HEADER ENDOCYTOSIS/EXOCYTOSIS 02-FEB-02 1KY3 TITLE GDP-BOUND YPT7P AT 1.35 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN YPT7P; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GTPASE DOMAIN; COMPND 5 SYNONYM: GTP-BINDING PROTEIN YPT7; COMPND 6 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 GENE: YPT7; 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: PET11 KEYWDS G PROTEIN, VESICULAR TRAFFIC, GTP HYDROLYSIS, YPT/RAB PROTEIN, KEYWDS 2 ENDOCYTOSIS, HYDROLASE, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.-T.CONSTANTINESCU,A.RAK,A.J.SCHEIDIG REVDAT 6 03-APR-24 1KY3 1 REMARK REVDAT 5 14-FEB-24 1KY3 1 REMARK LINK REVDAT 4 11-OCT-17 1KY3 1 REMARK REVDAT 3 24-FEB-09 1KY3 1 VERSN REVDAT 2 01-APR-03 1KY3 1 JRNL REVDAT 1 05-JUN-02 1KY3 0 JRNL AUTH A.T.CONSTANTINESCU,A.RAK,K.ALEXANDROV,H.ESTERS,R.S.GOODY, JRNL AUTH 2 A.J.SCHEIDIG JRNL TITL RAB-SUBFAMILY-SPECIFIC REGIONS OF YPT7P ARE STRUCTURALLY JRNL TITL 2 DIFFERENT FROM OTHER RABGTPASES. JRNL REF STRUCTURE V. 10 569 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 11937061 JRNL DOI 10.1016/S0969-2126(02)00737-2 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.166 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.163 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 6.600 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2413 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 36545 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1263 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.053 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.069 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.014 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.062 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.083 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 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 : MIRROR REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36543 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 15.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: YPT7-GPPNHP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, HEPES, GDP, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.76750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.08850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.08850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.76750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.71500 REMARK 290 SMTRY3 4 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 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 38 REMARK 465 ALA A 39 REMARK 465 THR A 40 REMARK 465 GLY A 67 REMARK 465 GLN A 68 REMARK 465 GLU A 69 REMARK 465 ARG A 70 REMARK 465 PHE A 71 REMARK 465 GLN A 72 REMARK 465 SER A 73 REMARK 465 LEU A 74 REMARK 465 GLY A 75 REMARK 465 VAL A 76 REMARK 465 ALA A 182 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 7 CB CG OD1 ND2 REMARK 480 GLN A 35 CB CG CD OE1 NE2 REMARK 480 GLN A 36 CG CD OE1 NE2 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 A 27 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP A 64 CB - CG - OD2 ANGL. DEV. = 5.8 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 ASP A 53 56.69 -33.61 REMARK 500 ASP A 55 -113.76 56.69 REMARK 500 LYS A 127 34.61 73.64 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 GDP A 400 O3B 89.3 REMARK 620 3 HOH A 583 O 90.1 175.1 REMARK 620 4 HOH A 584 O 91.8 87.0 88.2 REMARK 620 5 HOH A 585 O 175.8 94.9 85.7 88.5 REMARK 620 6 HOH A 586 O 90.4 96.9 88.0 175.6 89.0 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 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KY2 RELATED DB: PDB REMARK 900 1KY2 IS GPPNHP-BOUND YPT7P. DBREF 1KY3 A 1 182 UNP P32939 YPT7_YEAST 1 182 SEQRES 1 A 182 MET SER SER ARG LYS LYS ASN ILE LEU LYS VAL ILE ILE SEQRES 2 A 182 LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU MET HIS SEQRES 3 A 182 ARG TYR VAL ASN ASP LYS TYR SER GLN GLN TYR LYS ALA SEQRES 4 A 182 THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL THR VAL SEQRES 5 A 182 ASP GLY ASP LYS VAL ALA THR MET GLN VAL TRP ASP THR SEQRES 6 A 182 ALA GLY GLN GLU ARG PHE GLN SER LEU GLY VAL ALA PHE SEQRES 7 A 182 TYR ARG GLY ALA ASP CYS CYS VAL LEU VAL TYR ASP VAL SEQRES 8 A 182 THR ASN ALA SER SER PHE GLU ASN ILE LYS SER TRP ARG SEQRES 9 A 182 ASP GLU PHE LEU VAL HIS ALA ASN VAL ASN SER PRO GLU SEQRES 10 A 182 THR PHE PRO PHE VAL ILE LEU GLY ASN LYS ILE ASP ALA SEQRES 11 A 182 GLU GLU SER LYS LYS ILE VAL SER GLU LYS SER ALA GLN SEQRES 12 A 182 GLU LEU ALA LYS SER LEU GLY ASP ILE PRO LEU PHE LEU SEQRES 13 A 182 THR SER ALA LYS ASN ALA ILE ASN VAL ASP THR ALA PHE SEQRES 14 A 182 GLU GLU ILE ALA ARG SER ALA LEU GLN GLN ASN GLN ALA HET MG A 401 1 HET GDP A 400 28 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 HOH *172(H2 O) HELIX 1 1 GLY A 20 ASP A 31 1 12 HELIX 2 2 ASN A 93 ASN A 99 1 7 HELIX 3 3 ASN A 99 ASN A 112 1 14 HELIX 4 4 GLU A 131 LYS A 135 5 5 HELIX 5 5 SER A 138 LEU A 149 1 12 HELIX 6 6 ASN A 164 GLN A 181 1 18 SHEET 1 A 6 LEU A 46 VAL A 50 0 SHEET 2 A 6 ALA A 58 TRP A 63 -1 O ALA A 58 N VAL A 50 SHEET 3 A 6 ILE A 8 LEU A 14 1 N LEU A 9 O GLN A 61 SHEET 4 A 6 CYS A 84 ASP A 90 1 O VAL A 86 N LEU A 14 SHEET 5 A 6 PHE A 121 ASN A 126 1 O ASN A 126 N TYR A 89 SHEET 6 A 6 LEU A 154 THR A 157 1 O THR A 157 N GLY A 125 LINK OG1 THR A 22 MG MG A 401 1555 1555 2.08 LINK O3B GDP A 400 MG MG A 401 1555 1555 2.01 LINK MG MG A 401 O HOH A 583 1555 1555 2.06 LINK MG MG A 401 O HOH A 584 1555 1555 2.18 LINK MG MG A 401 O HOH A 585 1555 1555 2.16 LINK MG MG A 401 O HOH A 586 1555 1555 2.03 SITE 1 AC1 6 THR A 22 GDP A 400 HOH A 583 HOH A 584 SITE 2 AC1 6 HOH A 585 HOH A 586 SITE 1 AC2 20 GLY A 18 VAL A 19 GLY A 20 LYS A 21 SITE 2 AC2 20 THR A 22 SER A 23 TYR A 33 ASN A 126 SITE 3 AC2 20 LYS A 127 ASP A 129 SER A 158 ALA A 159 SITE 4 AC2 20 LYS A 160 MG A 401 HOH A 553 HOH A 584 SITE 5 AC2 20 HOH A 585 HOH A 586 HOH A 587 HOH A 649 CRYST1 49.535 55.430 60.177 90.00 90.00 90.00 P 21 21 21 4 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 0.020188 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016618 0.00000