HEADER STRUCTURAL GENOMICS 19-JUN-16 5GHD TITLE SOLUTION STRUCTURE OF LYS39 ACETYLATED HUMAN SUMO1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-97; COMPND 5 SYNONYM: SUMO-1,GAP-MODIFYING PROTEIN 1,GMP1,SMT3 HOMOLOG 3,SENTRIN, COMPND 6 UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1,UBIQUITIN-LIKE PROTEIN SMT3C, COMPND 7 SMT3C,UBIQUITIN-LIKE PROTEIN UBL1; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: LYS39 ACETYLATED MATURE SMALL UBIQUITIN-RELATED COMPND 10 MODIFIER 1 (SUMO1) RESIDUES 1-14 (MGSSHHHHHHSQDP) REPRESENT A NON- COMPND 11 NATIVE PURIFICATION TAG. THESE RESIDUES WERE NEITHER ASSIGNED NOR COMPND 12 INCLUDED IN STRUCTURE CALCULATION. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-CL.43; 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: PCDFDUET-1; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PCDFDUET-1; SOURCE 11 OTHER_DETAILS: PLASMID PCDF PYLT-1 WITH SUMO INSERT WITH K39STOP SOURCE 12 MUTATION (WITH AMBER CODON) AND PACKRS-3 AS DESCRIBED IN NEUMANN ET SOURCE 13 AL., MOL CELL, 36, 153, 2009 KEYWDS UBIQUITIN-LIKE PROTEIN, ACETYLATED PROTEIN, STRUCTURAL GENOMICS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.T.NAIK,N.NAIK,H.SHIH,T.HUANG REVDAT 3 15-NOV-23 5GHD 1 ATOM REVDAT 2 11-OCT-23 5GHD 1 REMARK REVDAT 1 07-JUN-17 5GHD 0 JRNL AUTH M.T.NAIK,N.NAIK,H.SHIH,T.HUANG JRNL TITL STRUCTURES OF HUMAN SUMO JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.34 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL STRUCTURE ENSEMBLE WAS REMARK 3 CALCULATED BY SEMI-AUTOMATED NOESY ASSIGNMENT BY CYANA. THE REMARK 3 ASSIGNMENTS WERE MANUALLY VERIFIED IN SPARKY AND FINAL STRUCTURE REMARK 3 ANNEALING WAS PERFORMED IN CYANA.STRUCTURE AND RESTRAINTS FROM REMARK 3 CYANA WERE IMPORTED IN XPLOR-NIH FOR EXPLICIT WATER REFINEMENT., REMARK 3 INITIAL STRUCTURE ENSEMBLE WAS CALCULATED BY SEMI-AUTOMATED REMARK 3 NOESY ASSIGNMENT BY CYANA. THE ASSIGNMENTS WERE MANUALLY REMARK 3 VERIFIED IN SPARKY AND FINAL STRUCTURE ANNEALING WAS PERFORMED REMARK 3 IN CYANA.STRUCTURE AND RESTRAINTS FROM CYANA WERE IMPORTED IN REMARK 3 XPLOR- NIH FOR EXPLICIT WATER REFINEMENT. REMARK 4 REMARK 4 5GHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000772. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : AMBIENT ATM ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 SUMO1 K39AC, 10 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 2 MM DTT, 0.1 MM EDTA, REMARK 210 0.001 % SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; 1 MM [U-100% 15N] SUMO1 REMARK 210 K39AC, 10 MM POTASSIUM PHOSPHATE, REMARK 210 100 MM POTASSIUM CHLORIDE, 2 MM REMARK 210 DTT, 0.1 MM EDTA, 0.001 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 