PDB Short entry for 1GL2 HEADER MEMBRANE PROTEIN 22-AUG-01 1GL2 TITLE CRYSTAL STRUCTURE OF AN ENDOSOMAL SNARE CORE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOBREVIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CORE FRAGMENT, RESIDUES 6-66; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SYNTAXIN 7; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: CORE FRAGMENT, RESIDUES 169-229; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1; COMPND 13 CHAIN: C; COMPND 14 FRAGMENT: CORE FRAGMENT, RESIDUES 140-200; COMPND 15 SYNONYM: VTI1B; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: SYNTAXIN 8; COMPND 19 CHAIN: D; COMPND 20 FRAGMENT: CORE FRAGMENT, RESIDUES 149-209; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 15 ORGANISM_COMMON: MOUSE; SOURCE 16 ORGANISM_TAXID: 10090; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 21 ORGANISM_COMMON: RAT; SOURCE 22 ORGANISM_TAXID: 10116; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE PROTEIN, MEMBRANE FUSION PROTEIN COMPLEX, COILED COIL, KEYWDS 2 TRANSMEMBRANE, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR W.ANTONIN,S.BECKER,R.JAHN,T.R.SCHNEIDER REVDAT 6 13-DEC-23 1GL2 1 REMARK REVDAT 5 08-MAY-19 1GL2 1 REMARK REVDAT 4 30-MAY-18 1GL2 1 TITLE REMARK ATOM REVDAT 3 24-FEB-09 1GL2 1 VERSN REVDAT 2 29-JAN-02 1GL2 1 JRNL REVDAT 1 15-JAN-02 1GL2 0 JRNL AUTH W.ANTONIN,D.FASSHAUER,S.BECKER,R.JAHN,T.R.SCHNEIDER JRNL TITL CRYSTAL STRUCTURE OF THE ENDOSOMAL SNARE COMPLEX REVEALS JRNL TITL 2 COMMON STRUCTURAL PRINCIPLES OF ALL SNARES. JRNL REF NAT.STRUCT.BIOL. V. 9 107 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11786915 JRNL DOI 10.1038/NSB746 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 0.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 14797 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) : 0.176 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 737 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) (%) : 85.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2143 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 118 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1792 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.34000 REMARK 3 B22 (A**2) : -2.53000 REMARK 3 B33 (A**2) : -4.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 13.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.580 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) : 1.120 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.580 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.710 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.980 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 66.79 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: NULL REMARK 4 REMARK 4 1GL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1290008503. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.20 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 : SIEMENS M18X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : COSMIC MIRRORS CMF12-38CU6 REMARK 200 OPTICS : COSMIC MIRRORS CMF12-38CU6 REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71259 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.03450 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.13700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.35 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1SFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 20 MG/ML OF REMARK 280 