PDB Short entry for 2BCG HEADER PROTEIN TRANSPORT 19-OCT-05 2BCG TITLE STRUCTURE OF DOUBLY PRENYLATED YPT1:GDI COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SECRETORY PATHWAY GDP DISSOCIATION INHIBITOR; COMPND 3 CHAIN: G; COMPND 4 FRAGMENT: RABGDI; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GTP-BINDING PROTEIN YPT1; COMPND 8 CHAIN: Y; COMPND 9 FRAGMENT: YPT1; COMPND 10 SYNONYM: PROTEIN YP2; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: 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 GENE: GDI1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET19; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 GENE: YPT1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTWIN-1 KEYWDS RABGTPASE, GERANYLGERANYLATION, VESICULAR TRANSPORT, PROTEIN KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR O.PYLYPENKO,A.RAK,K.ALEXANDROV REVDAT 6 23-AUG-23 2BCG 1 REMARK REVDAT 5 20-OCT-21 2BCG 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2BCG 1 REMARK REVDAT 3 24-FEB-09 2BCG 1 VERSN REVDAT 2 24-JAN-06 2BCG 1 JRNL REVDAT 1 17-JAN-06 2BCG 0 JRNL AUTH O.PYLYPENKO,A.RAK,T.DUREK,S.KUSHNIR,B.E.DURSINA,N.H.THOMAE, JRNL AUTH 2 A.T.CONSTANTINESCU,L.BRUNSVELD,A.WATZKE,H.WALDMANN, JRNL AUTH 3 R.S.GOODY,K.ALEXANDROV JRNL TITL STRUCTURE OF DOUBLY PRENYLATED YPT1:GDI COMPLEX AND THE JRNL TITL 2 MECHANISM OF GDI-MEDIATED RAB RECYCLING JRNL REF EMBO J. V. 25 13 2006 JRNL REFN ISSN 0261-4189 JRNL PMID 16395334 JRNL DOI 10.1038/SJ.EMBOJ.7600921 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 103719 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5459 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6020 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 316 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5079 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 923 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.00 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.609 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5448 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7360 ; 1.453 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 634 ; 5.760 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 258 ;34.495 ;24.845 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1040 ;13.621 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;18.665 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 828 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4012 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2645 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3767 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 759 ; 0.148 ; 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): 40 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 44 ; 0.123 ; 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): 3297 ; 1.345 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5249 ; 2.000 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2454 ; 2.919 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2111 ; 3.696 ; 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): 5751 ; 2.137 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 924 ; 5.636 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5345 ; 3.804 ; 3.000 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BCG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034931. 