HEADER GTPASE ACTIVATION 10-JUL-96 1GND TITLE GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ALPHA-ISOFORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 TISSUE: BRAIN; SOURCE 6 GENE: BOVGDI; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11DHIS; SOURCE 10 EXPRESSION_SYSTEM_GENE: BOVGDI KEYWDS GTPASE ACTIVATION EXPDTA X-RAY DIFFRACTION AUTHOR I.SCHALK,K.ZENG,S.-K.WU,E.A.STURA,J.METTESON,M.HUANG,A.TANDON, AUTHOR 2 I.A.WILSON,W.E.BALCH REVDAT 3 07-FEB-24 1GND 1 REMARK REVDAT 2 24-FEB-09 1GND 1 VERSN REVDAT 1 12-FEB-97 1GND 0 JRNL AUTH I.SCHALK,K.ZENG,S.K.WU,E.A.STURA,J.MATTESON,M.HUANG, JRNL AUTH 2 A.TANDON,I.A.WILSON,W.E.BALCH JRNL TITL STRUCTURE AND MUTATIONAL ANALYSIS OF RAB GDP-DISSOCIATION JRNL TITL 2 INHIBITOR. JRNL REF NATURE V. 381 42 1996 JRNL REFN ISSN 0028-0836 JRNL PMID 8609986 JRNL DOI 10.1038/381042A0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.J.SCHALK,E.A.STURA,J.MATTESON,I.A.WILSON,W.E.BALCH REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC DATA FOR REMARK 1 TITL 2 RAB GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR (RABGDI) FROM REMARK 1 TITL 3 BOVINE BRAIN REMARK 1 REF J.MOL.BIOL. V. 244 469 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.81 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) : 1.81 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 33282 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) : 0.198 REMARK 3 FREE R VALUE : 0.275 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 : 3405 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 418 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.20 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) : 0.20 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) : 1.660 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 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 1GND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-94 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN V. 2.1 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42588 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 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 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 (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 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 21.75000 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 PHE A 431 REMARK 465 GLU A 432 REMARK 465 ASN A 433 REMARK 465 MET A 434 REMARK 465 LYS A 435 REMARK 465 ARG A 436 REMARK 465 LYS A 437 REMARK 465 GLN A 438 REMARK 465 ASN A 439 REMARK 465 ASP A 440 REMARK 465 VAL A 441 REMARK 465 PHE A 442 REMARK 465 GLY A 443 REMARK 465 GLU A 444 REMARK 465 ALA A 445 REMARK 465 ASP A 446 REMARK 465 GLN A 447 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 GLU A 95 19.48 83.81 REMARK 500 GLU A 152 -7.16 -56.92 REMARK 500 ASN A 165 -37.56 -134.02 REMARK 500 LEU A 216 -73.15 -10.87 REMARK 500 ALA A 217 121.28 69.79 REMARK 500 ARG A 218 -177.17 -46.55 REMARK 500 TYR A 219 -9.60 62.53 REMARK 500 LYS A 221 -95.59 -79.32 REMARK 500 ASP A 257 144.99 -170.31 REMARK 500 MET A 260 142.71 170.61 REMARK 500 GLU A 261 -86.78 -134.54 REMARK 500 ASN A 262 -92.66 -62.62 REMARK 500 LYS A 264 -93.51 58.67 REMARK 500 VAL A 265 -150.92 40.85 REMARK 500 GLU A 374 -77.64 16.04 REMARK 500 PRO A 375 93.99 -65.59 REMARK 500 GLU A 395 -74.66 75.