15N] SUMO1 K39AC, 10 MM REMARK 210 POTASSIUM PHOSPHATE, 100 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM DTT, REMARK 210 0.1 MM EDTA, 0.001 % SODIUM REMARK 210 AZIDE, 10 MG/ML PF1 PHAGE, 90% REMARK 210 H2O/10% D2O; 1 MM SUMO1 K39AC, REMARK 210 10 MM POTASSIUM PHOSPHATE, 100 REMARK 210 MM POTASSIUM CHLORIDE, 2 MM DTT, REMARK 210 0.1 MM EDTA, 0.001 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 HBHA(CO)NH; 2D-HBCBCGCDHD; 2D- REMARK 210 HBCBCGCDCEHE; 3D 1H-15N TOCSY; REMARK 210 2D 1H-1H NOESY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 2D 1H-15N HSQC REMARK 210 IPAP; 2D NOESY F1 FILTERED; 2D REMARK 210 NOESY F2 FILTERED; 2D NOESY F1/ REMARK 210 F2 FILTERED; 2D TOCSY F1/F2 REMARK 210 FILTERED REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ; 850 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, TOPSPIN 3.2, SPARKY 3.113 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, DGSA- REMARK 210 DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 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: NMR DATA WAS ACQUIRED AT 295K USING SHIGEMI NMR TUBES. 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 -13 REMARK 465 GLY A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 SER A -3 REMARK 465 GLN A -2 REMARK 465 ASP A -1 REMARK 465 PRO A 0 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 SER A 2 -64.05 -148.56 REMARK 500 1 PRO A 8 -177.47 -65.70 REMARK 500 1 ALY A 39 -154.94 -109.93 REMARK 500 2 SER A 2 -75.33 -144.28 REMARK 500 2 SER A 9 129.51 -173.37 REMARK 500 2 LEU A 13 28.05 -160.84 REMARK 500 2 ALY A 39 -162.28 -107.29 REMARK 500 2 GLU A 93 -177.28 -68.83 REMARK 500 3 SER A 2 27.66 -153.96 REMARK 500 3 ASP A 3 -45.67 -153.17 REMARK 500 3 LEU A 13 -15.79 -146.04 REMARK 500 3 ALY A 39 -159.62 -104.43 REMARK 500 4 ASP A 15 77.46 -100.92 REMARK 500 4 ALY A 39 -158.00 -107.47 REMARK 500 4 GLN A 94 48.91 -158.80 REMARK 500 5 SER A 2 -70.68 -104.40 REMARK 500 5 ASP A 3 -72.06 -113.73 REMARK 500 5 ASP A 15 35.35 -81.89 REMARK 500 5 ALY A 39 -157.98 -108.32 REMARK 500 6 SER A 9 73.31 57.37 REMARK 500 6 GLU A 18 -58.61 -156.09 REMARK 500 6 ALY A 39 -161.97 -103.48 REMARK 500 6 THR A 95 65.62 -68.21 REMARK 500 7 ASP A 3 -61.56 -99.99 REMARK 500 7 ALY A 39 -156.77 -112.82 REMARK 500 8 ASP A 3 -71.29 -75.31 REMARK 500 8 LYS A 16 28.16 -140.86 REMARK 500 8 LYS A 17 -159.92 -128.18 REMARK 500 8 ALY A 39 -159.83 -105.01 REMARK 500 9 SER A 2 -61.28 -176.98 REMARK 500 9 GLN A 4 -167.79 -117.47 REMARK 500 9 ALA A 6 89.60 -158.83 REMARK 500 9 SER A 9 148.12 86.98 REMARK 500 9 ALY A 39 -154.86 -111.16 REMARK 500 10 ASP A 3 -73.95 -125.09 REMARK 500 10 GLN A 4 141.69 -174.61 REMARK 500 10 SER A 9 79.18 56.80 REMARK 