HEADER SIGNALING PROTEIN 03-SEP-05 2AX5 TITLE SOLUTION STRUCTURE OF URM1 FROM SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL 11.0 KDA PROTEIN IN FAA3-MAS3 INTERGENIC COMPND 3 REGION; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: UBIQUITIN-RELATED MODIFIER-1; 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: YIL008W; 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: PET22B(+) KEYWDS BETA GRASP FOLD, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.XU,H.HUANG,J.ZHANG,J.WU,Y.SHI REVDAT 3 09-MAR-22 2AX5 1 REMARK SEQADV REVDAT 2 24-FEB-09 2AX5 1 VERSN REVDAT 1 27-JUN-06 2AX5 0 JRNL AUTH J.XU,J.ZHANG,L.WANG,J.ZHOU,H.HUANG,J.WU,Y.ZHONG,Y.SHI JRNL TITL SOLUTION STRUCTURE OF URM1 AND ITS IMPLICATIONS FOR THE JRNL TITL 2 ORIGIN OF PROTEIN MODIFIERS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 11625 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16864801 JRNL DOI 10.1073/PNAS.0604876103 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.2, CNS 1.1 REMARK 3 AUTHORS : F.DELAGLIO (NMRPIPE), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS SOLVED USING A TOTAL REMARK 3 OF 1655 DISTANCE RESTRAINTS AND 79 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 2AX5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034419. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8MM [15N, 13C] LABELED URM1 REMARK 210 PROTEIN, 50MM PHOSPHATE BUFFER REMARK 210 (PH6.5), 50MM SODIUM CHLORIDE, REMARK 210 90% H2O, 10% D2O; 0.8MM [15N, REMARK 210 13C] LABELED URM1 PROTEIN, 50MM REMARK 210 PHOSPHATE BUFFER (PH6.5), 50MM REMARK 210 SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3, CNS 1.1, CSI 1.0, REMARK 210 MOLMOL 2K.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 LEU A 100 REMARK 465 GLU A 101 REMARK 465 HIS A 102 REMARK 465 HIS A 103 REMARK 465 HIS A 104 REMARK 465 HIS A 105 REMARK 465 HIS A 106 REMARK 465 HIS A 107 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 LYS A 28 -69.33 -149.37 REMARK 500 1 SER A 43 -77.52 -99.33 REMARK 500 1 ASN A 47 74.05 -157.15 REMARK 500 1 ASN A 50 -44.93 -171.86 REMARK 500 1 GLU A 77 -72.20 -76.15 REMARK 500 1 GLU A 79 -83.98 56.71 REMARK 500 1 ASP A 81 31.09 -91.56 REMARK 500 1 GLU A 85 101.06 -167.64 REMARK 500 1 THR A 95 53.99 -94.43 REMARK 500 2 LYS A 28 -50.49 -156.09 REMARK 500 2 SER A 43 -78.79 -81.87 REMARK 500 2 PRO A 49 77.56 -63.52 REMARK 500 2 ASN A 50 -54.32 -162.26 REMARK 500 2 GLU A 85 102.08 -165.42 REMARK 500 2 SER A 94 82.18 -155.34 REMARK 500 3 PHE A 16 -75.19 -67.38 REMARK 500 3 LYS A 28 -49.35 -155.49 REMARK 500 3 SER A 43 -74.83 -92.67 REMARK 500 3 ASN A 