HEADER PROTEIN TRANSPORT 31-MAR-08 3CPH TITLE CRYSTAL STRUCTURE OF SEC4 IN COMPLEX WITH RAB-GDI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB GDP-DISSOCIATION INHIBITOR; COMPND 3 CHAIN: G, H; COMPND 4 SYNONYM: RAB GDI, SECRETORY PATHWAY GDP DISSOCIATION INHIBITOR, YEAST COMPND 5 RAB-GDI; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAS-RELATED PROTEIN SEC4; COMPND 9 CHAIN: A; COMPND 10 SYNONYM: SUPPRESSOR OF RHO3 PROTEIN 6, SMALL GTPASE SEC4; COMPND 11 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: PET19; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET19 KEYWDS RAB GTPASE, PRENYLATION, VESICULAR TRANSPORT, CYTOPLASM, CYTOPLASMIC KEYWDS 2 VESICLE, EXOCYTOSIS, GTP-BINDING, LIPOPROTEIN, MEMBRANE, NUCLEOTIDE- KEYWDS 3 BINDING, PALMITATE, PHOSPHOPROTEIN, PROTEIN TRANSPORT, GTPASE KEYWDS 4 ACTIVATION EXPDTA X-RAY DIFFRACTION AUTHOR S.KRAVCHENKO,A.IGNATEV,R.S.GOODY,A.RAK,O.PYLYPENKO REVDAT 4 01-NOV-23 3CPH 1 REMARK REVDAT 3 24-FEB-09 3CPH 1 VERSN REVDAT 2 15-JUL-08 3CPH 1 JRNL REVDAT 1 06-MAY-08 3CPH 0 JRNL AUTH A.IGNATEV,S.KRAVCHENKO,A.RAK,R.S.GOODY,O.PYLYPENKO JRNL TITL A STRUCTURAL MODEL OF THE GDP DISSOCIATION INHIBITOR RAB JRNL TITL 2 MEMBRANE EXTRACTION MECHANISM. JRNL REF J.BIOL.CHEM. V. 283 18377 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18426803 JRNL DOI 10.1074/JBC.M709718200 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 46245 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 + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2437 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3291 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8373 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 87 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.534 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.339 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.264 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.504 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8582 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5879 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11604 ; 1.120 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14400 ; 0.824 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1049 ; 5.879 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 383 ;36.029 ;24.674 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1549 ;16.469 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;17.284 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1287 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9412 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1689 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1713 ; 0.199 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5762 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4115 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 4496 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 184 ; 