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 : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PRODC REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 109178 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 19.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.1 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: NULL REMARK 200 STARTING MODEL: 1UKV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG MME 2000, 100 MM TRIS-ACETATE, REMARK 280 PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 60.11500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, Y 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 G -1 REMARK 465 HIS G 0 REMARK 465 MET G 1 REMARK 465 ASP G 2 REMARK 465 GLN G 3 REMARK 465 GLU G 4 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 Y 1 REMARK 465 ASN Y 2 REMARK 465 SER Y 197 REMARK 465 LEU Y 198 REMARK 465 THR Y 199 REMARK 465 ASN Y 200 REMARK 465 THR Y 201 REMARK 465 GLY Y 202 REMARK 465 GLY Y 203 REMARK 465 CYS Y 204 REMARK 465 CYS Y 205 REMARK 465 CYS Y 206 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 O HOH G 4052 O HOH G 4406 2.07 REMARK 500 O HOH Y 3143 O HOH Y 3290 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ARG G 106 NE - CZ - NH2 ANGL. DEV. = -3.2 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 LYS G 229 -53.32 69.46 REMARK 500 THR G 272 -30.01 -132.44 REMARK 500 ASP Y 44 -75.25 -92.10 REMARK 500 LYS Y 122 32.79 70.41 REMARK 500 SER Y 155 -3.12 85.26 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 Y1208 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER Y 22 OG REMARK 620 2 GDP Y1207 O3B 90.4 REMARK 620 3 HOH Y3243 O 88.7 93.6 REMARK 620 4 HOH Y3244 O 176.9 92.1 89.5 REMARK 620 5 HOH Y3245 O 86.7 176.2 88.8 90.8 REMARK 620 6 HOH Y3246 O 89.8 89.0 177.0 92.0 88.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG Y 1208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP Y 1207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GER G 4000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GER G 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS Y 3000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UKV RELATED DB: PDB REMARK 900 MONO PRENYLATED YPT1:GDI COMPLEX DBREF 2BCG G 1 451 UNP P39958 GDI1_YEAST 1 451 DBREF 2BCG Y 1 206 UNP P01123 YPT1_YEAST 1 206 SEQADV 2BCG GLY G -1 UNP P39958 CLONING ARTIFACT SEQADV 2BCG HIS G 0 UNP P39958 CLONING ARTIFACT SEQADV 2BCG CYS Y 204 UNP P01123 GLY 204 ENGINEERED MUTATION SEQRES 1 G 453 GLY HIS MET ASP GLN GLU THR ILE ASP THR ASP TYR ASP SEQRES 2 G 453 VAL ILE VAL LEU GLY THR GLY ILE THR GLU CYS ILE LEU SEQRES 3 G 453 SER GLY LEU LEU SER VAL ASP GLY LYS LYS VAL LEU HIS SEQRES 4 G 453 ILE ASP LYS GLN ASP HIS TYR GLY GLY GLU ALA ALA SER SEQRES 5 G 