QUATERNARY COMPLEX IN 20MM TRIS-HCL AT PH 7.4 WELL SOLUTION: REMARK 280 0.1M NA-ACETATE AT PH 5.2, 2.5 M NA-FORMIAT, 15% GLYCEROL REMARK 280 HANGING DROPS WITH 2MUL + 2 MUL, PH 5.20, VAPOR DIFFUSION, REMARK 280 HANGING DROP 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 20.55000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 HIS A 4 REMARK 465 MET A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 GLY A 8 REMARK 465 ASN A 9 REMARK 465 ASP A 10 REMARK 465 ALA A 65 REMARK 465 ARG A 66 REMARK 465 GLY B 165 REMARK 465 SER B 166 REMARK 465 HIS B 167 REMARK 465 MET B 168 REMARK 465 ASN B 229 REMARK 465 GLY C 136 REMARK 465 SER C 137 REMARK 465 HIS C 138 REMARK 465 SER C 199 REMARK 465 ARG C 200 REMARK 465 GLY D 145 REMARK 465 SER D 146 REMARK 465 HIS D 147 REMARK 465 MET D 148 REMARK 465 GLN D 149 REMARK 465 GLU D 150 REMARK 465 GLN D 151 REMARK 465 VAL D 207 REMARK 465 ASP D 208 REMARK 465 ARG D 209 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 ARG A 11 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 13 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 14 CG OD1 ND2 REMARK 470 VAL A 64 O REMARK 470 ARG B 226 CG CD NE CZ NH1 NH2 REMARK 470 ALA B 228 O REMARK 470 MET C 198 O REMARK 470 ASP D 152 CG OD1 OD2 REMARK 470 ARG D 203 CG CD NE CZ NH1 NH2 REMARK 470 LEU D 206 O CG CD1 CD2 DBREF 1GL2 A 2 5 PDB 1GL2 1GL2 2 5 DBREF 1GL2 A 6 66 UNP Q9WUF4 Q9WUF4 6 66 DBREF 1GL2 B 165 168 PDB 1GL2 1GL2 165 168 DBREF 1GL2 B 169 229 UNP O70439 O70439 169 229 DBREF 1GL2 C 136 139 PDB 1GL2 1GL2 136 139 DBREF 1GL2 C 140 200 UNP O88384 VTL1_MOUSE 140 200 DBREF 1GL2 D 145 148 PDB 1GL2 1GL2 145 148 DBREF 1GL2 D 149 209 UNP Q9Z2Q7 STX8_RAT 149 209 SEQADV 1GL2 ASN B 229 UNP O70439 ASP 229 CONFLICT SEQRES 1 A 65 GLY SER HIS MET SER ALA GLY ASN ASP ARG VAL ARG ASN SEQRES 2 A 65 LEU GLN SER GLU VAL GLU GLY VAL LYS ASN ILE MET THR SEQRES 3 A 65 GLN ASN VAL GLU ARG ILE LEU ALA ARG GLY GLU ASN LEU SEQRES 4 A 65 ASP HIS LEU ARG ASN LYS THR GLU ASP LEU GLU ALA THR SEQRES 5 A 65 SER GLU HIS PHE LYS THR THR SER GLN LYS VAL ALA ARG SEQRES 1 B 65 GLY SER HIS MET HIS GLU ARG GLU SER SER ILE ARG GLN SEQRES 2 B 65 LEU GLU ALA ASP ILE MET ASP ILE ASN GLU ILE PHE LYS SEQRES 3 B 65 ASP LEU GLY MET MET ILE HIS GLU GLN GLY ASP VAL ILE SEQRES 4 B 65 ASP SER ILE GLU ALA ASN VAL GLU SER ALA GLU VAL HIS SEQRES 5 B 65 VAL GLN GLN ALA ASN GLN GLN LEU SER ARG ALA ALA ASN SEQRES 1 C 65 GLY SER HIS MET ASN ARG ALA THR GLN SER ILE GLU ARG SEQRES 2 C 65 SER HIS ARG ILE ALA THR GLU THR ASP GLN ILE GLY THR SEQRES 3 C 65 GLU ILE ILE GLU GLU LEU GLY GLU GLN ARG ASP GLN LEU SEQRES 4 C 65 GLU ARG THR LYS SER ARG LEU VAL ASN THR ASN GLU ASN SEQRES 5 C 65 LEU SER LYS SER ARG LYS ILE LEU ARG SER MET SER ARG SEQRES 1 D 65 GLY SER HIS MET GLN GLU GLN ASP ALA GLY LEU ASP ALA SEQRES 2 D 65 LEU SER SER ILE ILE SER ARG GLN LYS GLN MET GLY GLN SEQRES 3 D 65 GLU ILE GLY ASN GLU LEU ASP GLU GLN ASN GLU ILE ILE SEQRES 4 D 65 ASP ASP LEU ALA ASN LEU VAL GLU ASN THR ASP GLU LYS SEQRES 5 D 65 LEU ARG THR GLU ALA ARG ARG VAL THR LEU VAL ASP ARG FORMUL 5 HOH *234(H2 O) HELIX 1 1 ARG A 11 LYS A 63 1 53 HELIX 2 2 HIS B 169 ALA B 227 1 59 HELIX 3 3 ASN C 140 SER C 197 1 58 HELIX 4 4 ASP D 152 THR D 205 1 54 CRYST1 50.700 41.100 51.500 90.00 109.40 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 0.019724 0.000000 0.006946 0.00000 SCALE2 0.000000 0.024331 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020586 0.00000