10 20 30 40 50 60 70 80 1RSY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER CALCIUM/PHOSPHOLIPID BINDING PROTEIN 01-FEB-95 1RSY
TITLE STRUCTURE OF THE FIRST C2-DOMAIN OF SYNAPTOTAGMIN I: A TITLE 2 NOVEL CA2+(SLASH)PHOSPHOLIPID BINDING FOLD
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN I; COMPND 3 CHAIN: A; COMPND 4 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIAL; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-KG
KEYWDS CALCIUM/PHOSPHOLIPID BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR R.B.SUTTON,S.R.SPRANG
REVDAT 3 24-FEB-09 1RSY 1 VERSN REVDAT 2 01-APR-03 1RSY 1 JRNL REVDAT 1 08-MAY-95 1RSY 0
JRNL AUTH R.B.SUTTON,B.A.DAVLETOV,A.M.BERGHUIS,T.C.SUDHOF, JRNL AUTH 2 S.R.SPRANG JRNL TITL STRUCTURE OF THE FIRST C2 DOMAIN OF SYNAPTOTAGMIN JRNL TITL 2 I: A NOVEL CA2+/PHOSPHOLIPID-BINDING FOLD. JRNL REF CELL(CAMBRIDGE,MASS.) V. 80 929 1995 JRNL REFN ISSN 0092-8674 JRNL PMID 7697723 JRNL DOI 10.1016/0092-8674(95)90296-1
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.A.DAVLETOV,T.C.SUDHOF REMARK 1 TITL A SINGLE C2 DOMAIN FROM SYNAPTOTAGMIN I IS REMARK 1 TITL 2 SUFFICIENT FOR HIGH AFFINITY REMARK 1 TITL 3 CA2+(SLASH)PHOSPHOLIPID BINDING REMARK 1 REF J.BIOL.CHEM. V. 268 26386 1993 REMARK 1 REFN ISSN 0021-9258
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 9851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.58 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.39 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.35 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1RSY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11214 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 19.45000 REMARK 290 SMTRY3 2 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: 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 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 1 REMARK 465 SER A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 4 REMARK 465 ILE A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 GLU A 132 REMARK 465 LYS A 133 REMARK 465 GLU A 134 REMARK 465 GLU A 135 REMARK 465 PRO A 136 REMARK 465 LYS A 137 REMARK 465 GLU A 138 REMARK 465 GLU A 139 REMARK 465 GLU A 266
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 LYS A 192 CG CD CE NZ
REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 MET A 173 REMARK 475 GLY A 174 REMARK 475 LYS A 189 REMARK 475 LYS A 190 REMARK 475 LYS A 191 REMARK 475 LYS A 192
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 338 DISTANCE = 7.60 ANGSTROMS
REMARK 600 REMARK 600 HETEROGEN REMARK 600 HET GROUP TRIVIAL NAME: SULFATE REMARK 600 EMPIRICAL FORMULA: SO4 REMARK 600 NUMBER OF ATOMS IN GROUP: 5 REMARK 600 ADDITIONAL COMMENTS: SULFATE THOUGHT TO MIMIC PHOSPHOLIPID REMARK 600 BINDING SITE REMARK 600 REMARK 600 WATER HOH 154 IS THE SITE OF CALCIUM BINDING.
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 271
DBREF 1RSY A 132 266 UNP P21707 SYT1_RAT 132 266
SEQADV 1RSY ASP A 14F UNP P21707 THR 128 CONFLICT SEQADV 1RSY SER A 15F UNP P21707 ASP 129 CONFLICT SEQADV 1RSY MET A 16F UNP P21707 GLY 130 CONFLICT SEQADV 1RSY VAL A 17F UNP P21707 GLU 131 CONFLICT SEQADV 1RSY ASP A 188 UNP P21707 GLU 188 CONFLICT
SEQRES 1 A 152 GLY SER PRO GLY ILE SER GLY GLY GLY GLY GLY ILE LEU SEQRES 2 A 152 ASP SER MET VAL GLU LYS GLU GLU PRO LYS GLU GLU GLU SEQRES 3 A 152 LYS LEU GLY LYS LEU GLN TYR SER LEU ASP TYR ASP PHE SEQRES 4 A 152 GLN ASN ASN GLN LEU LEU VAL GLY ILE ILE GLN ALA ALA SEQRES 5 A 152 GLU LEU PRO ALA LEU ASP MET GLY GLY THR SER ASP PRO SEQRES 6 A 152 TYR VAL LYS VAL PHE LEU LEU PRO ASP LYS LYS LYS LYS SEQRES 7 A 152 PHE GLU THR LYS VAL HIS ARG LYS THR LEU ASN PRO VAL SEQRES 8 A 152 PHE ASN GLU GLN PHE THR PHE LYS VAL PRO TYR SER GLU SEQRES 9 A 152 LEU GLY GLY LYS THR LEU VAL MET ALA VAL TYR ASP PHE SEQRES 10 A 152 ASP ARG PHE SER LYS HIS ASP ILE ILE GLY GLU PHE LYS SEQRES 11 A 152 VAL PRO MET ASN THR VAL ASP PHE GLY HIS VAL THR GLU SEQRES 12 A 152 GLU TRP ARG ASP LEU GLN SER ALA GLU
HET SO4 A 271 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *80(H2 O)
HELIX 1 1 GLY A 10F SER A 15F 1 6 HELIX 2 2 TYR A 216 GLY A 221 1 6 HELIX 3 3 MET A 247 THR A 249 5 3
SHEET 1 A 4 THR A 256 ASP A 261 0 SHEET 2 A 4 LYS A 144 ASP A 152 -1 N LEU A 149 O THR A 256 SHEET 3 A 4 GLN A 157 ALA A 166 -1 N ALA A 166 O LYS A 144 SHEET 4 A 4 GLU A 208 PHE A 212 -1 N PHE A 212 O LEU A 158 SHEET 1 B 3 PRO A 179 LEU A 186 0 SHEET 2 B 3 THR A 223 ASP A 230 -1 N TYR A 229 O TYR A 180 SHEET 3 B 3 ASP A 238 PRO A 246 -1 N VAL A 245 O LEU A 224
CISPEP 1 LEU A 186 PRO A 187 0 0.33
SITE 1 AC1 2 ARG A 199 ARG A 233
CRYST1 42.300 38.900 44.600 90.00 96.90 90.00 P 1 21 1 2
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 0.023641 0.000000 0.002861 0.00000
SCALE2 0.000000 0.025707 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022585 0.00000