500 10 ALY A 39 -161.76 -103.56 REMARK 500 11 ASP A 12 -159.47 -79.74 REMARK 500 11 ALY A 39 -155.59 -112.59 REMARK 500 12 SER A 2 -88.51 -177.89 REMARK 500 12 ASP A 3 -11.68 66.43 REMARK 500 12 GLU A 18 -61.33 -140.42 REMARK 500 12 ALY A 39 -153.29 -110.69 REMARK 500 13 SER A 2 -59.43 -162.48 REMARK 500 13 ALA A 6 64.33 -104.68 REMARK 500 13 ASP A 15 60.86 67.07 REMARK 500 13 ALY A 39 -164.06 -105.85 REMARK 500 13 HIS A 43 108.32 -59.90 REMARK 500 14 ALY A 39 -160.11 -106.41 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2N1V RELATED DB: PDB REMARK 900 RELATED ID: 25576 RELATED DB: BMRB REMARK 900 RELATED ID: 36008 RELATED DB: BMRB REMARK 900 RELATED ID: 5GHB RELATED DB: PDB REMARK 900 RELATED ID: 5GHC RELATED DB: PDB REMARK 900 RELATED ID: 5B7A RELATED DB: PDB DBREF 5GHD A 1 97 UNP P63165 SUMO1_HUMAN 1 97 SEQADV 5GHD MET A -13 UNP P63165 INITIATING METHIONINE SEQADV 5GHD GLY A -12 UNP P63165 EXPRESSION TAG SEQADV 5GHD SER A -11 UNP P63165 EXPRESSION TAG SEQADV 5GHD SER A -10 UNP P63165 EXPRESSION TAG SEQADV 5GHD HIS A -9 UNP P63165 EXPRESSION TAG SEQADV 5GHD HIS A -8 UNP P63165 EXPRESSION TAG SEQADV 5GHD HIS A -7 UNP P63165 EXPRESSION TAG SEQADV 5GHD HIS A -6 UNP P63165 EXPRESSION TAG SEQADV 5GHD HIS A -5 UNP P63165 EXPRESSION TAG SEQADV 5GHD HIS A -4 UNP P63165 EXPRESSION TAG SEQADV 5GHD SER A -3 UNP P63165 EXPRESSION TAG SEQADV 5GHD GLN A -2 UNP P63165 EXPRESSION TAG SEQADV 5GHD ASP A -1 UNP P63165 EXPRESSION TAG SEQADV 5GHD PRO A 0 UNP P63165 EXPRESSION TAG SEQRES 1 A 111 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 111 PRO MET SER ASP GLN GLU ALA LYS PRO SER THR GLU ASP SEQRES 3 A 111 LEU GLY ASP LYS LYS GLU GLY GLU TYR ILE LYS LEU LYS SEQRES 4 A 111 VAL ILE GLY GLN ASP SER SER GLU ILE HIS PHE LYS VAL SEQRES 5 A 111 ALY MET THR THR HIS LEU LYS LYS LEU LYS GLU SER TYR SEQRES 6 A 111 CYS GLN ARG GLN GLY VAL PRO MET ASN SER LEU ARG PHE SEQRES 7 A 111 LEU PHE GLU GLY GLN ARG ILE ALA ASP ASN HIS THR PRO SEQRES 8 A 111 LYS GLU LEU GLY MET GLU GLU GLU ASP VAL ILE GLU VAL SEQRES 9 A 111 TYR GLN GLU GLN THR GLY GLY MODRES 5GHD ALY A 39 LYS MODIFIED RESIDUE HET ALY A 39 26 HETNAM ALY N(6)-ACETYLLYSINE FORMUL 1 ALY C8 H16 N2 O3 HELIX 1 AA1 HIS A 43 GLY A 56 1 14 HELIX 2 AA2 THR A 76 GLY A 81 1 6 SHEET 1 AA1 5 GLU A 33 VAL A 38 0 SHEET 2 AA1 5 ILE A 22 GLY A 28 -1 N ILE A 22 O VAL A 38 SHEET 3 AA1 5 ASP A 86 GLN A 92 1 O ILE A 88 N ILE A 27 SHEET 4 AA1 5 LEU A 62 PHE A 66 -1 N ARG A 63 O TYR A 91 SHEET 5 AA1 5 GLN A 69 ARG A 70 -1 O GLN A 69 N PHE A 66 LINK C VAL A 38 N ALY A 39 1555 1555 1.31 LINK C ALY A 39 N MET A 40 1555 1555 1.31 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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