HEADER ENDOCYTOSIS/EXOCYTOSIS 09-MAY-00 1EZ3 TITLE CRYSTAL STRUCTURE OF THE NEURONAL T-SNARE SYNTAXIN-1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTAXIN-1A; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 SYNONYM: SYNAPTOTAGMIN ASSOCIATED 35 KDA PROTEIN, P35A, NEURON- COMPND 6 SPECIFIC ANTIGEN HPC-1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: BRAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLM1 T7 PROMOTER PLASMID KEYWDS THREE HELIX BUNDLE, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.C.LERMAN,J.ROBBLEE,R.FAIRMAN,F.M.HUGHSON REVDAT 5 07-FEB-24 1EZ3 1 REMARK REVDAT 4 24-FEB-09 1EZ3 1 VERSN REVDAT 3 06-SEP-00 1EZ3 1 JRNL REVDAT 2 14-JUN-00 1EZ3 1 REMARK REVDAT 1 07-JUN-00 1EZ3 0 JRNL AUTH J.C.LERMAN,J.ROBBLEE,R.FAIRMAN,F.M.HUGHSON JRNL TITL STRUCTURAL ANALYSIS OF THE NEURONAL SNARE PROTEIN JRNL TITL 2 SYNTAXIN-1A. JRNL REF BIOCHEMISTRY V. 39 8470 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10913252 JRNL DOI 10.1021/BI0003994 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1185796.740 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 29081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1456 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4602 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 236 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3068 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 422 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.62000 REMARK 3 B22 (A**2) : -4.76000 REMARK 3 B33 (A**2) : -6.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.27000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 53.64 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED MAXIMUM LIKELIHOOD USING REMARK 3 AMPLITUDES AND PHASE PROBABILITY DISTRIBUTION. REMARK 4 REMARK 4 1EZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000011048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OTHER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48323 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.748 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.530 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, SODIUM ACETATE, DTT, PH 5.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296.0K 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 49.78000 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, 3 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 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 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 VAL A 24 REMARK 465 ASP A 25 REMARK 465 GLN A 150 REMARK 465 VAL B 24 REMARK 465 ASP B 25 REMARK 465 ARG B 26 REMARK 465 VAL C 24 REMARK 465 ASP C 25 REMARK 465 GLN C 150 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 148 N - CA - C ANGL. DEV. = 19.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1EZ3 A 24 150 UNP P32851 STX1A_RAT 24 150 DBREF 1EZ3 B 24 150 UNP P32851 STX1A_RAT 24 150 DBREF 1EZ3 C 24 150 UNP P32851 STX1A_RAT 24 150 SEQRES 1 A 127 VAL ASP ARG ASP ARG PHE MET ASP GLU PHE PHE GLU GLN SEQRES 2 A 127 VAL GLU GLU ILE ARG GLY PHE ILE ASP LYS ILE ALA GLU SEQRES 3 A 127 ASN VAL GLU GLU VAL LYS ARG LYS HIS SER ALA ILE LEU SEQRES 4 A 127 ALA SER PRO ASN PRO ASP GLU LYS THR LYS GLU GLU LEU SEQRES 5 A 127 GLU GLU LEU MET SER ASP ILE LYS LYS THR ALA ASN LYS SEQRES 6 A 127 VAL ARG SER LYS LEU LYS SER ILE GLU GLN SER ILE GLU SEQRES 7 A 127 GLN GLU GLU GLY LEU ASN ARG SER SER ALA ASP LEU ARG SEQRES 8 A 127 ILE ARG LYS THR GLN HIS SER THR LEU SER ARG LYS PHE SEQRES 9 A 127 VAL GLU VAL MET SER GLU TYR ASN ALA THR GLN SER ASP SEQRES 10 A 127 TYR ARG GLU ARG CYS LYS GLY ARG ILE GLN SEQRES 1 B 127 VAL ASP ARG ASP ARG PHE MET ASP GLU PHE PHE GLU GLN SEQRES 2 B 127 VAL GLU GLU ILE ARG GLY PHE ILE ASP LYS ILE ALA GLU SEQRES 3 B 127 ASN VAL GLU GLU VAL LYS ARG LYS HIS SER ALA ILE LEU SEQRES 4 B 127 ALA SER PRO ASN PRO ASP GLU LYS THR LYS GLU GLU LEU SEQRES 5 B 127 GLU GLU LEU MET SER ASP ILE LYS LYS THR ALA ASN LYS SEQRES 6 B 127 VAL ARG SER LYS LEU LYS SER ILE GLU GLN SER ILE GLU SEQRES 7 B 127 GLN GLU GLU GLY LEU ASN ARG SER SER ALA ASP LEU ARG SEQRES 8 B 127 ILE ARG LYS THR GLN HIS SER THR LEU SER ARG LYS PHE SEQRES 9 B 127 VAL GLU VAL MET SER GLU TYR ASN ALA THR GLN SER ASP SEQRES 10 B 127 TYR ARG GLU ARG CYS LYS GLY ARG ILE GLN SEQRES 1 C 127 VAL ASP ARG ASP ARG PHE MET ASP GLU PHE PHE GLU GLN SEQRES 2 C 127 VAL GLU GLU ILE ARG GLY PHE ILE ASP LYS ILE ALA GLU SEQRES 3 C 127 ASN VAL GLU GLU VAL LYS ARG LYS HIS SER ALA ILE LEU SEQRES 4 C 127 ALA SER PRO ASN PRO ASP GLU LYS THR LYS GLU GLU LEU SEQRES 5 C 127 GLU GLU LEU MET SER ASP ILE LYS LYS THR ALA ASN LYS SEQRES 6 C 127 VAL ARG SER LYS LEU LYS SER ILE GLU GLN SER ILE GLU SEQRES 7 C 127 GLN GLU GLU GLY LEU ASN ARG SER SER ALA ASP LEU ARG SEQRES 8 C 127 ILE ARG LYS THR GLN HIS SER THR LEU SER ARG LYS PHE SEQRES 9 C 127 VAL GLU VAL MET SER GLU TYR ASN ALA THR GLN SER ASP SEQRES 10 C 127 TYR ARG GLU ARG CYS LYS GLY ARG ILE GLN FORMUL 4 HOH *422(H2 O) HELIX 1 1 ASP A 27 SER A 64 1 38 HELIX 2 2 ASP A 68 GLY A 105 1 38 HELIX 3 3 SER A 110 GLY A 147 1 38 HELIX 4 4 ASP B 27 ALA B 63 1 37 HELIX 5 5 ASP B 68 GLY B 105 1 38 HELIX 6 6 SER B 110 LYS B 146 1 37 HELIX 7 7 ARG C 28 SER C 64 1 37 HELIX 8 8 ASP C 68 GLU C 104 1 37 HELIX 9 9 SER C 110 GLY C 147 1 38 CRYST1 35.410 99.560 54.960 90.00 97.46 90.00 P 1 21 1 6 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 0.028241 0.000000 0.003698 0.00000 SCALE2 0.000000 0.010044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018350 0.00000