PDB Short entry for 3CPJ HEADER PROTEIN TRANSPORT 31-MAR-08 3CPJ TITLE CRYSTAL STRUCTURE OF YPT31 IN COMPLEX WITH YEAST RAB-GDI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB GDP-DISSOCIATION INHIBITOR; COMPND 3 CHAIN: G; COMPND 4 SYNONYM: RAB GDI, SECRETORY PATHWAY GDP DISSOCIATION INHIBITOR; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GTP-BINDING PROTEIN YPT31/YPT8; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: RAB GTPASE YPT31; COMPND 10 ENGINEERED: YES; COMPND 11 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 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, ACETYLATION, GOLGI KEYWDS 2 APPARATUS, GTP-BINDING, LIPOPROTEIN, MEMBRANE, NUCLEOTIDE-BINDING, KEYWDS 3 PROTEIN TRANSPORT, CYTOPLASM, GTPASE ACTIVATION, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KRAVCHENKO,A.IGNATEV,R.S.GOODY,A.RAK,O.PYLYPENKO REVDAT 5 01-NOV-23 3CPJ 1 REMARK REVDAT 4 10-NOV-21 3CPJ 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 3CPJ 1 VERSN REVDAT 2 15-JUL-08 3CPJ 1 JRNL REVDAT 1 06-MAY-08 3CPJ 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. 2.35 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28714 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1512 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2072 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4749 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 452 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.17 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): 0.389 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.260 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.523 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4875 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6594 ; 1.102 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 595 ; 5.414 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 216 ;37.739 ;24.398 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 850 ;15.041 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.934 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 736 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3625 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2231 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3325 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 420 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.029 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.149 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.172 ; 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): 3075 ; 0.472 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4807 ; 0.832 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2065 ; 1.079 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1787 ; 1.791 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3CPJ 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_1000047058. 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 : 6.5 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) : 0.931 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 : 30683 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 19.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 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) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 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 (%): 48.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, PH 6.5, VAPOR DIFFUSION, REMARK 280 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 30.71500 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: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, B 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 THR G 5 REMARK 465 GLN G 444 REMARK 465 ARG G 445 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 B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 ASP B 5 REMARK 465 TYR B 6 REMARK 465 GLY B 7 REMARK 465 TYR B 8 REMARK 465 ASP B 9 REMARK 465 ASP B 41 REMARK 465 SER B 42 REMARK 465 LYS B 43 REMARK 465 SER B 44 REMARK 465 THR B 45 REMARK 465 ILE B 46 REMARK 465 ILE B 95 REMARK 465 ASP B 117 REMARK 465 ASN B 118 REMARK 465 ASN B 159 REMARK 465 SER B 179 REMARK 465 LYS B 180 REMARK 465 HIS B 181 REMARK 465 GLN B 182 REMARK 465 MET B 183 REMARK 465 ASP B 184 REMARK 465 LEU B 185 REMARK 465 GLY B 186 REMARK 465 ASP B 187 REMARK 465 SER B 188 REMARK 465 SER B 189 REMARK 465 ALA B 190 REMARK 465 ASN B 191 REMARK 465 GLY B 192 REMARK 465 ASN B 193 REMARK 465 ALA B 194 REMARK 465 ASN B 195 REMARK 465 GLY B 196 REMARK 465 ALA B 197 REMARK 465 SER B 198 REMARK 465 ALA B 199 REMARK 465 PRO B 200 REMARK 465 ASN B 201 REMARK 465 GLY B 202 REMARK 465 THR B 208 REMARK 465 PRO B 209 REMARK 465 THR B 210 REMARK 465 PRO B 211 REMARK 465 ASN B 212 REMARK 465 GLU B 213 REMARK 465 ASN B 214 