453 VAL THR LEU SER GLN LEU TYR GLU LYS PHE LYS GLN ASN SEQRES 6 G 453 PRO ILE SER LYS GLU GLU ARG GLU SER LYS PHE GLY LYS SEQRES 7 G 453 ASP ARG ASP TRP ASN VAL ASP LEU ILE PRO LYS PHE LEU SEQRES 8 G 453 MET ALA ASN GLY GLU LEU THR ASN ILE LEU ILE HIS THR SEQRES 9 G 453 ASP VAL THR ARG TYR VAL ASP PHE LYS GLN VAL SER GLY SEQRES 10 G 453 SER TYR VAL PHE LYS GLN GLY LYS ILE TYR LYS VAL PRO SEQRES 11 G 453 ALA ASN GLU ILE GLU ALA ILE SER SER PRO LEU MET GLY SEQRES 12 G 453 ILE PHE GLU LYS ARG ARG MET LYS LYS PHE LEU GLU TRP SEQRES 13 G 453 ILE SER SER TYR LYS GLU ASP ASP LEU SER THR HIS GLN SEQRES 14 G 453 GLY LEU ASP LEU ASP LYS ASN THR MET ASP GLU VAL TYR SEQRES 15 G 453 TYR LYS PHE GLY LEU GLY ASN SER THR LYS GLU PHE ILE SEQRES 16 G 453 GLY HIS ALA MET ALA LEU TRP THR ASN ASP ASP TYR LEU SEQRES 17 G 453 GLN GLN PRO ALA ARG PRO SER PHE GLU ARG ILE LEU LEU SEQRES 18 G 453 TYR CYS GLN SER VAL ALA ARG TYR GLY LYS SER PRO TYR SEQRES 19 G 453 LEU TYR PRO MET TYR GLY LEU GLY GLU LEU PRO GLN GLY SEQRES 20 G 453 PHE ALA ARG LEU SER ALA ILE TYR GLY GLY THR TYR MET SEQRES 21 G 453 LEU ASP THR PRO ILE ASP GLU VAL LEU TYR LYS LYS ASP SEQRES 22 G 453 THR GLY LYS PHE GLU GLY VAL LYS THR LYS LEU GLY THR SEQRES 23 G 453 PHE LYS ALA PRO LEU VAL ILE ALA ASP PRO THR TYR PHE SEQRES 24 G 453 PRO GLU LYS CYS LYS SER THR GLY GLN ARG VAL ILE ARG SEQRES 25 G 453 ALA ILE CYS ILE LEU ASN HIS PRO VAL PRO ASN THR SER SEQRES 26 G 453 ASN ALA ASP SER LEU GLN ILE ILE ILE PRO GLN SER GLN SEQRES 27 G 453 LEU GLY ARG LYS SER ASP ILE TYR VAL ALA ILE VAL SER SEQRES 28 G 453 ASP ALA HIS ASN VAL CYS SER LYS GLY HIS TYR LEU ALA SEQRES 29 G 453 ILE ILE SER THR ILE ILE GLU THR ASP LYS PRO HIS ILE SEQRES 30 G 453 GLU LEU GLU PRO ALA PHE LYS LEU LEU GLY PRO ILE GLU SEQRES 31 G 453 GLU LYS PHE MET GLY ILE ALA GLU LEU PHE GLU PRO ARG SEQRES 32 G 453 GLU ASP GLY SER LYS ASP ASN ILE TYR LEU SER ARG SER SEQRES 33 G 453 TYR ASP ALA SER SER HIS PHE GLU SER MET THR ASP ASP SEQRES 34 G 453 VAL LYS ASP ILE TYR PHE ARG VAL THR GLY HIS PRO LEU SEQRES 35 G 453 VAL LEU LYS GLN ARG GLN GLU GLN GLU LYS GLN SEQRES 1 Y 206 MET ASN SER GLU TYR ASP TYR LEU PHE LYS LEU LEU LEU SEQRES 2 Y 206 ILE GLY ASN SER GLY VAL GLY LYS SER CYS LEU LEU LEU SEQRES 3 Y 206 ARG PHE SER ASP ASP THR TYR THR ASN ASP TYR ILE SER SEQRES 4 Y 206 THR ILE GLY VAL ASP PHE LYS ILE LYS THR VAL GLU LEU SEQRES 5 Y 206 ASP GLY LYS THR VAL LYS LEU GLN ILE TRP ASP THR ALA SEQRES 6 Y 206 GLY GLN GLU ARG PHE ARG THR ILE THR SER SER TYR TYR SEQRES 7 Y 206 ARG GLY SER HIS GLY ILE ILE ILE VAL TYR ASP VAL THR SEQRES 8 Y 206 ASP GLN GLU SER PHE ASN GLY VAL LYS MET TRP LEU GLN SEQRES 9 Y 206 GLU ILE ASP ARG TYR ALA THR SER THR VAL LEU LYS LEU SEQRES 10 Y 206 LEU VAL GLY ASN LYS CYS ASP LEU LYS ASP LYS ARG VAL SEQRES 11 Y 206 VAL GLU TYR ASP VAL ALA LYS GLU PHE ALA ASP ALA ASN SEQRES 12 Y 206 LYS MET PRO PHE LEU GLU THR SER ALA LEU ASP SER THR SEQRES 13 Y 206 ASN VAL GLU ASP ALA PHE LEU THR MET ALA ARG GLN ILE SEQRES 14 Y 206 LYS GLU SER MET SER GLN GLN ASN LEU ASN GLU THR THR SEQRES 15 Y 206 GLN LYS