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GND A 1 447 UNP P21856 GDIA_BOVIN 1 447 SEQRES 1 A 447 MET ASP GLU GLU TYR ASP VAL ILE VAL LEU GLY THR GLY SEQRES 2 A 447 LEU THR GLU CYS ILE LEU SER GLY ILE MET SER VAL ASN SEQRES 3 A 447 GLY LYS LYS VAL LEU HIS MET ASP ARG ASN PRO TYR TYR SEQRES 4 A 447 GLY GLY GLU SER SER SER ILE THR PRO LEU GLU GLU LEU SEQRES 5 A 447 TYR LYS ARG PHE GLN LEU LEU GLU GLY PRO PRO GLU THR SEQRES 6 A 447 MET GLY ARG GLY ARG ASP TRP ASN VAL ASP LEU ILE PRO SEQRES 7 A 447 LYS PHE LEU MET ALA ASN GLY GLN LEU VAL LYS MET LEU SEQRES 8 A 447 LEU TYR THR GLU VAL THR ARG TYR LEU ASP PHE LYS VAL SEQRES 9 A 447 VAL GLU GLY SER PHE VAL TYR LYS GLY GLY LYS ILE TYR SEQRES 10 A 447 LYS VAL PRO SER THR GLU THR GLU ALA LEU ALA SER ASN SEQRES 11 A 447 LEU MET GLY MET PHE GLU LYS ARG ARG PHE ARG LYS PHE SEQRES 12 A 447 LEU VAL PHE VAL ALA ASN PHE ASP GLU ASN ASP PRO LYS SEQRES 13 A 447 THR PHE GLU GLY VAL ASP PRO GLN ASN THR SER MET ARG SEQRES 14 A 447 ASP VAL TYR ARG LYS PHE ASP LEU GLY GLN ASP VAL ILE SEQRES 15 A 447 ASP PHE THR GLY HIS ALA LEU ALA LEU TYR ARG THR ASP SEQRES 16 A 447 ASP TYR LEU ASP GLN PRO CYS LEU GLU THR ILE ASN ARG SEQRES 17 A 447 ILE LYS LEU TYR SER GLU SER LEU ALA ARG TYR GLY LYS SEQRES 18 A 447 SER PRO TYR LEU TYR PRO LEU TYR GLY LEU GLY GLU LEU SEQRES 19 A 447 PRO GLN GLY PHE ALA ARG LEU SER ALA ILE TYR GLY GLY SEQRES 20 A 447 THR TYR MET LEU ASN LYS PRO VAL ASP ASP ILE ILE MET SEQRES 21 A 447 GLU ASN GLY LYS VAL VAL GLY VAL LYS SER GLU GLY GLU SEQRES 22 A 447 VAL ALA ARG CYS LYS GLN LEU ILE CYS ASP PRO SER TYR SEQRES 23 A 447 VAL PRO ASP ARG VAL ARG LYS ALA GLY GLN VAL ILE ARG SEQRES 24 A 447 ILE ILE CYS ILE LEU SER HIS PRO ILE LYS ASN THR ASN SEQRES 25 A 447 ASP ALA ASN SER CYS GLN ILE ILE ILE PRO GLN ASN GLN SEQRES 26 A 447 VAL ASN ARG LYS SER ASP ILE TYR VAL CYS MET ILE SER SEQRES 27 A 447 TYR ALA HIS ASN VAL ALA ALA GLN GLY LYS TYR ILE ALA SEQRES 28 A 447 ILE ALA SER THR THR VAL GLU THR THR ASP PRO GLU LYS SEQRES 29 A 447 GLU VAL GLU PRO ALA LEU GLU LEU LEU GLU PRO ILE ASP SEQRES 30 A 447 GLN LYS PHE VAL ALA ILE SER ASP LEU TYR GLU PRO ILE SEQRES 31 A 447 ASP ASP GLY SER GLU SER GLN VAL PHE CYS SER CYS SER SEQRES 32 A 447 TYR ASP ALA THR THR HIS PHE GLU THR THR CYS ASN ASP SEQRES 33 A 447 ILE LYS ASP ILE TYR LYS ARG MET ALA GLY SER ALA PHE SEQRES 34 A 447 ASP PHE GLU ASN MET LYS ARG LYS GLN ASN ASP VAL PHE SEQRES 35 A 447 GLY GLU ALA ASP GLN FORMUL 2 HOH *418(H2 O) HELIX 1 1 LEU A 14 VAL A 25 1 12 HELIX 2 2 LEU A 49 ARG A 55 1 7 HELIX 3 3 GLU A 64 MET A 66 5 3 HELIX 4 4 GLY A 69 ASP A 71 5 3 HELIX 5 5 GLN A 86 THR A 94 1 9 HELIX 6 6 VAL A 96 ARG A 98 5 3 HELIX 7 7 GLU A 123 ALA A 126 1 4 HELIX 8 8 MET A 134 ASN A 149 1 16 HELIX 9 9 MET A 168 LYS A 174 1 7 HELIX 10 10 GLN A 179 ALA A 188 1 10 HELIX 11 11 ASP A 196 ASP A 199 5 4 HELIX 12 12 CYS A 202 GLU A 214 1 13 HELIX 13 13 ARG A 218 GLY A 220 5 3 HELIX 14 14 LEU A 231 TYR A 245 5 15 HELIX 15 15 PRO A 284 TYR A 286 5 3 HELIX 16 16 PRO A 288 ARG A 290 5 3 HELIX 17 17 GLN A 323 VAL A 326 5 4 HELIX 18 18 TYR A 339 HIS A 341 5 3 HELIX 19 19 PRO A 362 GLU A 365 1 4 HELIX 20 20 GLU A 367 LEU A 372 1 6 HELIX 21 21 GLU A 411 ALA A 425 1 15 SHEET 1 A 5 VAL A 398 CYS A 400 0 SHEET 2 A 5 GLN A 279 CYS A 282 1 N LEU A 280 O PHE A 399 SHEET 3 A 5 VAL A 7 LEU A 10 1 N ILE A 8 O GLN A 279 SHEET 4 A 5 VAL A 30 MET A 33 1 N LEU A 31 O VAL A 7 SHEET 5 A 5 THR A 248 MET A 250 1 N THR A 248 O HIS A 32 SHEET 1 B 2 PHE A 102 VAL A 104 0 SHEET 2 B 2 LEU A 225 PRO A 227 -1 N TYR A 226 O LYS A 103 SHEET 1 C 7 LYS A 115 LYS A 118 0 SHEET 2 C 7 GLY A 107 LYS A 112 -1 N LYS A 112 O LYS A 115 SHEET 3 C 7 CYS A 317 ILE A 321 1 N GLN A 318 O GLY A 107 SHEET 4 C 7 ILE A 332 SER A 338 -1 N MET A 336 O CYS A 317 SHEET 5 C 7 TYR A 349 THR A 356 -1 N SER A 354 O TYR A 333 SHEET 6 C 7 VAL A 291 LEU A 304 -1 N LEU A 304 O TYR A 349 SHEET 7 C 7 GLN A 378 PRO A 389 -1 N GLU A 388 O ARG A 292 SHEET 1 D 2 VAL A 268 SER A 270 0 SHEET 2 D 2 GLU A 273 ALA A 275 -1 N ALA A 275 O VAL A 268 CRYST1 91.800 43.500 63.200 90.00 104.50 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 0.010893 0.000000 0.002817 0.00000 SCALE2 0.000000 0.022989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016343 0.00000