47 74.96 -162.24 REMARK 500 3 PRO A 49 79.53 -61.67 REMARK 500 3 ASN A 50 -51.33 -172.88 REMARK 500 3 GLU A 57 -162.97 -71.85 REMARK 500 3 ASP A 58 86.93 -64.43 REMARK 500 3 GLU A 77 -50.90 -120.96 REMARK 500 3 GLU A 85 100.96 -165.88 REMARK 500 4 PHE A 16 -70.40 -58.61 REMARK 500 4 ASP A 27 48.52 -91.93 REMARK 500 4 SER A 43 -64.59 -95.33 REMARK 500 4 ASN A 47 72.51 -173.87 REMARK 500 4 ASN A 50 -49.00 -158.85 REMARK 500 4 GLU A 77 -58.53 -137.31 REMARK 500 4 GLU A 79 -71.42 -49.61 REMARK 500 4 GLU A 85 99.71 -162.74 REMARK 500 4 ASP A 86 105.05 -43.50 REMARK 500 4 HIS A 97 114.27 73.08 REMARK 500 5 PHE A 16 -70.44 -69.65 REMARK 500 5 ASP A 27 76.13 56.59 REMARK 500 5 LYS A 28 -67.57 -136.67 REMARK 500 5 SER A 43 -68.81 -92.70 REMARK 500 5 ASN A 47 51.41 -143.91 REMARK 500 5 PRO A 49 74.41 -63.32 REMARK 500 5 ASN A 50 -58.35 -167.63 REMARK 500 5 GLU A 79 -78.50 61.76 REMARK 500 5 ASP A 81 47.52 -93.52 REMARK 500 5 LEU A 84 173.78 -59.75 REMARK 500 5 GLU A 85 100.50 -161.65 REMARK 500 5 ASP A 86 105.03 -43.07 REMARK 500 5 LEU A 96 102.19 61.49 REMARK 500 6 LYS A 28 -53.41 -166.29 REMARK 500 6 GLU A 29 -166.59 -174.07 REMARK 500 REMARK 500 THIS ENTRY HAS 209 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2AX5 A 1 99 UNP P40554 URM1_YEAST 1 99 SEQADV 2AX5 LEU A 100 UNP P40554 EXPRESSION TAG SEQADV 2AX5 GLU A 101 UNP P40554 EXPRESSION TAG SEQADV 2AX5 HIS A 102 UNP P40554 EXPRESSION TAG SEQADV 2AX5 HIS A 103 UNP P40554 EXPRESSION TAG SEQADV 2AX5 HIS A 104 UNP P40554 EXPRESSION TAG SEQADV 2AX5 HIS A 105 UNP P40554 EXPRESSION TAG SEQADV 2AX5 HIS A 106 UNP P40554 EXPRESSION TAG SEQADV 2AX5 HIS A 107 UNP P40554 EXPRESSION TAG SEQRES 1 A 107 MET VAL ASN VAL LYS VAL GLU PHE LEU GLY GLY LEU ASP SEQRES 2 A 107 ALA ILE PHE GLY LYS GLN ARG VAL HIS LYS ILE LYS MET SEQRES 3 A 107 ASP LYS GLU ASP PRO VAL THR VAL GLY ASP LEU ILE ASP SEQRES 4 A 107 HIS ILE VAL SER THR MET ILE ASN ASN PRO ASN ASP VAL SEQRES 5 A 107 SER ILE PHE ILE GLU ASP ASP SER ILE ARG PRO GLY ILE SEQRES 6 A 107 ILE THR LEU ILE ASN ASP THR ASP TRP GLU LEU GLU GLY SEQRES 7 A 107 GLU LYS ASP TYR ILE LEU GLU ASP GLY ASP ILE ILE SER SEQRES 8 A 107 PHE THR SER THR LEU HIS GLY GLY LEU GLU HIS HIS HIS SEQRES 9 A 107 HIS HIS HIS HELIX 1 1 LEU A 12 GLY A 17 1 6 HELIX 2 2 THR A 33 THR A 44 1 12 HELIX 3 3 ASP A 51 ILE A 56 1 6 HELIX 4 4 ASP A 73 GLY A 78 1 6 SHEET 1 A 4 HIS A 22 ILE A 24 0 SHEET 2 A 4 VAL A 4 PHE A 8 -1 N VAL A 6 O HIS A 22 SHEET 3 A 4 ASP A 88 SER A 94 1 O PHE A 92 N GLU A 7 SHEET 4 A 4 ILE A 65 ILE A 69 -1 N ILE A 66 O THR A 93 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 MODEL 1