HEADER PROTEIN TRANSPORT 03-MAR-14 4PQO TITLE STRUCTURE OF THE HUMAN SNX14 PX DOMAIN IN SPACE GROUP I41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-14; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PX DOMAIN (UNP RESIDUES 561-686); COMPND 5 SYNONYM: SNX14; COMPND 6 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: SNX14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SORTING NEXIN, PHOX HOMOLOGY DOMAIN, PHOSPHOINOSITIDE BINDING, KEYWDS 2 PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.MAS,S.NORWOOD,A.BUGARCIC,G.KINNA,N.LENEVA,O.KOVTUN,R.TEASDALE, AUTHOR 2 B.COLLINS REVDAT 3 28-FEB-24 4PQO 1 SEQADV REVDAT 2 29-OCT-14 4PQO 1 JRNL REVDAT 1 03-SEP-14 4PQO 0 JRNL AUTH C.MAS,S.J.NORWOOD,A.BUGARCIC,G.KINNA,N.LENEVA,O.KOVTUN, JRNL AUTH 2 R.GHAI,L.E.ONA YANEZ,J.L.DAVIS,R.D.TEASDALE,B.M.COLLINS JRNL TITL STRUCTURAL BASIS FOR DIFFERENT PHOSPHOINOSITIDE JRNL TITL 2 SPECIFICITIES OF THE PX DOMAINS OF SORTING NEXINS REGULATING JRNL TITL 3 G-PROTEIN SIGNALING. JRNL REF J.BIOL.CHEM. V. 289 28554 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 25148684 JRNL DOI 10.1074/JBC.M114.595959 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9067 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 432 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 20.2669 - 3.6757 0.96 2921 136 0.1518 0.1855 REMARK 3 2 3.6757 - 2.9203 0.96 2871 131 0.2122 0.2274 REMARK 3 3 2.9203 - 2.5500 0.94 2810 165 0.3051 0.3026 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.120 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 : 0.010 919 REMARK 3 ANGLE : 1.260 1242 REMARK 3 CHIRALITY : 0.089 128 REMARK 3 PLANARITY : 0.006 158 REMARK 3 DIHEDRAL : 18.770 342 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 562:630) REMARK 3 ORIGIN FOR THE GROUP (A): 35.2659 51.6003 13.9911 REMARK 3 T TENSOR REMARK 3 T11: 0.2302 T22: 0.3289 REMARK 3 T33: 0.3954 T12: 0.0301 REMARK 3 T13: 0.0896 T23: -0.0816 REMARK 3 L TENSOR REMARK 3 L11: 4.7876 L22: 4.0211 REMARK 3 L33: 6.3408 L12: -2.9513 REMARK 3 L13: 3.9960 L23: -1.6349 REMARK 3 S TENSOR REMARK 3 S11: 0.3097 S12: -0.2469 S13: -0.1235 REMARK 3 S21: -0.1008 S22: 0.2087 S23: 0.1827 REMARK 3 S31: 0.0604 S32: 0.0823 S33: -0.4248 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 631:686) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0094 52.2796 11.9390 REMARK 3 T TENSOR REMARK 3 T11: 0.1995 T22: 0.2980 REMARK 3 T33: 0.4520 T12: 0.0204 REMARK 3 T13: -0.0710 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 4.0950 L22: 5.2989 REMARK 3 L33: 4.8344 L12: -1.3473 REMARK 3 L13: -0.2614 L23: 0.4459 REMARK 3 S TENSOR REMARK 3 S11: 0.0395 S12: -0.1662 S13: 0.0546 REMARK 3 S21: -0.1713 S22: 0.1301 S23: 0.3953 REMARK 3 S31: 0.2015 S32: -0.3182 S33: -0.1583 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 4PQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085102. