HEADER LIGASE 03-DEC-09 2KR4 TITLE U-BOX DOMAIN OF THE E3 UBIQUITIN LIGASE E4B COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CONJUGATION FACTOR E4 B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: U-BOX DOMAIN (UNP RESIDUES 1092-1173); COMPND 5 SYNONYM: UBIQUITIN FUSION DEGRADATION PROTEIN 2, UFD2A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: UBE4B, UFD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PBG102; SOURCE 9 OTHER_DETAILS: 6XHIS-SUMO TAG WITH H3C PROTEASE CLEAVAGE SITE KEYWDS U-BOX, E4B, UFD2, RING, UBIQUITIN, E3 LIGASE, UBL CONJUGATION KEYWDS 2 PATHWAY, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.NORDQUIST,S.SOSS,W.CHAZIN REVDAT 2 16-MAR-22 2KR4 1 REMARK SEQADV REVDAT 1 26-JAN-10 2KR4 0 JRNL AUTH K.A.NORDQUIST,Y.N.DIMITROVA,P.S.BRZOVIC,W.B.RIDENOUR, JRNL AUTH 2 K.A.MUNRO,S.E.SOSS,R.M.CAPRIOLI,R.E.KLEVIT,W.J.CHAZIN JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE MONOMERIC JRNL TITL 2 U-BOX DOMAIN FROM E4B. JRNL REF BIOCHEMISTRY V. 49 347 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20017557 JRNL DOI 10.1021/BI901620V REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2009.015.15.35, AMBER 9 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CASE, DARDEN, CHEATHAM, III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, ... AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: COMPUTED THROUGH AMBER9 IN WATER, REMARK 3 COMPUTED THROUGH AMBER9 IN WATER. SINGLE RESIDUES IN SOME MODELS REMARK 3 HAVE PHI-PSI ANGLE COMBINATIONS THAT ARE OUTSIDE THE NORM. THESE REMARK 3 ARE FOUND ONLY FOR RESIDUES THAT LACK EXPERIMENTAL CONSTRAINTS REMARK 3 AND WHICH ARE THEREFORE POORLY DEFINED IN THE STRUCTURE. REMARK 4 REMARK 4 2KR4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000101469. 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 : 25 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 750 UM [U-100% 13C; U-100% 15N] REMARK 210 U-BOX DOMAIN OF E4B, 90% H2O/10% REMARK 210 D2O; 1 MM U-BOX DOMAIN OF E4B, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D DQF-COSY; 2D 1H-1H NOESY; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HN(CO) REMARK 210 CA; 3D H(CCO)NH; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.113, CYANA 2..1 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: 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: 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 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 2 PRO A 1 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 2 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 4 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 5 PRO A 1 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 6 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 7 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 8 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 PRO A 1 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 10 PRO A 1 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 11 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 PRO A 1 CA - N - CD ANGL. DEV. = -9.2 DEGREES REMARK 500 13 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 PRO A 1 