HEADER PROTEIN TRANSPORT 04-FEB-13 4J2C TITLE GARP-SNARE INTERACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTAXIN-6; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 3-110; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 51 HOMOLOG; COMPND 8 CHAIN: B, D; COMPND 9 FRAGMENT: UNP RESIDUES 33-49; COMPND 10 SYNONYM: ANOTHER NEW GENE 2 PROTEIN, PROTEIN FAT-FREE HOMOLOG; COMPND 11 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: STX6; 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 TETHERING COMPLEX, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.ABASCAL-PALACIOS,C.SCHINDLER,A.L.ROJAS,J.S.BONIFACINO,A.HIERRO REVDAT 3 28-FEB-24 4J2C 1 REMARK SEQADV REVDAT 2 15-NOV-17 4J2C 1 REMARK REVDAT 1 25-DEC-13 4J2C 0 JRNL AUTH G.ABASCAL-PALACIOS,C.SCHINDLER,A.L.ROJAS,J.S.BONIFACINO, JRNL AUTH 2 A.HIERRO JRNL TITL STRUCTURAL BASIS FOR THE INTERACTION OF THE GOLGI-ASSOCIATED JRNL TITL 2 RETROGRADE PROTEIN COMPLEX WITH THE T-SNARE SYNTAXIN 6. JRNL REF STRUCTURE V. 21 1698 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23932592 JRNL DOI 10.1016/J.STR.2013.06.025 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.1_357 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 19085 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.410 REMARK 3 FREE R VALUE TEST SET COUNT : 1032 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 27.2219 - 3.4453 0.93 2780 172 0.1166 0.1566 REMARK 3 2 3.4453 - 2.7354 0.93 2719 159 0.1309 0.1788 REMARK 3 3 2.7354 - 2.3899 0.92 2692 138 0.1601 0.2084 REMARK 3 4 2.3899 - 2.1715 0.90 2592 161 0.1672 0.2218 REMARK 3 5 2.1715 - 2.0159 0.89 2608 133 0.1952 0.2400 REMARK 3 6 2.0159 - 1.8971 0.87 2487 112 0.2075 0.2728 REMARK 3 7 1.8971 - 1.8021 0.76 2200 115 0.2528 0.2809 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 : 0.36 REMARK 3 B_SOL : 31.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.01250 REMARK 3 B22 (A**2) : -2.90390 REMARK 3 B33 (A**2) : -1.10860 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.54380 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.4980 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1965 REMARK 3 ANGLE : 0.827 2654 REMARK 3 CHIRALITY : 0.052 301 REMARK 3 PLANARITY : 0.003 342 REMARK 3 DIHEDRAL : 14.187 738 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 4J2C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19877 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.35800 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 (%): 35.