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 2013 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9067 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 61.405 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM CITRATE TRIBASIC, PH 5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 43.42000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 43.42000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.22000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.61000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.42000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.83000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.42000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.42000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.22000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 43.42000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 55.83000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 43.42000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 18.61000 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 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 GLY A 559 REMARK 465 SER A 560 REMARK 465 ASN A 561 REMARK 465 PRO A 577A REMARK 465 SER A 577B REMARK 465 SER A 577C REMARK 465 GLU A 577D REMARK 465 ARG A 577E REMARK 465 LYS A 577F REMARK 465 GLU A 577G REMARK 465 LYS A 577H REMARK 465 LYS A 577I REMARK 465 GLU A 577J REMARK 465 ARG A 577K REMARK 465 ASN A 599 REMARK 465 ASP A 600 REMARK 465 ARG A 601 REMARK 465 ARG A 602 REMARK 465 ALA A 603 REMARK 465 VAL A 604 REMARK 465 GLY A 605 REMARK 465 HIS A 606 REMARK 465 GLU A 607 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 GLU A 624 OG1 THR A 628 2.01 REMARK 500 O PHE A 634 O HOH A 713 2.14 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 ALA A 633 65.28 -154.76 REMARK 500 PRO A 635 -126.01 -101.88 REMARK 500 ASP A 636 -54.60 71.19 REMARK 500 GLU A 672 -36.69 64.96 REMARK 500 SER A 674 -1.42 -45.11 REMARK 500 ASN A 675 20.99 -150.39 REMARK 500 LEU A 678 -47.66 -24.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 574 PHE A 575 148.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PQP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SNX14 PX DOMAIN IN SPACE GROUP P43212 DBREF 4PQO A 561 686 UNP Q9Y5W7 SNX14_HUMAN 561 686 SEQADV 4PQO GLY A 559 UNP Q9Y5W7 EXPRESSION TAG SEQADV 4PQO SER A 560 UNP Q9Y5W7 EXPRESSION TAG SEQRES 1 A 128 GLY SER ASN LEU ALA ALA TRP LYS ILE SER ILE PRO TYR SEQRES 2 A 128 VAL ASP PHE PHE GLU ASP PRO SER SER GLU ARG LYS GLU SEQRES 3 A 128 LYS LYS GLU ARG ILE PRO VAL PHE CYS ILE ASP VAL GLU SEQRES 4 A 128 ARG ASN ASP ARG ARG ALA VAL GLY HIS GLU PRO GLU HIS SEQRES 5 A 128 TRP SER VAL TYR ARG ARG TYR LEU GLU PHE TYR VAL LEU SEQRES 6 A 128 GLU SER LYS LEU THR GLU PHE HIS GLY ALA PHE PRO ASP SEQRES 7 A 128 ALA GLN LEU PRO SER LYS ARG ILE ILE GLY PRO LYS ASN SEQRES 8 A 128 TYR GLU PHE LEU LYS SER LYS ARG GLU GLU PHE GLN GLU SEQRES 9 A 128 TYR LEU GLN LYS LEU LEU GLN HIS PRO GLU LEU SER ASN SEQRES 10 A 128 SER GLN LEU LEU ALA ASP PHE LEU SER PRO ASN FORMUL 2 HOH *23(H2 O) HELIX 1 1 ARG A 616 HIS A 631 1 16 HELIX 2 2 ASN A 649 SER A 655 1 7 HELIX 3 3 LYS A 656 HIS A 670 1 15 HELIX 4 4 SER A 676 LEU A 683 1 8 SHEET 1 A 3 LYS A 566 PHE A 574 0 SHEET 2 A 3 PRO A 587 GLU A 594 -1 O VAL A 588 N ASP A 573 SHEET 3 A 3 TRP A 611 ARG A 615 -1 O VAL A 613 N ILE A 591 CISPEP 1 GLY A 646 PRO A 647 0 -4.08 CRYST1 86.840 86.840 74.440 90.00 90.00 90.00 I 41 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 0.011515 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013434 0.00000