PDB Short entry for 2K5U HEADER SIGNALING PROTEIN 30-JUN-08 2K5U TITLE SOLUTION STRUCTURE OF MYIRSTOYLATED YEAST ARF1 PROTEIN, GDP-BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLATION FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: ARF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET20(B) KEYWDS ARF, ARF1, MYRISTOYL, MYRSITOYLATED, GDP, ER-GOLGI TRANSPORT, GOLGI KEYWDS 2 APPARATUS, GTP-BINDING, LIPOPROTEIN, MYRISTATE, NUCLEOTIDE-BINDING, KEYWDS 3 PROTEIN TRANSPORT, TRANSPORT, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR J.PRESTEGARD,Y.LIU REVDAT 2 16-MAR-22 2K5U 1 REMARK SEQADV LINK REVDAT 1 27-JAN-09 2K5U 0 JRNL AUTH Y.LIU,R.A.KAHN,J.H.PRESTEGARD JRNL TITL STRUCTURE AND MEMBRANE INTERACTION OF MYRISTOYLATED ARF1 JRNL REF STRUCTURE V. 17 79 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19141284 JRNL DOI 10.1016/J.STR.2008.10.020 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR, CNS REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER, ADAMS, CLORE, GROS, NILGES REMARK 3 AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K5U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100713. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-13C; U-15N; U-2H] MYR REMARK 210 -YARF1.GDP, 95% H2O/5% D2O; 0.8 REMARK 210 MM [U-98% 13C; U-98% 15N] MYR- REMARK 210 YARF1.GDP, 95% H2O/5% D2O; 0.8 REMARK 210 MM [U-100% 13C; U-100% 15N; 80% REMARK 210 2H] MYR-YARF1.GDP, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CBCA(CO)NH; 3D HNCA; 3D HNCO; REMARK 210 3D HNCACB; 3D HN(CO)CA; 3D REMARK 210 HN(COCA)CB; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 3D 13C-FILTERED- REMARK 210 NOESY-13C-EDITED NOESY; 3D REMARK 210 DOUBLY-ENHANCED 13C EXICTED C- REMARK 210 CMHM-TOCSY; 2D HSQC-TROSY; 3D REMARK 210 HNCO-JNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, CNS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 LEU A 3 -76.25 -102.57 REMARK 500 1 PHE A 4 93.10 59.21 REMARK 500 1 SER A 6 -82.44 62.26 REMARK 500 1 LYS A 7 -80.58 62.09 REMARK 500 1 ASN A 15 33.69 -168.67 REMARK 500 1 GLU A 17 111.31 62.63 REMARK 500 1 LYS A 38 -35.19 83.87 REMARK 500 1 LEU A 39 81.54 79.27 REMARK 500 1 ILE A 49 -108.29 38.94 REMARK 500 1 LYS A 59 -84.12 58.30 REMARK 500 1 TRP A 66 143.31 -174.35 REMARK 500 1 ARG A 75 -149.99 -155.27 REMARK 500 1 ASP A 96 65.69 -114.36 REMARK 500 1 LYS A 127 32.33 132.66 REMARK 500 1 ARG A 149 154.28 -44.36 REMARK 500 1 ARG A 151 -46.35 123.92 REMARK 500 2 PHE A 4 97.18 60.57 REMARK 500 2 SER A 6 102.90 60.70 REMARK 500 2 LYS A 7 159.66 59.88 REMARK 500 2 PHE A 9 -78.39 -145.69 REMARK 500 2 ASN A 11 20.55 -151.66 REMARK 500 2 LEU A 12 135.31 64.03 REMARK 500 2 PHE A 13 -155.21 -132.95 REMARK 500 2 GLU A 17 90.54 50.80 REMARK 500 2 LYS A 38 -54.06 78.08 REMARK 500 2 LEU A 39 86.43 85.65 REMARK 500 2 ILE A 49 -49.49 -12.24 REMARK 500 2 ARG A 75 47.49 173.57 REMARK 500 2 SER A 76 -96.57 -177.89 REMARK 500 2 ASP A 96 67.94 -114.26 REMARK 500 2 LYS A 127 33.65 132.71 REMARK 500 2 ARG A 151 -45.45 123.15 REMARK 