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 100MM AMMONIUM REMARK 280 DIHYDROGEN PHOSPHATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.83000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 1160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 109 REMARK 465 SER A 110 REMARK 465 GLU B 45 REMARK 465 GLY B 46 REMARK 465 GLU B 47 REMARK 465 ALA B 48 REMARK 465 ALA B 49 REMARK 465 SER C 36 REMARK 465 THR C 37 REMARK 465 ALA C 38 REMARK 465 SER C 110 REMARK 465 GLU D 45 REMARK 465 GLY D 46 REMARK 465 GLU D 47 REMARK 465 ALA D 48 REMARK 465 ALA D 49 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE C 57 CA CB CG1 CG2 CD1 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 OD2 ASP A 63 O HOH A 218 2.17 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 PRO A 35 33.18 -66.76 REMARK 500 MET A 106 -68.11 -105.17 REMARK 500 ASN C 74 63.35 -150.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 4J2C A 3 110 UNP O43752 STX6_HUMAN 3 110 DBREF 4J2C B 33 49 UNP Q9UID3 VPS51_HUMAN 33 49 DBREF 4J2C C 3 110 UNP O43752 STX6_HUMAN 3 110 DBREF 4J2C D 33 49 UNP Q9UID3 VPS51_HUMAN 33 49 SEQADV 4J2C GLY A 1 UNP O43752 EXPRESSION TAG SEQADV 4J2C ALA A 2 UNP O43752 EXPRESSION TAG SEQADV 4J2C GLY C 1 UNP O43752 EXPRESSION TAG SEQADV 4J2C ALA C 2 UNP O43752 EXPRESSION TAG SEQRES 1 A 110 GLY ALA MET GLU ASP PRO PHE PHE VAL VAL LYS GLY GLU SEQRES 2 A 110 VAL GLN LYS ALA VAL ASN THR ALA GLN GLY LEU PHE GLN SEQRES 3 A 110 ARG TRP THR GLU LEU LEU GLN ASP PRO SER THR ALA THR SEQRES 4 A 110 ARG GLU GLU ILE ASP TRP THR THR ASN GLU LEU ARG ASN SEQRES 5 A 110 ASN LEU ARG SER ILE GLU TRP ASP LEU GLU ASP LEU ASP SEQRES 6 A 110 GLU THR ILE SER ILE VAL GLU ALA ASN PRO ARG LYS PHE SEQRES 7 A 110 ASN LEU ASP ALA THR GLU LEU SER ILE ARG LYS ALA PHE SEQRES 8 A 110 ILE THR SER THR ARG GLN VAL VAL ARG ASP MET LYS ASP SEQRES 9 A 110 GLN MET SER THR SER SER SEQRES 1 B 17 ALA HIS GLY MET LEU LYS LEU TYR TYR GLY LEU SER GLU SEQRES 2 B 17 GLY GLU ALA ALA SEQRES 1 C 110 GLY ALA MET GLU ASP PRO PHE PHE VAL VAL LYS GLY GLU SEQRES 2 C 110 VAL GLN LYS ALA VAL ASN THR ALA GLN GLY LEU PHE GLN SEQRES 3 C 110 ARG TRP THR GLU LEU LEU GLN ASP PRO SER THR ALA THR SEQRES 4 C 110 ARG GLU GLU ILE ASP TRP THR THR ASN GLU LEU ARG ASN SEQRES 5 C 110 ASN LEU ARG SER ILE GLU TRP ASP LEU GLU ASP LEU ASP SEQRES 6 C 110 GLU THR ILE SER ILE VAL GLU ALA ASN PRO ARG LYS PHE SEQRES 7 C 110 ASN LEU ASP ALA THR GLU LEU SER ILE ARG LYS ALA PHE SEQRES 8 C 110 ILE THR SER THR ARG GLN VAL VAL ARG ASP MET LYS ASP SEQRES 9 C 110 GLN MET SER THR SER SER SEQRES 1 D 17 ALA HIS GLY MET LEU LYS LEU TYR TYR GLY LEU SER GLU SEQRES 2 D 17 GLY GLU ALA ALA FORMUL 5 HOH *507(H2 O) HELIX 1 1 PRO A 6 ASP A 34 1 29 HELIX 2 2 THR A 39 ASN A 74 1 36 HELIX 3 3 ASN A 74 ASN A 79 1 6 HELIX 4 4 ASP A 81 THR A 108 1 28 HELIX 5 5 HIS B 34 GLY B 42 1 9 HELIX 6 6 PRO C 6 ASP C 34 1 29 HELIX 7 7 ARG C 40 ASN C 74 1 35 HELIX 8 8 ASN C 74 ASN C 79 1 6 HELIX 9 9 ASP C 81 SER C 109 1 29 HELIX 10 10 HIS D 34 GLY D 42 1 9 CRYST1 41.636 45.660 58.338 90.00 90.04 90.00 P 1 21 1 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 0.024018 0.000000 0.000016 0.00000 SCALE2 0.000000 0.021901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017141 0.00000