REMARK 465 LYS B 215 REMARK 465 LYS B 216 REMARK 465 ALA B 217 REMARK 465 ASN B 218 REMARK 465 GLY B 219 REMARK 465 ASN B 220 REMARK 465 ASN B 221 REMARK 465 CYS B 222 REMARK 465 CYS B 223 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 GLN G 62 CG CD OE1 NE2 REMARK 470 GLU G 131 CG CD OE1 OE2 REMARK 470 LYS G 443 CG CD CE NZ REMARK 470 ASP B 11 CG OD1 OD2 REMARK 470 LYS B 35 CG CD CE NZ REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 MET B 40 CG SD CE REMARK 470 ILE B 57 CG1 CG2 CD1 REMARK 470 SER B 96 OG REMARK 470 SER B 99 OG REMARK 470 GLU B 168 CG CD OE1 OE2 REMARK 470 GLU B 169 CG CD OE1 OE2 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 4015 O HOH G 4253 2.19 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 TYR G 227 -24.21 -145.28 REMARK 500 LYS G 229 -62.86 65.50 REMARK 500 LYS G 270 -60.27 -21.79 REMARK 500 ASN G 321 38.80 70.37 REMARK 500 ALA B 115 -142.38 -78.84 REMARK 500 LEU B 130 51.89 -100.11 REMARK 500 VAL B 136 114.68 67.71 REMARK 500 GLU B 161 109.14 -51.91 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 B1208 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 27 OG REMARK 620 2 GDP B1207 O3B 83.6 REMARK 620 3 HOH B4388 O 94.4 174.0 REMARK 620 4 HOH B4389 O 168.4 97.5 83.4 REMARK 620 5 HOH B4390 O 96.3 88.9 85.7 72.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL G 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL G 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 1207 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CPH RELATED DB: PDB REMARK 900 RELATED ID: 3CPI RELATED DB: PDB DBREF 3CPJ G 1 451 UNP P39958 GDI1_YEAST 1 451 DBREF 3CPJ B 1 223 UNP P38555 YPT31_YEAST 1 223 SEQADV 3CPJ GLU B 58 UNP P38555 ASP 58 ENGINEERED MUTATION 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 B 223 MET SER SER GLU ASP TYR GLY TYR ASP TYR ASP LEU LEU SEQRES 2 B 223 PHE LYS ILE VAL LEU ILE GLY ASP SER GLY VAL GLY LYS SEQRES 3 B 223 SER ASN LEU LEU SER ARG PHE THR LYS ASN GLU PHE ASN SEQRES 4 B 223 MET ASP SER LYS SER THR ILE GLY VAL GLU PHE ALA THR SEQRES 5 B 223 ARG THR LEU GLU ILE GLU GLY LYS ARG ILE LYS ALA GLN SEQRES 6 B 223 ILE TRP ASP THR ALA GLY GLN GLU ARG TYR ARG ALA ILE SEQRES 7 B 223 THR SER ALA TYR TYR ARG GLY ALA VAL GLY ALA LEU ILE SEQRES 8 B 223 VAL TYR ASP ILE SER LYS SER SER SER TYR GLU ASN CYS SEQRES 9 B 223 ASN HIS TRP LEU SER GLU LEU ARG GLU ASN ALA ASP ASP SEQRES 10 B 223 ASN VAL ALA VAL GLY LEU ILE GLY ASN LYS SER ASP LEU SEQRES 11 B 223 ALA HIS LEU ARG ALA VAL PRO THR GLU GLU SER LYS THR SEQRES 12 B 223 PHE ALA GLN GLU ASN GLN LEU LEU PHE THR GLU THR SER SEQRES 13 B 223 ALA LEU ASN SER GLU ASN VAL ASP LYS ALA PHE GLU GLU SEQRES 14 B 223 LEU ILE ASN THR ILE TYR GLN LYS VAL SER LYS HIS GLN SEQRES 15 B 223 MET ASP LEU GLY ASP SER SER ALA ASN GLY ASN ALA ASN SEQRES 16 B 223 GLY ALA SER ALA PRO ASN GLY PRO THR ILE SER LEU THR SEQRES 17 B 223 PRO THR PRO ASN GLU ASN LYS LYS ALA ASN GLY ASN ASN SEQRES 18 B 223 CYS CYS HET CL G2001 1 HET CL G2002 1 HET MG B1208 1 HET GDP B1207 28 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 CL 2(CL 1-) FORMUL 5 MG MG 2+ FORMUL 6 GDP C10 H15 N5 O11 P2 FORMUL 7 HOH *452(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 PHE G 421 GLY G 437 1 17 HELIX 22 22 GLY B 25 ASN B 36 1 12 HELIX 23 23 THR B 79 TYR B 83 5 5 HELIX 24 24 LYS B 97 ALA B 115 1 19 HELIX 25 25 LYS B 127 ARG B 134 5 8 HELIX 26 26 PRO B 137 ASN B 148 1 12 HELIX 27 27 ASN B 162 TYR B 175 1 14 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 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 ALA G 311 O ILE G 364 SHEET 7 D 7 GLU G 389 PRO G 400 -1 O GLU G 399 N LYS G 302 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 B 50 ILE B 57 0 SHEET 2 F 6 LYS B 60 TRP B 67 -1 O ILE B 62 N LEU B 55 SHEET 3 F 6 LEU B 12 ILE B 19 1 N ILE B 16 O GLN B 65 SHEET 4 F 6 GLY B 88 TYR B 93 1 O LEU B 90 N ILE B 19 SHEET 5 F 6 ALA B 120 GLY B 125 1 O ALA B 120 N ALA B 89 SHEET 6 F 6 LEU B 151 GLU B 154 1 O LEU B 151 N LEU B 123 LINK OG SER B 27 MG MG B1208 1555 1555 2.09 LINK O3B GDP B1207 MG MG B1208 1555 1555 1.96 LINK MG MG B1208 O HOH B4388 1555 1555 2.02 LINK MG MG B1208 O HOH B4389 1555 1555 2.21 LINK MG MG B1208 O HOH B4390 1555 1555 2.19 SITE 1 AC1 1 SER B 27 SITE 1 AC2 3 ARG G 147 GLY G 186 THR G 189 SITE 1 AC3 3 LEU G 89 MET G 90 PHE G 421 SITE 1 AC4 17 ASP B 21 SER B 22 GLY B 23 GLY B 25 SITE 2 AC4 17 LYS B 26 SER B 27 ASN B 28 PHE B 38 SITE 3 AC4 17 ASN B 39 MET B 40 ASN B 126 LYS B 127 SITE 4 AC4 17 ASP B 129 LEU B 130 SER B 156 ALA B 157 SITE 5 AC4 17 LEU B 158 CRYST1 65.940 61.430 92.750 90.00 103.68 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 0.015165 0.000000 0.003690 0.00000 SCALE2 0.000000 0.016279 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011096 0.00000