HEADER ENDOCYTOSIS/EXOCYTOSIS 16-SEP-05 2D2S TITLE CRYSTAL STRUCTURE OF THE EXO84P C-TERMINAL DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXOCYST COMPLEX COMPONENT EXO84; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXO84P C-TERMINAL DOMAINS; COMPND 5 SYNONYM: EXOCYST COMPLEX PROTEIN OF 84 KDA, U1-SNP1 ASSOCIATING COMPND 6 PROTEIN 3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS TETHERING COMPLEX, EXOCYST, EXO84P, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.DONG,A.H.HUTAGALUNG,C.FU,P.NOVICK,K.M.REINISCH REVDAT 4 13-MAR-24 2D2S 1 SEQADV REVDAT 3 24-FEB-09 2D2S 1 VERSN REVDAT 2 17-JAN-06 2D2S 1 JRNL REVDAT 1 01-NOV-05 2D2S 0 JRNL AUTH G.DONG,A.H.HUTAGALUNG,C.FU,P.NOVICK,K.M.REINISCH JRNL TITL THE STRUCTURES OF EXOCYST SUBUNIT EXO70P AND THE EXO84P JRNL TITL 2 C-TERMINAL DOMAINS REVEAL A COMMON MOTIF JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 1094 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 16249794 JRNL DOI 10.1038/NSMB1017 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12362 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.269 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1101 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 : 1742 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 2D2S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000024916. 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 : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13025 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL 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) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.2 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3000, ISO-PROPANOL, SODIUM REMARK 280 CLORIDE, DITHIOTHREITOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 104.56500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.42500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 156.84750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.42500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.28250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.42500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.42500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 156.84750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.42500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.42500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.28250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 104.56500 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 519 REMARK 465 SER A 520 REMARK 465 HIS A 521 REMARK 465 MET A 522 REMARK 465 SER A 523 REMARK 465 ARG A 524 REMARK 465 GLU A 571 REMARK 465 ARG A 572 REMARK 465 ILE A 573 REMARK 465 SER A 574 REMARK 465 ASP A 575 REMARK 465 GLU A 576 REMARK 465 GLU A 577 REMARK 465 GLY A 648 REMARK 465 SER A 649 REMARK 465 ASP A 712 REMARK 465 GLU A 713 REMARK 465 MET A 714 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 PRO A 653 CA - N - CD ANGL. DEV. = -11.5 DEGREES 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 LEU A 604 -16.00 -47.65 REMARK 500 ASN A 607 -69.87 -94.00 REMARK 500 LYS A 613 -70.67 -50.42 REMARK 500 GLN A 646 40.39 -64.14 REMARK 500 VAL A 662 -75.99 -41.55 REMARK 500 ILE A 663 -70.75 -26.28 REMARK 500 ARG A 664 -83.66 -48.30 REMARK 500 PHE A 679 34.74 -83.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B1E RELATED DB: PDB REMARK 900 EXO70P DBREF 2D2S A 523 753 UNP P38261 EXO84_YEAST 523 753 SEQADV 2D2S GLY A 519 UNP P38261 CLONING ARTIFACT SEQADV 2D2S SER A 520 UNP P38261 CLONING ARTIFACT SEQADV 2D2S HIS A 521 UNP P38261 CLONING ARTIFACT SEQADV 2D2S MET A 522 UNP P38261 CLONING ARTIFACT SEQRES 1 A 235 GLY SER HIS MET SER ARG ASP MET SER SER THR ALA GLN SEQRES 2 A 235 ARG LEU LYS PHE LEU ASP GLU GLY VAL GLU GLU ILE ASP SEQRES 3 A 235 ILE GLU LEU ALA ARG LEU ARG PHE GLU SER ALA VAL GLU SEQRES 4 A 235 THR LEU LEU ASP ILE GLU SER GLN LEU GLU ASP LEU SER SEQRES 5 A 235 GLU ARG ILE SER ASP GLU GLU LEU MET LEU LEU ASN LEU SEQRES 6 A 235 ILE SER LEU LYS ILE GLU GLN ARG ARG GLU ALA ILE SER SEQRES 7 A 235 SER LYS LEU SER GLN SER ILE LEU SER SER ASN GLU ILE SEQRES 8 A 235 VAL HIS LEU LYS SER GLY THR GLU ASN MET ILE LYS LEU SEQRES 9 A 235 GLY LEU PRO GLU GLN ALA LEU ASP LEU PHE LEU GLN ASN SEQRES 10 A 235 ARG SER ASN PHE ILE GLN ASP LEU ILE LEU GLN ILE GLY SEQRES 11 A 235 SER VAL ASP ASN PRO THR ASN TYR LEU THR GLN LEU ALA SEQRES 12 A 235 VAL ILE ARG PHE GLN THR ILE LYS LYS THR VAL GLU ASP SEQRES 13 A 235 PHE GLN ASP ILE PHE LYS GLU LEU GLY ALA LYS ILE SER SEQRES 14 A 235 SER ILE LEU VAL ASP TRP CYS SER ASP GLU VAL ASP ASN SEQRES 15 A 235 HIS PHE LYS LEU ILE ASP LYS GLN LEU LEU ASN ASP GLU SEQRES 16 A 235 MET LEU SER PRO GLY SER ILE LYS SER SER ARG LYS GLN SEQRES 17 A 235 ILE ASP GLY LEU LYS ALA VAL GLY LEU ASP PHE VAL TYR SEQRES 18 A 235 LYS LEU ASP GLU PHE ILE LYS LYS ASN SER ASP LYS ILE SEQRES 19 A 235 ARG HELIX 1 1 SER A 527 ARG A 549 1 23 HELIX 2 2 ARG A 551 LEU A 569 1 19 HELIX 3 3 LEU A 578 SER A 605 1 28 HELIX 4 4 GLU A 608 LEU A 622 1 15 HELIX 5 5 LEU A 624 GLN A 646 1 23 HELIX 6 6 ASN A 652 PHE A 679 1 28 HELIX 7 7 GLY A 683 LEU A 709 1 27 HELIX 8 8 SER A 716 GLY A 729 1 14 HELIX 9 9 LEU A 730 GLY A 734 5 5 HELIX 10 10 PHE A 737 LYS A 747 1 11 HELIX 11 11 ASN A 748 ILE A 752 5 5 CRYST1 54.850 54.850 209.130 90.00 90.00 90.00 P 43 21 2 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 0.018232 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018232 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004782 0.00000