HEADER LIGASE 27-APR-06 2DO6 TITLE SOLUTION STRUCTURE OF RSGI RUH-065, A UBA DOMAIN FROM HUMAN CDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE CBL-B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UBA DOMAIN; COMPND 5 SYNONYM: SIGNAL TRANSDUCTION PROTEIN CBL-B, SH3-BINDING PROTEIN CBL- COMPND 6 B, CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE B, RING FINGER PROTEIN COMPND 7 56, RSGI RUH-065; COMPND 8 EC: 6.3.2.-; COMPND 9 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: CBLB, RNF56; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050620-17; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS UBA DOMAIN, DIMER, PROTEIN BINDING, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 2 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.HAMADA,H.HIROTA,Y.-J.LIN,P.GUNTERT,M.SATO,S.KOSHIBA,T.KIGAWA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DO6 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DO6 1 VERSN REVDAT 1 08-MAY-07 2DO6 0 JRNL AUTH T.HAMADA,Y.-J.LIN,M.SATO,S.KOSHIBA,M.INOUE,T.KIGAWA, JRNL AUTH 2 F.HAYASHI,Y.MUTO,M.YOSHIDA,R.AKASAKA,M.KUKIMOTO,T.TERADA, JRNL AUTH 3 M.SHIROUZU,A.TANAKA,P.GUNTERT,S.YOKOYAMA,H.HIROTA JRNL TITL SOLUTION STRUCTURE OF RSGI RUH-065, A UBA DOMAIN FROM HUMAN JRNL TITL 2 CDNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, OPALP 1.4 REMARK 3 AUTHORS : BRUKER (XWINNMR), KORADI, R., BILLETER, M., REMARK 3 GUNTERT, P. (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DO6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000025644. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1MM UBA DOMAIN U-15N,13C, 20MM REMARK 210 D-TRIS-HCL BUFFER (PH 7.0), REMARK 210 100MM NACL, 1MM D-DTT, 0.02% REMARK 210 NAN3, 90% H2O, 10% D2O; 1.0MM REMARK 210 UBA DOMAIN U-15N,13C, 1.0MM UBA REMARK 210 DOMAIN, 20MM D-TRIS-HCL BUFFER REMARK 210 (PH 7.0), 100MM NACL, 1MM D-DTT, REMARK 210 0.02% NAN3, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C_F1-FILTERED_F3-EDITED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, CYANA 2.2.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 3D NMR TECHNIQUES 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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: 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 12 ARG B 41 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 16 ARG B 41 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG B 45 NE - CZ - NH2 ANGL. DEV. = -3.1 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 SER A 6 -164.43 48.84 REMARK 500 1 VAL A 9 -52.70 -120.27 REMARK 500 1 ALA A 33 12.76 -66.75 REMARK 500 1 SER B 6 -118.20 44.98 REMARK 500 1 SER B 48 -60.92 -124.86 REMARK 500 2 SER A 2 -167.20 57.09 REMARK 500 2 SER A 6 -134.14 49.41 REMARK 500 2 ALA A 33 12.47 -66.69 REMARK 500 2 SER B 2 171.11 70.87 REMARK 500 2 SER B 6 172.41 69.31 REMARK 500 3 SER A 2 -36.59 -135.86 REMARK 500 3 VAL A 9 -30.07 -135.65 REMARK 500 3 SER B 2 -76.82 -117.52 REMARK 500 3 SER B 5 18.27 54.10 REMARK 500 3 ASN B 8 109.33 -46.29 REMARK 500 4 SER A 5 -135.01 -154.21 REMARK 500 4 SER A 6 -179.37 -69.91 REMARK 500 4 ALA A 33 7.67 -67.54 REMARK 500 4 SER B 5 -77.03 -117.31 REMARK 500 4 ASN B 35 17.83 59.95 REMARK 500 5 SER A 6 -160.27 -160.21 REMARK 500 5 ASN A 8 96.28 -20.01 REMARK 500 5 ALA B 33 9.76 -67.79 REMARK 500 6 SER A 48 -70.57 -113.41 REMARK 500 6 SER B 5 39.49 -76.90 REMARK 500 6 ALA B 33 3.59 -67.20 REMARK 500 6 SER B 48 -76.94 -89.02 REMARK 500 7 SER A 48 -77.36 -88.71 REMARK 500 7 SER A 51 41.66 -140.32 REMARK 500 7 SER A 52 70.55 44.78 REMARK 500 7 SER B 6 1.31 -152.54 REMARK 500 7 