500 2 ASN A 179 65.69 -112.94 REMARK 500 3 PHE A 9 108.58 61.39 REMARK 500 3 ASN A 11 -53.79 -142.06 REMARK 500 3 PHE A 13 39.46 -179.67 REMARK 500 3 LYS A 16 92.95 47.14 REMARK 500 3 GLU A 17 108.05 58.49 REMARK 500 3 LYS A 38 -48.72 86.00 REMARK 500 3 LEU A 39 79.18 74.13 REMARK 500 3 ILE A 49 -110.32 39.03 REMARK 500 3 LYS A 59 -93.25 43.29 REMARK 500 3 TRP A 66 141.06 -171.11 REMARK 500 3 ASP A 72 154.38 61.23 REMARK 500 3 TYR A 82 -71.10 -55.85 REMARK 500 3 ASP A 96 66.54 -112.03 REMARK 500 3 LYS A 127 34.73 132.22 REMARK 500 3 ARG A 149 166.07 -45.36 REMARK 500 3 ARG A 151 -42.56 118.73 REMARK 500 3 LYS A 178 -79.90 -85.65 REMARK 500 REMARK 500 THIS ENTRY HAS 320 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYR A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 182 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15809 RELATED DB: BMRB DBREF 2K5U A 2 181 UNP P11076 ARF1_YEAST 2 181 SEQADV 2K5U MYR A 1 UNP P11076 INSERTION SEQRES 1 A 181 MYR GLY LEU PHE ALA SER LYS LEU PHE SER ASN LEU PHE SEQRES 2 A 181 GLY ASN LYS GLU MET ARG ILE LEU MET VAL GLY LEU ASP SEQRES 3 A 181 GLY ALA GLY LYS THR THR VAL LEU TYR LYS LEU LYS LEU SEQRES 4 A 181 GLY GLU VAL ILE THR THR ILE PRO THR ILE GLY PHE ASN SEQRES 5 A 181 VAL GLU THR VAL GLN TYR LYS ASN ILE SER PHE THR VAL SEQRES 6 A 181 TRP ASP VAL GLY GLY GLN ASP ARG ILE ARG SER LEU TRP SEQRES 7 A 181 ARG HIS TYR TYR ARG ASN THR GLU GLY VAL ILE PHE VAL SEQRES 8 A 181 VAL ASP SER ASN ASP ARG SER ARG ILE GLY GLU ALA ARG SEQRES 9 A 181 GLU VAL MET GLN ARG MET LEU ASN GLU ASP GLU LEU ARG SEQRES 10 A 181 ASN ALA ALA TRP LEU VAL PHE ALA ASN LYS GLN ASP LEU SEQRES 11 A 181 PRO GLU ALA MET SER ALA ALA GLU ILE THR GLU LYS LEU SEQRES 12 A 181 GLY LEU HIS SER ILE ARG ASN ARG PRO TRP PHE ILE GLN SEQRES 13 A 181 ALA THR CYS ALA THR SER GLY GLU GLY LEU TYR GLU GLY SEQRES 14 A 181 LEU GLU TRP LEU SER ASN SER LEU LYS ASN SER THR HET MYR A 1 42 HET GDP A 182 40 HETNAM MYR MYRISTIC ACID HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 1 MYR C14 H28 O2 FORMUL 2 GDP C10 H15 N5 O11 P2 HELIX 1 1 GLY A 29 LYS A 38 1 10 HELIX 2 2 SER A 76 THR A 85 1 10 HELIX 3 3 ASP A 96 SER A 98 5 3 HELIX 4 4 ARG A 99 ASN A 112 1 14 HELIX 5 5 GLU A 113 ARG A 117 5 5 HELIX 6 6 SER A 135 LEU A 143 1 9 HELIX 7 7 GLY A 144 ILE A 148 5 5 HELIX 8 8 GLY A 165 ASN A 179 1 15 SHEET 1 A 7 ILE A 43 THR A 45 0 SHEET 2 A 7 VAL A 53 TYR A 58 -1 O VAL A 53 N THR A 45 SHEET 3 A 7 ILE A 61 VAL A 65 -1 O PHE A 63 N VAL A 56 SHEET 4 A 7 ARG A 19 VAL A 23 1 N MET A 22 O THR A 64 SHEET 5 A 7 GLY A 87 ASP A 93 1 O GLY A 87 N ARG A 19 SHEET 6 A 7 ALA A 120 ASN A 126 1 O LEU A 122 N PHE A 90 SHEET 7 A 7 TRP A 153 THR A 158 1 O PHE A 154 N VAL A 123 LINK C1 MYR A 1 N GLY A 2 1555 1555 1.33 SITE 1 AC1 4 GLY A 2 LYS A 36 LEU A 37 LYS A 38 SITE 1 AC2 14 LEU A 25 ASP A 26 GLY A 27 ALA A 28 SITE 2 AC2 14 GLY A 29 LYS A 30 THR A 31 ASN A 95 SITE 3 AC2 14 ASN A 126 LYS A 127 GLN A 128 ASP A 129 SITE 4 AC2 14 LEU A 130 ALA A 160 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000