HEADER STRUCTURAL GENOMICS, SIGNALING PROTEIN 26-JUL-02 1M94 TITLE SOLUTION STRUCTURE OF THE YEAST UBIQUITIN-LIKE MODIFIER PROTEIN HUB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN YNR032C-A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HUB1; COMPND 5 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: YNR032C-A/HUB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-(GOLD LAMDADE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS UBIQUITIN-LIKE FOLD OR BETA-GRASP FOLD, STRUCTURAL GENOMICS, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.A.RAMELOT,J.R.CORT,A.A.YEE,A.SEMESI,A.M.EDWARDS,C.H.ARROWSMITH, AUTHOR 2 M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 8 22-MAY-24 1M94 1 REMARK REVDAT 7 23-FEB-22 1M94 1 REMARK SEQADV REVDAT 6 24-FEB-09 1M94 1 VERSN REVDAT 5 25-JAN-05 1M94 1 AUTHOR KEYWDS REMARK REVDAT 4 02-SEP-03 1M94 1 AUTHOR REVDAT 3 05-AUG-03 1M94 1 JRNL REVDAT 2 18-MAR-03 1M94 1 JRNL REVDAT 1 11-DEC-02 1M94 0 JRNL AUTH T.A.RAMELOT,J.R.CORT,A.A.YEE,A.SEMESI,A.M.EDWARDS, JRNL AUTH 2 C.H.ARROWSMITH,M.A.KENNEDY JRNL TITL SOLUTION STRUCTURE OF THE YEAST UBIQUITIN-LIKE MODIFIER JRNL TITL 2 PROTEIN HUB1 JRNL REF J.STRUCT.FUNCT.GENOM. V. 4 25 2003 JRNL REFN ISSN 1345-711X JRNL PMID 12943364 JRNL DOI 10.1023/A:1024674220425 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.84, X-PLOR 3.84 REMARK 3 AUTHORS : BRUNGER, A.T. (X-PLOR), BRUNGER, A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 869 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE REMARK 3 CONSTRAINTS: TOTAL = 783; INTRA-RESIDUE [I=J] = 4; SEQUENTIAL REMARK 3 [(I-J)=1] = 229; MEDIUM RANGE [1<(I-J)<5] = 159; LONG RANGE [(I- REMARK 3 J)>=5] = 333; HYDROGEN BOND CONSTRAINTS = 58 (2 PER H-BOND); REMARK 3 NUMBER OF DISTANCE CONSTRAINTS PER RESIDUE = 10.7; DIHEDRAL- REMARK 3 ANGLE CONSTRAINTS = 86 (50 PHI, 36 PSI); TOTAL NUMBER OF REMARK 3 CONSTRAINTS PER RESIDUE = 11.9; NUMBER OF LONG RANGE CONSTRAINTS REMARK 3 PER RESIDUE = 4.6; NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF REMARK 3 STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0 ANG = 22.9; REMARK 3 AVERAGE R.M.S. DISTANCE VIOLATION = 0.006 ANG; MAXIMUM NUMBER OF REMARK 3 DISTANCE VIOLATIONS 28. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 REMARK 3 DEG = 4.6; MAX NUMBER OF ANGLE VIOLATION = 7 DEG; AVERAGE R.M.S. REMARK 3 ANGLE VIOLATION = 0.14 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', REMARK 3 O) = 0.61 ANG; ALL HEAVY ATOMS = 1.17 ANG; PROCHECK: MOST REMARK 3 FAVORED REGIONS = 92%; ADDITIONAL ALLOWED REGIONS = 4%; REMARK 3 GENEROUSLY ALLOWED REGIONS = 2%; DISALLOWED REGIONS = 2%. REMARK 4 REMARK 4 1M94 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016750. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 10 MM NAOAC, 300 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-3 MM HUB1, U-15N, 13C, NAOAC, REMARK 210 PH 5.0; 1-3 MM HUB1, U-15N, 13C, REMARK 210 NAOAC, PH* 4.6; 1-3 MM HUB1, U- REMARK 210 15N, NAOAC, PH 5.0; 1-3 MM HUB1, REMARK 210 U-15N, 10%-13C, NAOAC, PH 5.