REMARK 3 23 0.9642 - 0.9500 1.00 2581 137 0.2433 0.2534 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.680 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 : 0.008 833 REMARK 3 ANGLE : 1.278 1136 REMARK 3 CHIRALITY : 0.068 132 REMARK 3 PLANARITY : 0.006 152 REMARK 3 DIHEDRAL : 11.446 327 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 4Z8J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208821. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.88560 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64036 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 15.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 1.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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: 3QDO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS/TRIS (PH 5.5) AND 2 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 18.53500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.86250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.31250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.86250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.53500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.31250 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: 1050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 33 REMARK 465 SER A 34 REMARK 465 HIS A 35 REMARK 465 GLY A 36 REMARK 465 GLY A 37 REMARK 465 GLN B 586 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 A 273 O HOH A 301 1.42 REMARK 500 O HOH A 333 O HOH A 362 1.93 REMARK 500 O HOH A 303 O HOH A 349 1.95 REMARK 500 O HOH A 202 O HOH A 287 1.99 REMARK 500 O HOH B 606 O HOH B 609 2.02 REMARK 500 N GLU B 587 O HOH B 601 2.06 REMARK 500 O GLY A 85 NH1 ARG A 90 2.09 REMARK 500 O HOH A 351 O HOH A 366 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 329 O HOH A 362 3554 1.73 REMARK 500 O ALA A 121 O HOH A 216 3554 2.16 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 124 -11.45 -143.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ELQ RELATED DB: PDB REMARK 900 RELATED ID: 5EM9 RELATED DB: PDB REMARK 900 RELATED ID: 5EMA RELATED DB: PDB REMARK 900 RELATED ID: 5EMB RELATED DB: PDB REMARK 900 RELATED ID: 5EMY RELATED DB: PDB DBREF 4Z8J A 39 133 UNP Q8K4V4 SNX27_RAT 39 133 DBREF 4Z8J B 586 593 PDB 4Z8J 4Z8J 586 593 SEQADV 4Z8J GLY A 33 UNP Q8K4V4 EXPRESSION TAG SEQADV 4Z8J SER A 34 UNP Q8K4V4 EXPRESSION TAG SEQADV 4Z8J HIS A 35 UNP Q8K4V4 EXPRESSION TAG SEQADV 4Z8J GLY A 36 UNP Q8K4V4 EXPRESSION TAG SEQADV 4Z8J GLY A 37 UNP Q8K4V4 EXPRESSION TAG SEQADV 4Z8J SER A 38 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 GLN GLU GLU TRP GLU THR VAL MET FORMUL 3 HOH *185(H2 O) HELIX 1 AA1 GLY A 86 GLY A 92 1 7 HELIX 2 AA2 THR A 111 ARG A 120 1 10 SHEET 1 AA1 4 ARG A 40 VAL A 45 0 SHEET 2 AA1 4 GLU A 125 LEU A 131 -1 O LEU A 126 N ILE A 44 SHEET 3 AA1 4 ARG A 98 VAL A 102 -1 N ARG A 98 O LEU A 131 SHEET 4 AA1 4 VAL A 105 ASN A 106 -1 O VAL A 105 N VAL A 102 SHEET 1 AA2 3 HIS A 78 VAL A 82 0 SHEET 2 AA2 3 PHE A 53 GLN A 58 -1 N ARG A 56 O HIS A 78 SHEET 3 AA2 3 GLU B 588 MET B 593 -1 O MET B 593 N PHE A 53 SHEET 1 AA3 2 ARG A 66 ILE A 68 0 SHEET 2 AA3 2 GLU A 71 TYR A 73 -1 O TYR A 73 N ARG A 66 CRYST1 37.070 48.625 55.725 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 0.026976 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020566 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017945 0.00000