0.161 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 2 ; 0.102 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.139 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.186 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 6794 ; 0.616 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2132 ; 0.050 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8473 ; 0.675 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4003 ; 0.714 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3131 ; 1.135 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9816 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48896 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 19.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 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) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1UKV, CHAIN G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG MME 2000, PH 5.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 145.04133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.52067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.52067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 145.04133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: H 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 MET G 1 REMARK 465 ASP G 2 REMARK 465 GLN G 3 REMARK 465 GLU G 4 REMARK 465 GLN G 446 REMARK 465 GLU G 447 REMARK 465 GLN G 448 REMARK 465 GLU G 449 REMARK 465 LYS G 450 REMARK 465 GLN G 451 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 LEU A 4 REMARK 465 ARG A 5 REMARK 465 THR A 6 REMARK 465 VAL A 7 REMARK 465 SER A 8 REMARK 465 ALA A 9 REMARK 465 SER A 10 REMARK 465 SER A 11 REMARK 465 GLY A 12 REMARK 465 ASN A 13 REMARK 465 GLY A 14 REMARK 465 LYS A 15 REMARK 465 SER A 16 REMARK 465 TYR A 17 REMARK 465 ASP A 18 REMARK 465 SER A 19 REMARK 465 GLY A 195 REMARK 465 LYS A 196 REMARK 465 GLU A 197 REMARK 465 GLY A 198 REMARK 465 ASN A 199 REMARK 465 ILE A 200 REMARK 465 SER A 201 REMARK 465 ILE A 202 REMARK 465 ASN A 203 REMARK 465 SER A 204 REMARK 465 GLY A 205 REMARK 465 SER A 206 REMARK 465 GLY A 207 REMARK 465 ASN A 208 REMARK 465 SER A 209 REMARK 465 SER A 210 REMARK 465 LYS A 211 REMARK 465 SER A 212 REMARK 465 ASN A 213 REMARK 465 MET H 1 REMARK 465 ASP H 2 REMARK 465 GLN H 3 REMARK 465 GLU H 4 REMARK 465 THR H 5 REMARK 465 ILE H 6 REMARK 465 LYS H 443 REMARK 465 GLN H 444 REMARK 465 ARG H 445 REMARK 465 GLN H 446 REMARK 465 GLU H 447 REMARK 465 GLN H 448 REMARK 465 GLU H 449 REMARK 465 LYS H 450 REMARK 465 GLN H 451 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER H 365 O ALA H 417 2.18 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 THR G 17 46.76 -104.05 REMARK 500 ASP G 103 19.33 55.48 REMARK 500 GLN G 121 25.38 48.73 REMARK 500 ARG G 211 -67.55 -19.93 REMARK 500 LYS G 270 113.61 -5.67 REMARK 500 ASP G 271 -44.94 68.80 REMARK 500 PHE G 297 57.17 -144.84 REMARK 500 LEU