PDB Short entry for 2KTF HEADER PROTEIN BINDING 01-FEB-10 2KTF TITLE SOLUTION NMR STRUCTURE OF HUMAN POLYMERASE IOTA UBM2 IN COMPLEX WITH TITLE 2 UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA POLYMERASE IOTA; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UBIQUITIN BIDING MOTIF UBM2; COMPND 9 SYNONYM: RAD30 HOMOLOG B, ETA2; COMPND 10 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: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSUB; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: POLI, RAD30B; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PTEV KEYWDS TRANSLESION SYNTHESIS DNA POLYMERASE, Y-FAMILY DNA POLYMERASE, KEYWDS 2 UBIQUITIN BINDING MOTIF, UBIQUITIN, ISOPEPTIDE BOND, NUCLEUS, KEYWDS 3 PHOSPHOPROTEIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.CUI,R.BENIRSCHKE,G.MER REVDAT 3 08-DEC-10 2KTF 1 JRNL REVDAT 2 01-DEC-10 2KTF 1 JRNL REVDAT 1 03-NOV-10 2KTF 0 JRNL AUTH G.CUI,R.C.BENIRSCHKE,H.F.TUAN,N.JURANIC,S.MACURA, JRNL AUTH 2 M.V.BOTUYAN,G.MER JRNL TITL STRUCTURAL BASIS OF UBIQUITIN RECOGNITION BY TRANSLESION JRNL TITL 2 SYNTHESIS DNA POLYMERASE IOTA. JRNL REF BIOCHEMISTRY V. 49 10198 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 21049971 JRNL DOI 10.1021/BI101303T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8 REMARK 3 AUTHORS : CASE, D. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KTF COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-10. REMARK 100 THE RCSB ID CODE IS RCSB101551. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.08 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 3.5 MM PEPTIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 30 MM SODIUM REMARK 210 CHLORIDE, 0.001 % SODIUM AZIDE, REMARK 210 90% H2O/10% D2O; 2.5 MM PROTEIN, REMARK 210 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 PEPTIDE, 20 MM SODIUM PHOSPHATE, REMARK 210 30 MM SODIUM CHLORIDE, 0.001 % REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HCACO; 3D C(CO)NH; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HBHA(CO)NH; 3D 13C EDITED DOUBLE- REMARK 210 FILTERED 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 : NMRPIPE 2.1, NMRVIEW 5.0.4, REMARK 210 CYANA 2.1, SANE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: 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: 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 4 ARG B 705 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 7 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 7 ARG B 705 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 17 ARG B 705 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 18 ARG B 705 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 19 ARG B 705 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 GLN A 62 -169.24 -124.74 REMARK 500 1 LEU A 73 -57.24 70.20 REMARK 500 1 PHE B 679 -75.94 -142.97 REMARK 500 2 GLU A 64 50.70 39.86 REMARK 500 2 LEU A 73 -43.80 65.70 REMARK 500 2 PRO B 680 -175.46 -65.19 REMARK 500 3 LEU A 73 -16.10 46.46 REMARK 500 3 SER B 681 11.72 -60.40 REMARK 500 3 GLU B 690 4.19 -66.32 REMARK 500 4 GLN A 62 -168.62 -126.47 REMARK 500 4 GLU A 64 46.71 39.38 REMARK 500 4 LEU A 73 -59.52 68.19 REMARK 500 4 PHE B 679 53.33 36.66 REMARK 500 4 PRO B 680 -176.67 -61.01 REMARK 500 5 GLN A 62 -169.86 -127.23 REMARK 500 5 LEU A 73 -56.66 70.38 REMARK 500 5 ASP B 682 -7.31 -57.64 REMARK 500 6 GLN A 62 -167.62 -126.72 REMARK 500 6 LEU A 73 -50.05 65.44 REMARK 500 6 ASP B 682 -6.41 -58.43 REMARK 500 7 GLN A 62 -169.58 -128.07 REMARK 500 7 GLU A 64 46.98 39.62 REMARK 500 7 LEU A 73 -22.33 59.47 REMARK 500 7 SER B 681 4.49 -58.89 REMARK 500 8 GLN A 62 -168.70 -126.71 REMARK 500 8 LEU A 73 -20.24 63.37 REMARK 500 8 ASP B 682 -5.08 -58.57 REMARK 500 9 ASN A 60 19.67 59.54 REMARK 500 9 GLN A 62 -169.60 -125.19 REMARK 500 9 LEU A 73 -63.55 70.71 REMARK 500 9 ASP B 682 -4.08 -59.10 REMARK 500 10 ASN A 60 18.48 59.76 REMARK 500 10 GLN A 62 -167.85 -125.85 REMARK 500 10 LEU A 73 -57.25 69.31 REMARK 500 10 PHE B 679 -92.95 -120.29 REMARK 500 11 GLN A 62 -168.74 -127.88 REMARK 500 11 GLU A 64 50.28 39.52 REMARK 500 11 LEU A 73 -33.43 65.49 REMARK 500 11 PHE B 679 -78.62 -135.96 REMARK 500 12 ASN A 60 19.39 59.15 REMARK 500 12 GLN A 62 -168.35 -126.03 REMARK 500 12 LEU A 73 -33.91 63.75 REMARK 500 12 PRO B 680 -169.77 -74.61 REMARK 500 12 SER B 681 15.83 -60.88 REMARK 500 13 GLN A 62 -166.85 -125.73 REMARK 500 13 LEU A 73 -52.69 66.47 REMARK 500 13 SER B 681 17.01 -60.43 REMARK 500 14 GLN A 62 -169.15 -127.81 REMARK 500 14 LEU A 73 -44.98 64.48 REMARK 500 14 ASP B 682 -3.96 -58.81 REMARK 500 REMARK 500 THIS ENTRY HAS 77 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 74 0.09 SIDE CHAIN REMARK 500 3 ARG A 42 0.11 SIDE CHAIN REMARK 500 12 ARG A 42 0.10 SIDE CHAIN REMARK 500 12 ARG A 54 0.08 SIDE CHAIN REMARK 500 13 ARG A 42 0.11 SIDE CHAIN REMARK 500 15 ARG A 42 0.08 SIDE CHAIN REMARK 500 16 ARG A 74 0.08 SIDE CHAIN REMARK 500 20 ARG A 54 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 3 LEU A 73 24.6 L L OUTSIDE RANGE REMARK 500 18 LYS B 697 24.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL DBREF 2KTF A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2KTF B 679 707 UNP Q9UNA4 POLI_HUMAN 679 707 SEQADV 2KTF GLY B -3 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KTF HIS B -2 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KTF MET B -1 UNP Q9UNA4 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 32 GLY HIS MET PHE PRO SER ASP ILE ASP PRO GLN VAL PHE SEQRES 2 B 32 TYR GLU LEU PRO GLU ALA VAL GLN LYS GLU LEU LEU ALA SEQRES 3 B 32 GLU TRP LYS ARG THR GLY HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 HELIX 4 4 PRO B 685 GLU B 690 1 6 HELIX 5 5 PRO B 692 GLY B 707 1 16 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 SER A 65 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 LEU A 50 -1 O LEU A 50 N LEU A 43 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