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 14 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 PRO A 1 CA - N - CD ANGL. DEV. = -9.2 DEGREES REMARK 500 16 PRO A 1 CA - N - CD ANGL. DEV. = -9.2 DEGREES REMARK 500 18 PRO A 1 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 19 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 19 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 20 PRO A 1 CA - N - CD ANGL. DEV. = -8.9 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 THR A 25 -35.49 71.70 REMARK 500 1 ASN A 54 -27.40 -154.00 REMARK 500 2 TYR A 8 48.99 -77.75 REMARK 500 2 THR A 25 -16.87 55.04 REMARK 500 2 ASP A 26 73.54 -117.86 REMARK 500 2 SER A 82 -5.89 70.79 REMARK 500 2 ASP A 84 163.15 81.26 REMARK 500 3 TYR A 8 27.87 -77.65 REMARK 500 3 THR A 25 -27.73 67.36 REMARK 500 4 ASP A 21 -2.87 73.78 REMARK 500 4 THR A 25 -42.27 72.23 REMARK 500 5 TYR A 8 43.31 -77.31 REMARK 500 5 THR A 25 -40.78 75.39 REMARK 500 5 SER A 83 -26.30 70.11 REMARK 500 6 LEU A 19 -53.04 -132.90 REMARK 500 6 THR A 25 -31.70 71.50 REMARK 500 7 THR A 25 -20.64 57.18 REMARK 500 7 ASP A 84 158.47 90.03 REMARK 500 8 TYR A 8 31.43 -77.79 REMARK 500 8 THR A 25 -39.71 71.87 REMARK 500 9 GLU A 5 171.73 66.47 REMARK 500 9 ASP A 21 -1.62 68.64 REMARK 500 9 THR A 25 -29.90 59.66 REMARK 500 9 ASN A 54 -17.93 -159.33 REMARK 500 10 THR A 25 -19.70 57.06 REMARK 500 11 THR A 25 -26.12 65.48 REMARK 500 12 THR A 25 -23.84 57.47 REMARK 500 12 ASP A 84 -81.96 66.03 REMARK 500 13 ASP A 21 -1.64 74.56 REMARK 500 13 THR A 25 -26.50 64.22 REMARK 500 13 ASP A 26 78.67 -119.45 REMARK 500 13 SER A 82 -38.79 76.65 REMARK 500 13 SER A 83 -3.89 77.07 REMARK 500 14 THR A 25 -29.48 71.48 REMARK 500 15 SER A 3 -4.59 75.41 REMARK 500 15 THR A 25 -28.82 66.96 REMARK 500 15 SER A 82 138.66 131.27 REMARK 500 16 ASP A 7 -9.79 75.01 REMARK 500 16 THR A 25 -34.52 73.35 REMARK 500 17 THR A 25 -36.16 74.07 REMARK 500 18 THR A 25 -31.70 65.19 REMARK 500 18 SER A 82 -25.40 -167.52 REMARK 500 19 THR A 25 -23.00 66.69 REMARK 500 20 THR A 25 -37.34 73.31 REMARK 500 20 ASP A 26 79.69 -115.90 REMARK 500 20 SER A 82 -139.86 -166.70 REMARK 500 20 SER A 83 -37.86 73.03 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 15 ARG A 55 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2KR4 A 4 85 UNP Q9ES00 UBE4B_MOUSE 1092 1173 SEQADV 2KR4 PRO A 1 UNP Q9ES00 EXPRESSION TAG SEQADV 2KR4 GLY A 2 UNP Q9ES00 EXPRESSION TAG SEQADV 2KR4 SER A 3 UNP Q9ES00 EXPRESSION TAG SEQRES 1 A 85 PRO GLY SER ALA GLU ILE ASP TYR SER ASP ALA PRO ASP SEQRES 2 A 85 GLU PHE ARG ASP PRO LEU MET ASP THR LEU MET THR ASP SEQRES 3 A 85 PRO VAL ARG LEU PRO SER GLY THR VAL MET ASP ARG SER SEQRES 4 A 85 ILE ILE LEU ARG HIS LEU LEU ASN SER PRO THR ASP PRO SEQRES 5 A 85 PHE ASN ARG GLN MET LEU THR GLU SER MET LEU GLU PRO SEQRES 6 A 85 VAL PRO GLU LEU LYS GLU GLN ILE GLN ALA TRP MET ARG SEQRES 7 A 85 GLU LYS GLN SER SER ASP HIS HELIX 1 1 ARG A 38 SER A 48 1 11 HELIX 2 2 THR A 59 LEU A 63 5 5 HELIX 3 3 VAL A 66 SER A 83 1 18 SHEET 1 A 3 VAL A 35 ASP A 37 0 SHEET 2 A 3 PRO A 27 ARG A 29 -1 N VAL A 28 O MET A 36 SHEET 3 A 3 GLU A 64 PRO A 65 -1 O GLU A 64 N ARG A 29 CISPEP 1 PRO A 1 GLY A 2 15 -1.03 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