G 328 140.42 -172.21 REMARK 500 SER A 48 10.66 -62.69 REMARK 500 PHE A 49 -30.31 66.95 REMARK 500 ASP A 56 -72.32 -104.14 REMARK 500 THR H 8 -40.81 70.40 REMARK 500 THR H 17 40.10 -109.68 REMARK 500 ALA H 48 63.88 -109.59 REMARK 500 PHE H 60 -46.93 -147.58 REMARK 500 VAL H 82 107.33 -53.86 REMARK 500 ASP H 103 14.42 85.98 REMARK 500 LYS H 120 116.45 -162.23 REMARK 500 ARG H 211 -66.11 -20.10 REMARK 500 TYR H 237 -6.49 78.56 REMARK 500 ASP H 260 73.40 17.97 REMARK 500 LYS H 274 -133.30 -74.53 REMARK 500 PRO H 294 -30.38 -35.56 REMARK 500 SER H 327 136.57 -174.99 REMARK 500 GLU H 369 -34.07 -142.71 REMARK 500 ASN H 408 29.24 41.11 REMARK 500 SER H 414 -178.88 -64.00 REMARK 500 PHE H 421 32.64 -99.18 REMARK 500 LEU H 440 103.71 -58.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 34 OG REMARK 620 2 GDP A 302 O2B 81.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CPI RELATED DB: PDB REMARK 900 RELATED ID: 3CPJ RELATED DB: PDB DBREF 3CPH G 1 451 UNP P39958 GDI1_YEAST 1 451 DBREF 3CPH A 1 213 UNP P07560 SEC4_YEAST 1 213 DBREF 3CPH H 1 451 UNP P39958 GDI1_YEAST 1 451 SEQRES 1 G 451 MET ASP GLN GLU THR ILE ASP THR ASP TYR ASP VAL ILE SEQRES 2 G 451 VAL LEU GLY THR GLY ILE THR GLU CYS ILE LEU SER GLY SEQRES 3 G 451 LEU LEU SER VAL ASP GLY LYS LYS VAL LEU HIS ILE ASP SEQRES 4 G 451 LYS GLN ASP HIS TYR GLY GLY GLU ALA ALA SER VAL THR SEQRES 5 G 451 LEU SER GLN LEU TYR GLU LYS PHE LYS GLN ASN PRO ILE SEQRES 6 G 451 SER LYS GLU GLU ARG GLU SER LYS PHE GLY LYS ASP ARG SEQRES 7 G 451 ASP TRP ASN VAL ASP LEU ILE PRO LYS PHE LEU MET ALA SEQRES 8 G 451 ASN GLY GLU LEU THR ASN ILE LEU ILE HIS THR ASP VAL SEQRES 9 G 451 THR ARG TYR VAL ASP PHE LYS GLN VAL SER GLY SER TYR SEQRES 10 G 451 VAL PHE LYS GLN GLY LYS ILE TYR LYS VAL PRO ALA ASN SEQRES 11 G 451 GLU ILE GLU ALA ILE SER SER PRO LEU MET GLY ILE PHE SEQRES 12 G 451 GLU LYS ARG ARG MET LYS LYS PHE LEU GLU TRP ILE SER SEQRES 13 G 451 SER TYR LYS GLU ASP ASP LEU SER THR HIS GLN GLY LEU SEQRES 14 G 451 ASP LEU ASP LYS ASN THR MET ASP GLU VAL TYR TYR LYS SEQRES 15 G 451 PHE GLY LEU GLY ASN SER THR LYS GLU PHE ILE GLY HIS SEQRES 16 G 451 ALA MET ALA LEU TRP THR ASN ASP ASP TYR LEU GLN GLN SEQRES 17 G 451 PRO ALA ARG PRO SER PHE GLU ARG ILE LEU LEU TYR CYS SEQRES 18 G 451 GLN SER VAL ALA ARG TYR GLY LYS SER PRO TYR LEU TYR SEQRES 19 G 451 PRO MET TYR GLY LEU GLY GLU LEU PRO GLN GLY PHE ALA SEQRES 20 G 451 ARG LEU SER ALA ILE TYR GLY GLY THR TYR MET LEU ASP SEQRES 21 G 451 THR PRO ILE ASP GLU VAL LEU TYR LYS LYS ASP THR GLY SEQRES 22 G 451 LYS PHE GLU GLY VAL LYS THR LYS LEU GLY THR PHE LYS SEQRES 23 G 451 ALA PRO LEU VAL ILE ALA ASP PRO THR TYR PHE PRO GLU SEQRES 24 G 451 LYS CYS LYS SER THR GLY GLN ARG VAL ILE ARG ALA ILE SEQRES 25 G 451 CYS ILE LEU ASN HIS PRO VAL PRO ASN THR SER ASN ALA SEQRES 26 G 451 ASP SER LEU GLN ILE ILE ILE PRO GLN SER GLN LEU GLY SEQRES 27 G 451 ARG LYS SER ASP ILE TYR VAL ALA ILE VAL SER ASP