LYS GLU ASP LYS GLY ASN VAL ASN LEU LYS GLY SEQRES 16 Y 206 GLN SER LEU THR ASN THR GLY GLY CYS CYS CYS HET GER G4000 20 HET GER G2000 20 HET MG Y1208 1 HET GDP Y1207 28 HET TRS Y3000 8 HETNAM GER GERAN-8-YL GERAN HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 3 GER 2(C20 H34) FORMUL 5 MG MG 2+ FORMUL 6 GDP C10 H15 N5 O11 P2 FORMUL 7 TRS C4 H12 N O3 1+ FORMUL 8 HOH *923(H2 O) HELIX 1 1 GLY G 18 ASP G 31 1 14 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 PHE G 183 1 9 HELIX 12 12 GLY G 186 MET G 197 1 12 HELIX 13 13 ASP G 203 GLN G 208 5 6 HELIX 14 14 ALA G 210 GLY G 228 1 19 HELIX 15 15 GLY G 240 TYR G 253 1 14 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 LYS G 382 1 6 HELIX 21 21 LEU G 383 GLY G 385 5 3 HELIX 22 22 PHE G 421 GLY G 437 1 17 HELIX 23 23 GLY Y 20 ASP Y 31 1 12 HELIX 24 24 THR Y 74 ARG Y 79 5 6 HELIX 25 25 ASP Y 92 ALA Y 110 1 19 HELIX 26 26 GLU Y 132 ASN Y 143 1 12 HELIX 27 27 ASN Y 157 MET Y 173 1 17 HELIX 28 28 SER Y 174 GLU Y 180 1 7 HELIX 29 29 THR Y 181 GLU Y 186 5 6 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 ILE G 38 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 SER G 116 LYS G 120 -1 N LYS G 120 O LYS G 123 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 343 N ILE G 332 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 LEU G 315 O TYR G 360 SHEET 7 D 7 GLU G 389 PRO G 400 -1 O GLY G 393 N ARG G 310 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 PHE G 285 N VAL G 278 SHEET 1 F 6 PHE Y 45 LEU Y 52 0 SHEET 2 F 6 LYS Y 55 TRP Y 62 -1 O LYS Y 55 N LEU Y 52 SHEET 3 F 6 TYR Y 7 GLY Y 15 1 N TYR Y 7 O LYS Y 58 SHEET 4 F 6 GLY Y 83 ASP Y 89 1 O ILE Y 85 N LEU Y 12 SHEET 5 F 6 LEU Y 115 ASN Y 121 1 O ASN Y 121 N TYR Y 88 SHEET 6 F 6 PHE Y 147 GLU Y 149 1 O LEU Y 148 N GLY Y 120 LINK OG SER Y 22 MG MG Y1208 1555 1555 2.09 LINK O3B GDP Y1207 MG MG Y1208 1555 1555 2.05 LINK MG MG Y1208 O HOH Y3243 1555 1555 2.07 LINK MG MG Y1208 O HOH Y3244 1555 1555 2.03 LINK MG MG Y1208 O HOH Y3245 1555 1555 2.11 LINK MG MG Y1208 O HOH Y3246 1555 1555 2.10 SITE 1 AC1 6 SER Y 22 GDP Y1207 HOH Y3243 HOH Y3244 SITE 2 AC1 6 HOH Y3245 HOH Y3246 SITE 1 AC2 27 GLY Y 18 VAL Y 19 GLY Y 20 LYS Y 21 SITE 2 AC2 27 SER Y 22 CYS Y 23 TYR Y 33 THR Y 34 SITE 3 AC2 27 ASP Y 36 TYR Y 37 ASN Y 121 LYS Y 122 SITE 4 AC2 27 ASP Y 124 LEU Y 125 SER Y 151 ALA Y 152 SITE 5 AC2 27 LEU Y 153 MG Y1208 HOH Y3002 HOH Y3004 SITE 6 AC2 27 HOH Y3024 HOH Y3043 HOH Y3054 HOH Y3057 SITE 7 AC2 27 HOH Y3243 HOH Y3244 HOH Y3246 SITE 1 AC3 7 PRO G 128 ALA G 134 LYS G 145 PHE G 192 SITE 2 AC3 7 CYS G 221 VAL G 224 GER G2000 SITE 1 AC4 8 ALA G 134 LYS G 145 MET G 148 LEU G 152 SITE 2 AC4 8 ILE G 155 CYS G 221 ASP G 371 GER G4000 SITE 1 AC5 10 VAL G 435 THR G 436 GLY G 437 HOH G4132 SITE 2 AC5 10 HOH G4259 HOH G4281 ASP Y 141 HOH Y3267 SITE 3 AC5 10 HOH Y3269 HOH Y3270 CRYST1 47.660 120.230 60.550 90.00 90.67 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 0.020982 0.000000 0.000245 0.00000 SCALE2 0.000000 0.008317 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016516 0.00000