ALA B 33 4.37 -65.99 REMARK 500 7 SER B 48 -72.41 -82.00 REMARK 500 8 ALA A 33 4.67 -69.39 REMARK 500 8 SER A 48 78.50 -100.12 REMARK 500 9 ASN A 8 93.82 5.52 REMARK 500 9 SER A 48 -62.33 -132.11 REMARK 500 9 PRO A 50 -175.25 -64.50 REMARK 500 9 SER A 51 -73.71 -116.22 REMARK 500 9 SER A 52 -165.65 56.33 REMARK 500 9 ALA B 33 6.87 -66.85 REMARK 500 9 SER B 48 -91.60 -83.07 REMARK 500 9 SER B 52 161.91 64.87 REMARK 500 10 VAL A 9 -52.41 -124.52 REMARK 500 10 VAL B 9 -55.04 -127.26 REMARK 500 11 SER A 2 127.62 -173.25 REMARK 500 11 SER A 6 28.05 -156.82 REMARK 500 11 ASN A 8 161.01 62.80 REMARK 500 11 VAL A 9 -55.22 -146.92 REMARK 500 11 ALA A 33 6.22 -66.77 REMARK 500 REMARK 500 THIS ENTRY HAS 113 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 4 ARG B 45 0.11 SIDE CHAIN REMARK 500 5 ARG A 45 0.08 SIDE CHAIN REMARK 500 8 ARG A 41 0.08 SIDE CHAIN REMARK 500 11 ARG A 28 0.08 SIDE CHAIN REMARK 500 13 ARG A 28 0.08 SIDE CHAIN REMARK 500 13 TYR B 21 0.08 SIDE CHAIN REMARK 500 15 ARG B 45 0.11 SIDE CHAIN REMARK 500 18 ARG A 45 0.09 SIDE CHAIN REMARK 500 20 ARG A 45 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2DO6 A 8 47 UNP Q13191 CBLB_HUMAN 931 970 DBREF 2DO6 B 8 47 UNP Q13191 CBLB_HUMAN 931 970 SEQADV 2DO6 GLY A 1 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER A 2 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER A 3 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY A 4 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER A 5 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER A 6 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY A 7 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER A 48 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY A 49 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 PRO A 50 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER A 51 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER A 52 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY A 53 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY B 1 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER B 2 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER B 3 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY B 4 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER B 5 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER B 6 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY B 7 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER B 48 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY B 49 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 PRO B 50 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER B 51 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 SER B 52 UNP Q13191 CLONING ARTIFACT SEQADV 2DO6 GLY B 53 UNP Q13191 CLONING ARTIFACT SEQRES 1 A 53 GLY SER SER GLY SER SER GLY ASN VAL ASP ALA LYS ILE SEQRES 2 A 53 ALA LYS LEU MET GLY GLU GLY TYR ALA PHE GLU GLU VAL SEQRES 3 A 53 LYS ARG ALA LEU GLU ILE ALA GLN ASN ASN VAL GLU VAL SEQRES 4 A 53 ALA ARG SER ILE LEU ARG GLU PHE SER GLY PRO SER SER SEQRES 5 A 53 GLY SEQRES 1 B 53 GLY SER SER GLY SER SER GLY ASN VAL ASP ALA LYS ILE SEQRES 2 B 53 ALA LYS LEU MET GLY GLU GLY TYR ALA PHE GLU GLU VAL SEQRES 3 B 53 LYS ARG ALA LEU GLU ILE ALA GLN ASN ASN VAL GLU VAL SEQRES 4 B 53 ALA ARG SER ILE LEU ARG GLU PHE SER GLY PRO SER SER SEQRES 5 B 53 GLY HELIX 1 1 VAL A 9 GLY A 18 1 10 HELIX 2 2 ALA A 22 ALA A 33 1 12 HELIX 3 3 ASN A 36 SER A 48 1 13 HELIX 4 4 VAL B 9 MET B 17 1 9 HELIX 5 5 ALA B 22 ALA B 33 1 12 HELIX 6 6 ASN B 36 SER B 48 1 13 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