ALA SEQRES 28 G 451 HIS ASN VAL CYS SER LYS GLY HIS TYR LEU ALA ILE ILE SEQRES 29 G 451 SER THR ILE ILE GLU THR ASP LYS PRO HIS ILE GLU LEU SEQRES 30 G 451 GLU PRO ALA PHE LYS LEU LEU GLY PRO ILE GLU GLU LYS SEQRES 31 G 451 PHE MET GLY ILE ALA GLU LEU PHE GLU PRO ARG GLU ASP SEQRES 32 G 451 GLY SER LYS ASP ASN ILE TYR LEU SER ARG SER TYR ASP SEQRES 33 G 451 ALA SER SER HIS PHE GLU SER MET THR ASP ASP VAL LYS SEQRES 34 G 451 ASP ILE TYR PHE ARG VAL THR GLY HIS PRO LEU VAL LEU SEQRES 35 G 451 LYS GLN ARG GLN GLU GLN GLU LYS GLN SEQRES 1 A 213 MET SER GLY LEU ARG THR VAL SER ALA SER SER GLY ASN SEQRES 2 A 213 GLY LYS SER TYR ASP SER ILE MET LYS ILE LEU LEU ILE SEQRES 3 A 213 GLY ASP SER GLY VAL GLY LYS SER CYS LEU LEU VAL ARG SEQRES 4 A 213 PHE VAL GLU ASP LYS PHE ASN PRO SER PHE ILE THR THR SEQRES 5 A 213 ILE GLY ILE ASP PHE LYS ILE LYS THR VAL ASP ILE ASN SEQRES 6 A 213 GLY LYS LYS VAL LYS LEU GLN LEU TRP ASP THR ALA GLY SEQRES 7 A 213 GLN GLU ARG PHE ARG THR ILE THR THR ALA TYR TYR ARG SEQRES 8 A 213 GLY ALA MET GLY ILE ILE LEU VAL TYR ASP VAL THR ASP SEQRES 9 A 213 GLU ARG THR PHE THR ASN ILE LYS GLN TRP PHE LYS THR SEQRES 10 A 213 VAL ASN GLU HIS ALA ASN ASP GLU ALA GLN LEU LEU LEU SEQRES 11 A 213 VAL GLY ASN LYS SER ASP MET GLU THR ARG VAL VAL THR SEQRES 12 A 213 ALA ASP GLN GLY GLU ALA LEU ALA LYS GLU LEU GLY ILE SEQRES 13 A 213 PRO PHE ILE GLU SER SER ALA LYS ASN ASP ASP ASN VAL SEQRES 14 A 213 ASN GLU ILE PHE PHE THR LEU ALA LYS LEU ILE GLN GLU SEQRES 15 A 213 LYS ILE ASP SER ASN LYS LEU VAL GLY VAL GLY ASN GLY SEQRES 16 A 213 LYS GLU GLY ASN ILE SER ILE ASN SER GLY SER GLY ASN SEQRES 17 A 213 SER SER LYS SER ASN SEQRES 1 H 451 MET ASP GLN GLU THR ILE ASP THR ASP TYR ASP VAL ILE SEQRES 2 H 451 VAL LEU GLY THR GLY ILE THR GLU CYS ILE LEU SER GLY SEQRES 3 H 451 LEU LEU SER VAL ASP GLY LYS LYS VAL LEU HIS ILE ASP SEQRES 4 H 451 LYS GLN ASP HIS TYR GLY GLY GLU ALA ALA SER VAL THR SEQRES 5 H 451 LEU SER GLN LEU TYR GLU LYS PHE LYS GLN ASN PRO ILE SEQRES 6 H 451 SER LYS GLU GLU ARG GLU SER LYS PHE GLY LYS ASP ARG SEQRES 7 H 451 ASP TRP ASN VAL ASP LEU ILE PRO LYS PHE LEU MET ALA SEQRES 8 H 451 ASN GLY GLU LEU THR ASN ILE LEU ILE HIS THR ASP VAL SEQRES 9 H 451 THR ARG TYR VAL ASP PHE LYS GLN VAL SER GLY SER TYR SEQRES 10 H 451 VAL PHE LYS GLN GLY LYS ILE TYR LYS VAL PRO ALA ASN SEQRES 11 H 451 GLU ILE GLU ALA ILE SER SER PRO LEU MET GLY ILE PHE SEQRES 12 H 451 GLU LYS ARG ARG MET LYS LYS PHE LEU GLU TRP ILE SER SEQRES 13 H 451 SER TYR LYS GLU ASP ASP LEU SER THR HIS GLN GLY LEU SEQRES 14 H 451 ASP LEU ASP LYS ASN THR MET ASP GLU VAL TYR TYR LYS SEQRES 15 H 451 PHE GLY LEU GLY ASN SER THR LYS GLU PHE ILE GLY HIS SEQRES 16 H 451 ALA MET ALA LEU TRP THR ASN ASP ASP TYR LEU GLN GLN SEQRES 17 H 451 PRO ALA ARG PRO SER PHE GLU ARG ILE LEU LEU TYR CYS SEQRES 18 H 451 GLN SER VAL ALA ARG TYR GLY LYS SER PRO TYR LEU TYR SEQRES 19 H 451 PRO MET TYR GLY LEU GLY GLU LEU PRO