HEADER PROTEIN TRANSPORT 28-JAN-20 6XXU TITLE SOLUTION NMR STRUCTURE OF THE NATIVE FORM OF UBCH7 (UBE2L3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 L3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME L3,L-UBC,UBCH7,UBIQUITIN COMPND 5 CARRIER PROTEIN L3,UBIQUITIN-CONJUGATING ENZYME E2-F1,UBIQUITIN- COMPND 6 PROTEIN LIGASE L3; COMPND 7 EC: 2.3.2.23; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2L3, UBCE7, UBCH7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS UBCH7, E2 ENZYME, UBC, UBE2L3, SOLUTION NMR SPECTROSCOPY, PROTEIN KEYWDS 2 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR K.D.MAROUSIS,A.SELIAMI,M.BIRKOU,V.EPISKOPOU,G.A.SPYROULIAS REVDAT 3 25-MAR-20 6XXU 1 JRNL REVDAT 2 19-FEB-20 6XXU 1 JRNL REVDAT 1 05-FEB-20 6XXU 0 JRNL AUTH K.D.MAROUSIS,M.BIRKOU,A.ASIMAKOPOULOU,G.A.SPYROULIAS JRNL TITL 1H,13C,15N BACKBONE AND SIDE-CHAIN RESONANCE ASSIGNMENT OF JRNL TITL 2 THE NATIVE FORM OF UBCH7 (UBE2L3) THROUGH SOLUTION NMR JRNL TITL 3 SPECTROSCOPY. JRNL REF BIOMOL.NMR ASSIGN. V. 14 73 2020 JRNL REFN ESSN 1874-270X JRNL PMID 31792831 JRNL DOI 10.1007/S12104-019-09923-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XXU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106463. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-99% 15N] UBCH7 E2 REMARK 210 ENZYME, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 0.25 MM DSS, 90% H2O/ REMARK 210 10% D2O; 0.9 MM [U-99% 13C; U-99% REMARK 210 15N] UBCH7 E2 ENZYME, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 0.25 MM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D HNHA; 2D 1H-13C HSQC; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HN(CO) REMARK 210 CA; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D REMARK 210 HCCH-TOCSY; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.8.4, DYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 21 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 1 TYR A 147 CB - CG - CD1 ANGL. DEV. = -3.6 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 1 MET A 19 82.06 -66.13 REMARK 500 1 LYS A 20 -79.83 -114.01 REMARK 500 1 ASN A 31 46.20 -87.66 REMARK 500 1 PRO A 45 84.92 -62.61 REMARK 500 1 HIS A 119 70.50 -162.94 REMARK 500 2 MET A 19 81.08 -62.04 REMARK 500 2 LYS A 20 -75.12 -110.60 REMARK 500 2 ASP A 42 -54.93 -126.19 REMARK 500 2 PRO A 45 76.51 -64.98 REMARK 500 2 GLU A 60 21.40 -72.95 REMARK 500 2 HIS A 119 64.70 -167.50 REMARK 500 2 ASP A 132 85.28 -155.25 REMARK 500 3 LYS A 20 -75.42 -107.73 REMARK 500 3 ASN A 31 46.49 -87.00 REMARK 500 3 ASP A 42 -46.92 -131.47 REMARK 500 3 PRO A 45 91.72 -56.87 REMARK 500 3 PHE A 57 79.02 -117.27 REMARK 500 3 GLU A 60 20.24 -73.87 REMARK 500 3 LYS A 73 152.29 -49.16 REMARK 500 3 HIS A 119 63.11 -154.64 REMARK 500 4 MET A 19 81.56 -62.55 REMARK 500 4 LYS A 20 -81.23 -109.79 REMARK 500 4 PRO A 45 82.50 -60.79 REMARK 500 4 GLU A 60 23.03 -72.04 REMARK 500 4 HIS A 119 71.94 -161.89 REMARK 500 5 