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HNHA; REMARK 210 3D_13C-SEPARATED_NOESY; 4D_13C/ REMARK 210 15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, VNMR 6.1C, SPARKY 3.98 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 1H-13C HSQC ON 10% C13, U-15N SAMPLE FOR STEREOSPECIFIC REMARK 210 ASSIGNMENTS OF LEU AND VAL 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 CYS A 18 -153.51 -163.10 REMARK 500 1 GLN A 38 152.29 66.31 REMARK 500 1 GLU A 61 67.07 78.52 REMARK 500 2 GLN A 38 155.95 67.69 REMARK 500 2 ASN A 40 -43.71 -166.61 REMARK 500 2 GLU A 61 75.95 73.04 REMARK 500 3 ASP A 8 -77.44 -78.30 REMARK 500 3 ARG A 9 -54.52 -174.11 REMARK 500 3 GLN A 38 152.10 66.00 REMARK 500 3 GLU A 61 55.97 75.85 REMARK 500 4 GLN A 38 149.71 68.18 REMARK 500 4 GLU A 61 56.01 75.46 REMARK 500 5 GLN A 38 150.86 70.81 REMARK 500 5 ASN A 40 -45.75 -152.31 REMARK 500 5 GLU A 61 64.84 71.93 REMARK 500 6 LEU A 10 -57.17 -134.06 REMARK 500 6 GLN A 38 154.09 65.35 REMARK 500 6 GLU A 61 68.50 72.30 REMARK 500 7 GLN A 38 153.55 71.50 REMARK 500 7 ASN A 40 -41.75 -173.90 REMARK 500 7 GLU A 61 62.76 77.33 REMARK 500 8 GLN A 38 156.32 66.69 REMARK 500 8 GLU A 61 71.87 83.04 REMARK 500 9 GLN A 38 150.15 67.85 REMARK 500 9 ASN A 40 -42.85 -160.82 REMARK 500 9 GLU A 61 76.29 72.37 REMARK 500 10 ARG A 9 -64.46 -162.26 REMARK 500 10 GLN A 38 156.02 67.36 REMARK 500 10 GLU A 61 54.21 72.48 REMARK 500 11 ARG A 9 -66.66 -138.96 REMARK 500 11 GLN A 38 154.90 65.44 REMARK 500 11 GLU A 61 75.52 82.12 REMARK 500 12 ARG A 9 -66.63 -136.31 REMARK 500 12 LEU A 10 114.44 -161.65 REMARK 500 12 GLN A 38 156.07 70.78 REMARK 500 12 ASN A 40 -46.61 -164.66 REMARK 500 12 GLU A 61 68.56 77.22 REMARK 500 13 LEU A 10 -60.64 -155.29 REMARK 500 13 GLN A 38 149.78 71.22 REMARK 500 13 ASN A 40 -43.69 -167.48 REMARK 500 13 GLU A 61 76.59 74.15 REMARK 500 14 GLN A 38 155.88 63.67 REMARK 500 14 ASN A 40 -41.73 -169.27 REMARK 500 14 GLU A 61 64.77 73.79 REMARK 500 15 GLN A 38 154.53 66.96 REMARK 500 15 GLU A 61 63.42 83.85 REMARK 500 16 LEU A 10 72.65 57.00 REMARK 500 16 GLN A 38 153.97 68.05 REMARK 500 16 GLU A 61 76.42 73.39 REMARK 500 17 ARG A 9 -63.06 -128.79 REMARK 500 REMARK 500 THIS ENTRY HAS 63 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 9 0.30 SIDE CHAIN REMARK 500 1 ARG A 15 0.31 SIDE CHAIN REMARK 500 2 ARG A 9 0.26 SIDE CHAIN REMARK 500 2 ARG A 15 0.30 SIDE CHAIN REMARK 500 3 ARG A 9 0.31 SIDE CHAIN REMARK 500 3 ARG A 15 0.25 SIDE CHAIN REMARK 500 4 ARG A 9 0.32 SIDE CHAIN REMARK 500 4 ARG A 15 0.31 SIDE CHAIN REMARK 500 5 ARG A 9 0.32 SIDE CHAIN REMARK 500 5 ARG A 15 0.32 SIDE CHAIN REMARK 500 6 ARG A 9 0.32 SIDE CHAIN REMARK 500 6 ARG A 15 0.30 SIDE CHAIN REMARK 500 7 ARG A 9 0.31 SIDE CHAIN REMARK 500 7 ARG A 15 0.32 SIDE CHAIN REMARK 500 8 ARG A 9 0.31 SIDE CHAIN REMARK 500 8 ARG A 15 0.31 SIDE CHAIN REMARK 500 9 ARG A 9 0.32 SIDE CHAIN REMARK 500 9 ARG A 15 0.29 SIDE CHAIN REMARK 500 10 ARG A 9 0.32 SIDE CHAIN REMARK 