GLN GLY PHE ALA SEQRES 20 H 451 ARG LEU SER ALA ILE TYR GLY GLY THR TYR MET LEU ASP SEQRES 21 H 451 THR PRO ILE ASP GLU VAL LEU TYR LYS LYS ASP THR GLY SEQRES 22 H 451 LYS PHE GLU GLY VAL LYS THR LYS LEU GLY THR PHE LYS SEQRES 23 H 451 ALA PRO LEU VAL ILE ALA ASP PRO THR TYR PHE PRO GLU SEQRES 24 H 451 LYS CYS LYS SER THR GLY GLN ARG VAL ILE ARG ALA ILE SEQRES 25 H 451 CYS ILE LEU ASN HIS PRO VAL PRO ASN THR SER ASN ALA SEQRES 26 H 451 ASP SER LEU GLN ILE ILE ILE PRO GLN SER GLN LEU GLY SEQRES 27 H 451 ARG LYS SER ASP ILE TYR VAL ALA ILE VAL SER ASP ALA SEQRES 28 H 451 HIS ASN VAL CYS SER LYS GLY HIS TYR LEU ALA ILE ILE SEQRES 29 H 451 SER THR ILE ILE GLU THR ASP LYS PRO HIS ILE GLU LEU SEQRES 30 H 451 GLU PRO ALA PHE LYS LEU LEU GLY PRO ILE GLU GLU LYS SEQRES 31 H 451 PHE MET GLY ILE ALA GLU LEU PHE GLU PRO ARG GLU ASP SEQRES 32 H 451 GLY SER LYS ASP ASN ILE TYR LEU SER ARG SER TYR ASP SEQRES 33 H 451 ALA SER SER HIS PHE GLU SER MET THR ASP ASP VAL LYS SEQRES 34 H 451 ASP ILE TYR PHE ARG VAL THR GLY HIS PRO LEU VAL LEU SEQRES 35 H 451 LYS GLN ARG GLN GLU GLN GLU LYS GLN HET MG A 301 1 HET GDP A 302 28 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 4 MG MG 2+ FORMUL 5 GDP C10 H15 N5 O11 P2 FORMUL 6 HOH *87(H2 O) HELIX 1 1 GLY G 18 GLY G 32 1 15 HELIX 2 2 GLY G 45 ALA G 48 5 4 HELIX 3 3 THR G 52 LYS G 61 1 10 HELIX 4 4 SER G 66 GLY G 75 1 10 HELIX 5 5 LYS G 76 TRP G 80 5 5 HELIX 6 6 GLY G 93 THR G 102 1 10 HELIX 7 7 ASP G 103 TYR G 107 5 5 HELIX 8 8 ASN G 130 SER G 137 1 8 HELIX 9 9 GLY G 141 TYR G 158 1 18 HELIX 10 10 ASP G 162 HIS G 166 5 5 HELIX 11 11 THR G 175 GLY G 184 1 10 HELIX 12 12 GLY G 186 MET G 197 1 12 HELIX 13 13 ASP G 203 GLN G 207 5 5 HELIX 14 14 ALA G 210 GLY G 228 1 19 HELIX 15 15 GLY G 240 GLY G 254 1 15 HELIX 16 16 PRO G 294 GLU G 299 5 6 HELIX 17 17 PRO G 333 LEU G 337 5 5 HELIX 18 18 ALA G 351 ASN G 353 5 3 HELIX 19 19 LYS G 372 LEU G 377 1 6 HELIX 20 20 LEU G 377 LEU G 384 1 8 HELIX 21 21 PHE G 421 GLY G 437 1 17 HELIX 22 22 GLY A 32 ASP A 43 1 12 HELIX 23 23 GLY A 78 ARG A 83 5 6 HELIX 24 24 THR A 86 ARG A 91 1 6 HELIX 25 25 ASP A 104 ASN A 110 1 7 HELIX 26 26 ASN A 110 ALA A 122 1 13 HELIX 27 27 THR A 143 GLY A 155 1 13 HELIX 28 28 VAL A 169 SER A 186 1 18 HELIX 29 29 GLY H 18 VAL H 30 1 13 HELIX 30 30 THR H 52 LYS H 59 1 8 HELIX 31 31 GLU H 68 LYS H 73 1 6 HELIX 32 32 GLY H 93 ASP H 103 1 11 HELIX 33 33 VAL H 104 TYR H 107 5 4 HELIX 34 34 ASN H 130 ILE H 135 1 6 HELIX 35 35 GLY H 141 TYR H 158 1 18 HELIX 36 36 ASP H 162 HIS H 166 5 5 HELIX 37 37 THR H 175 GLY H 184 1 10 HELIX 38 38 GLY H 186 MET H 197 1 12 HELIX 39 39 ASN H 202 GLN H 207 5 6 HELIX 40 40 PRO H 209 GLY H 228 1 20 HELIX 41 41 GLY H 240 ILE H 252 1 13 HELIX 42 42 PHE H 297 GLU H 299 5 3 HELIX 43 43 PRO H 333 LEU H 337 5 5 HELIX 44 44 ALA H 351 ASN H 353 5 3 HELIX 45 45 LYS H 372 LEU H 377 1 6 HELIX 46 46 LEU H 377 LEU H 383 1 7 HELIX 47 47 PHE H 421 GLY H 437 1 17 