MET A 19 87.54 -59.98 REMARK 500 5 LYS A 20 -78.74 -108.52 REMARK 500 5 ASN A 31 43.14 -85.77 REMARK 500 5 PRO A 41 -178.61 -67.47 REMARK 500 5 ASP A 42 -55.23 -134.73 REMARK 500 5 PRO A 45 89.72 -60.58 REMARK 500 5 GLU A 60 24.34 -76.65 REMARK 500 5 LYS A 82 22.63 -77.07 REMARK 500 5 HIS A 119 65.65 -161.10 REMARK 500 6 MET A 19 78.45 -60.80 REMARK 500 6 LYS A 20 -76.86 -110.20 REMARK 500 6 PRO A 45 104.97 -59.46 REMARK 500 6 ALA A 50 -155.40 -152.38 REMARK 500 6 GLU A 118 -70.60 -61.85 REMARK 500 6 HIS A 119 66.85 -150.23 REMARK 500 7 MET A 19 83.39 -64.39 REMARK 500 7 LYS A 20 -78.20 -111.88 REMARK 500 7 ASN A 31 39.67 -83.67 REMARK 500 7 ASP A 42 -52.34 -122.98 REMARK 500 7 PRO A 45 91.88 -62.65 REMARK 500 7 GLU A 60 25.18 -76.72 REMARK 500 7 HIS A 119 59.56 -155.94 REMARK 500 7 ASP A 132 80.96 -151.30 REMARK 500 8 MET A 19 84.90 -63.57 REMARK 500 8 ASN A 31 39.23 -85.11 REMARK 500 REMARK 500 THIS ENTRY HAS 153 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 3 ARG A 151 0.09 SIDE CHAIN REMARK 500 4 ARG A 151 0.09 SIDE CHAIN REMARK 500 7 ARG A 151 0.09 SIDE CHAIN REMARK 500 8 ARG A 6 0.12 SIDE CHAIN REMARK 500 8 ARG A 23 0.11 SIDE CHAIN REMARK 500 9 TYR A 46 0.10 SIDE CHAIN REMARK 500 9 ARG A 151 0.08 SIDE CHAIN REMARK 500 10 ARG A 151 0.08 SIDE CHAIN REMARK 500 12 ARG A 151 0.08 SIDE CHAIN REMARK 500 14 TYR A 46 0.09 SIDE CHAIN REMARK 500 17 ARG A 151 0.10 SIDE CHAIN REMARK 500 18 ARG A 151 0.10 SIDE CHAIN REMARK 500 19 PHE A 143 0.08 SIDE CHAIN REMARK 500 19 ARG A 151 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 28028 RELATED DB: BMRB DBREF 6XXU A 1 154 UNP P68036 UB2L3_HUMAN 1 154 SEQRES 1 A 154 MET ALA ALA SER ARG ARG LEU MET LYS GLU LEU GLU GLU SEQRES 2 A 154 ILE ARG LYS CYS GLY MET LYS ASN PHE ARG ASN ILE GLN SEQRES 3 A 154 VAL ASP GLU ALA ASN LEU LEU THR TRP GLN GLY LEU ILE SEQRES 4 A 154 VAL PRO ASP ASN PRO PRO TYR ASP LYS GLY ALA PHE ARG SEQRES 5 A 154 ILE GLU ILE ASN PHE PRO ALA GLU TYR PRO PHE LYS PRO SEQRES 6 A 154 PRO LYS ILE THR PHE LYS THR LYS ILE TYR HIS PRO ASN SEQRES 7 A 154 ILE ASP GLU LYS GLY GLN VAL CYS LEU PRO VAL ILE SER SEQRES 8 A 154 ALA GLU ASN TRP LYS PRO ALA THR LYS THR ASP GLN VAL SEQRES 9 A 154 ILE GLN SER LEU ILE ALA LEU VAL ASN ASP PRO GLN PRO SEQRES 10 A 154 GLU HIS PRO LEU ARG ALA ASP LEU ALA GLU GLU TYR SER SEQRES 11 A 154 LYS ASP ARG LYS LYS PHE CYS LYS ASN ALA GLU GLU PHE SEQRES 12 A 154 THR LYS LYS TYR GLY GLU LYS ARG PRO VAL ASP HELIX 1 AA1 ALA A 2 MET A 19 1 18 HELIX 2 AA2 PRO A 45 GLY A 49 5 5 HELIX 3 AA3 GLU A 60 LYS A 64 5 5 HELIX 4 AA4 LEU A 87 TRP A 95 5 9 HELIX 5 AA5 LYS A 100 ASP A 114 1 15 HELIX 6 AA6 ARG A 122 ASP A 132 1 11 HELIX 7 AA7 ASP A 132 GLY A 148 1 17 SHEET 1 AA1 4 PHE A 22 VAL A 27 0 SHEET 2 AA1 4 THR A 34 ILE A 39 -1 O LEU A 38 N ARG A 23 SHEET 3 AA1 4 PHE A 51 ASN A 56 -1 O ILE A 55 N TRP A 35 SHEET 4 AA1 4 LYS A 67 PHE A 70 -1 O THR A 69 N GLU A 54 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