500 10 ARG A 15 0.31 SIDE CHAIN REMARK 500 11 ARG A 9 0.31 SIDE CHAIN REMARK 500 11 ARG A 15 0.32 SIDE CHAIN REMARK 500 12 ARG A 9 0.29 SIDE CHAIN REMARK 500 12 ARG A 15 0.32 SIDE CHAIN REMARK 500 13 ARG A 9 0.25 SIDE CHAIN REMARK 500 13 ARG A 15 0.30 SIDE CHAIN REMARK 500 14 ARG A 9 0.31 SIDE CHAIN REMARK 500 14 ARG A 15 0.32 SIDE CHAIN REMARK 500 15 ARG A 9 0.30 SIDE CHAIN REMARK 500 15 ARG A 15 0.32 SIDE CHAIN REMARK 500 16 ARG A 9 0.32 SIDE CHAIN REMARK 500 16 ARG A 15 0.31 SIDE CHAIN REMARK 500 17 ARG A 9 0.32 SIDE CHAIN REMARK 500 17 ARG A 15 0.32 SIDE CHAIN REMARK 500 18 ARG A 9 0.31 SIDE CHAIN REMARK 500 18 ARG A 15 0.29 SIDE CHAIN REMARK 500 19 ARG A 9 0.31 SIDE CHAIN REMARK 500 19 ARG A 15 0.31 SIDE CHAIN REMARK 500 20 ARG A 9 0.31 SIDE CHAIN REMARK 500 20 ARG A 15 0.32 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: YTYST190 RELATED DB: TARGETDB DBREF 1M94 A 1 73 UNP Q6Q546 HUB1_YEAST 1 73 SEQADV 1M94 MET A -19 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 GLY A -18 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 SER A -17 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 SER A -16 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 HIS A -15 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 HIS A -14 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 HIS A -13 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 HIS A -12 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 HIS A -11 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 HIS A -10 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 SER A -9 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 SER A -8 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 GLY A -7 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 LEU A -6 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 VAL A -5 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 PRO A -4 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 ARG A -3 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 GLY A -2 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 SER A -1 UNP Q6Q546 EXPRESSION TAG SEQADV 1M94 HIS A 0 UNP Q6Q546 EXPRESSION TAG SEQRES 1 A 93 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 93 LEU VAL PRO ARG GLY SER HIS MET ILE GLU VAL VAL VAL SEQRES 3 A 93 ASN ASP ARG LEU GLY LYS LYS VAL ARG VAL LYS CYS LEU SEQRES 4 A 93 ALA GLU ASP SER VAL GLY ASP PHE LYS LYS VAL LEU SER SEQRES 5 A 93 LEU GLN ILE GLY THR GLN PRO ASN LYS ILE VAL LEU GLN SEQRES 6 A 93 LYS GLY GLY SER VAL LEU LYS ASP HIS ILE SER LEU GLU SEQRES 7 A 93 ASP TYR GLU VAL HIS ASP GLN THR ASN LEU GLU LEU TYR SEQRES 8 A 93 TYR LEU HELIX 1 1 SER A 23 GLY A 36 1 14 HELIX 2 2 SER A 56 GLU A 61 1 6 SHEET 1 A 5 LYS A 12 CYS A 18 0 SHEET 2 A 5 ILE A 2 ASP A 8 -1 N ILE A 2 O CYS A 18 SHEET 3 A 5 THR A 66 TYR A 72 1 O LEU A 68 N VAL A 5 SHEET 4 A 5 ILE A 42 GLN A 45 -1 N VAL A 43 O TYR A 71 SHEET 5 A 5 VAL A 50 LEU A 51 -1 O LEU A 51 N LEU A 44 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