SHEET 1 A 5 THR G 256 MET G 258 0 SHEET 2 A 5 VAL G 35 ILE G 38 1 N HIS G 37 O THR G 256 SHEET 3 A 5 VAL G 12 LEU G 15 1 N VAL G 14 O LEU G 36 SHEET 4 A 5 VAL G 290 ALA G 292 1 O ILE G 291 N LEU G 15 SHEET 5 A 5 ILE G 409 LEU G 411 1 O TYR G 410 N VAL G 290 SHEET 1 B 2 SER G 50 VAL G 51 0 SHEET 2 B 2 VAL G 82 ASP G 83 -1 O VAL G 82 N VAL G 51 SHEET 1 C 3 LEU G 89 MET G 90 0 SHEET 2 C 3 TYR G 232 PRO G 235 -1 O LEU G 233 N LEU G 89 SHEET 3 C 3 PHE G 110 GLN G 112 -1 N LYS G 111 O TYR G 234 SHEET 1 D 7 LYS G 123 LYS G 126 0 SHEET 2 D 7 GLY G 115 LYS G 120 -1 N VAL G 118 O TYR G 125 SHEET 3 D 7 LEU G 328 ILE G 332 1 O GLN G 329 N TYR G 117 SHEET 4 D 7 ILE G 343 SER G 349 -1 O ILE G 347 N LEU G 328 SHEET 5 D 7 TYR G 360 ILE G 367 -1 O LEU G 361 N VAL G 348 SHEET 6 D 7 CYS G 301 LEU G 315 -1 N CYS G 313 O ALA G 362 SHEET 7 D 7 ILE G 387 PRO G 400 -1 O GLU G 388 N ILE G 314 SHEET 1 E 3 GLU G 265 TYR G 268 0 SHEET 2 E 3 PHE G 275 THR G 280 -1 O GLY G 277 N LEU G 267 SHEET 3 E 3 GLY G 283 LYS G 286 -1 O GLY G 283 N THR G 280 SHEET 1 F 6 PHE A 57 ILE A 64 0 SHEET 2 F 6 LYS A 67 TRP A 74 -1 O LYS A 67 N ILE A 64 SHEET 3 F 6 MET A 21 ILE A 26 1 N MET A 21 O GLN A 72 SHEET 4 F 6 GLY A 95 ASP A 101 1 O VAL A 99 N ILE A 26 SHEET 5 F 6 GLN A 127 ASN A 133 1 O LEU A 129 N LEU A 98 SHEET 6 F 6 PHE A 158 GLU A 160 1 O ILE A 159 N LEU A 130 SHEET 1 G 4 VAL H 35 ILE H 38 0 SHEET 2 G 4 VAL H 12 LEU H 15 1 N VAL H 14 O ILE H 38 SHEET 3 G 4 LEU H 289 ALA H 292 1 O ILE H 291 N LEU H 15 SHEET 4 G 4 ILE H 409 LEU H 411 1 O TYR H 410 N VAL H 290 SHEET 1 H 2 SER H 50 VAL H 51 0 SHEET 2 H 2 VAL H 82 ASP H 83 -1 O VAL H 82 N VAL H 51 SHEET 1 I 3 LEU H 89 MET H 90 0 SHEET 2 I 3 TYR H 232 PRO H 235 -1 O LEU H 233 N LEU H 89 SHEET 3 I 3 PHE H 110 GLN H 112 -1 N LYS H 111 O TYR H 234 SHEET 1 J 7 LYS H 123 LYS H 126 0 SHEET 2 J 7 GLY H 115 LYS H 120 -1 N LYS H 120 O LYS H 123 SHEET 3 J 7 LEU H 328 ILE H 332 1 O GLN H 329 N TYR H 117 SHEET 4 J 7 ILE H 343 SER H 349 -1 O ILE H 343 N ILE H 332 SHEET 5 J 7 TYR H 360 ILE H 367 -1 O ILE H 363 N ALA H 346 SHEET 6 J 7 CYS H 301 LEU H 315 -1 N CYS H 313 O ALA H 362 SHEET 7 J 7 ALA H 395 PRO H 400 -1 O GLU H 399 N LYS H 302 SHEET 1 K 3 ILE H 263 LEU H 267 0 SHEET 2 K 3 GLY H 277 THR H 280 -1 O GLY H 277 N LEU H 267 SHEET 3 K 3 GLY H 283 LYS H 286 -1 O GLY H 283 N THR H 280 LINK OG SER A 34 MG MG A 301 1555 1555 2.30 LINK MG MG A 301 O2B GDP A 302 1555 1555 2.27 SITE 1 AC1 2 SER A 34 THR A 51 SITE 1 AC2 17 SER A 29 GLY A 30 GLY A 32 LYS A 33 SITE 2 AC2 17 SER A 34 CYS A 35 PHE A 45 ASN A 46 SITE 3 AC2 17 PRO A 47 PHE A 49 ASN A 133 LYS A 134 SITE 4 AC2 17 ASP A 136 MET A 137 SER A 162 ALA A 163 SITE 5 AC2 17 LYS A 164 CRYST1 131.900 131.900 217.562 90.00 90.00 120.00 P 32 2 1 12 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 0.007582 0.004377 0.000000 0.00000 SCALE2 0.000000 0.008754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004596 0.00000