HEADER TRANSFERASE 24-JUL-07 2V6Z TITLE SOLUTION STRUCTURE OF AMINO-TERMINAL DOMAIN OF HUMAN DNA POLYMERASE TITLE 2 EPSILON SUBUNIT B COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE EPSILON SUBUNIT 2; COMPND 3 CHAIN: M; COMPND 4 FRAGMENT: AMINO TERMINAL DOMAIN, RESIDUES 1-75; COMPND 5 SYNONYM: DNA POLYMERASE II SUBUNIT 2, DNA POLYMERASE EPSILON, SUBUNIT COMPND 6 B, DPOE2; COMPND 7 EC: 2.7.7.7; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSFDUET-1 KEYWDS DNA REPLICATION, DNA POLYMERASE EPSILON, DPOE2, TRANSFERASE, AAA KEYWDS 2 PROTEIN FAMILY EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.NUUTINEN,K.FREDRIKSSON,H.TOSSAVAINEN,H.POSPIECH,P.PIRILA,P.PERMI, AUTHOR 2 A.ANNILA,J.E.SYVAOJA REVDAT 9 19-JUN-24 2V6Z 1 REMARK REVDAT 8 14-JUN-23 2V6Z 1 REMARK REVDAT 7 15-JAN-20 2V6Z 1 REMARK REVDAT 6 17-JAN-18 2V6Z 1 TITLE JRNL REMARK ATOM REVDAT 5 24-JUL-13 2V6Z 1 SOURCE REMARK SCALE1 SCALE2 REVDAT 4 30-NOV-11 2V6Z 1 REMARK DBREF SEQADV HELIX REVDAT 4 2 1 SHEET ATOM VERSN REVDAT 3 24-FEB-09 2V6Z 1 VERSN REVDAT 2 09-SEP-08 2V6Z 1 JRNL REVDAT 1 05-AUG-08 2V6Z 0 JRNL AUTH T.NUUTINEN,H.TOSSAVAINEN,K.FREDRIKSSON,P.PIRILA,P.PERMI, JRNL AUTH 2 H.POSPIECH,J.E.SYVAOJA JRNL TITL THE SOLUTION STRUCTURE OF THE AMINO-TERMINAL DOMAIN OF HUMAN JRNL TITL 2 DNA POLYMERASE EPSILON SUBUNIT B IS HOMOLOGOUS TO C-DOMAINS JRNL TITL 3 OF AAA+ PROTEINS. JRNL REF NUCLEIC ACIDS RES. V. 36 5102 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18676977 JRNL DOI 10.1093/NAR/GKN497 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8 REMARK 3 AUTHORS : D.A.CASE,T.A.DARDEN,T.E CHEATHAM III,C.L. REMARK 3 SIMMERLING,J.WANG,R.E.DUKE,R.LUO,K.M.MERZ, B.WANG, REMARK 3 D.A.PEARLMAN,M.CROWLEY,S.BROZELL, V.TSUI,H.GOHLKE, REMARK 3 J.MONGAN,V.HORNAK,G.CUI, P.BEROZA,C.SCHAFMEISTER, REMARK 3 J.W.CALDWELL,W.S.ROSS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1488 DISTANCE RESTRAINTS. REMARK 4 REMARK 4 2V6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1290031977. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.62 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM PROTEIN; 155 MM NACL; 25 REMARK 210 MM TRIS-HCL; 25 MM IMIDAZOLE; REMARK 210 1.25 MM EDTA; 93% H2O, 7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D-15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, AMBER 8, PROCHECK / REMARK 210 PROCHECK-NMR NMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST NOE RESTRAINT VIOLATION REMARK 210 ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NONE 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: M 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN M, CYS 74 TO SER 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 M 1 REMARK 465 GLY M 2 REMARK 465 SER M 3 REMARK 465 SER M 4 REMARK 465 HIS M 5 REMARK 465 HIS M 6 REMARK 465 HIS M 7 REMARK 465 HIS M 8 REMARK 465 HIS M 9 REMARK 465 HIS M 10 REMARK 465 SER M 11 REMARK 465 GLN M 12 REMARK 465 ASP M 13 REMARK 465 PRO M 14 REMARK 465 ASN M 15 REMARK 465 SER M 16 REMARK 465 SER M 17 REMARK 465 SER M 18 REMARK 465 ALA M 19 REMARK 465 ARG M 20 REMARK 465 LEU M 21 REMARK 465 GLN M 22 REMARK 465 VAL M 23 REMARK 465 ASP M 24 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 ARG M 41 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG M 41 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG M 41 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG M 33 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG M 33 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG M 46 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG M 33 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG M 33 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG M 41 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 13 ARG M 33 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG M 33 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG M 33 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG M 41 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 18 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG M 41 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG M 88 NE - CZ - NH1 ANGL. DEV. = 3.2 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 2 SER M 32 33.99 -78.05 REMARK 500 7 ARG M 31 -81.92 -121.22 REMARK 500 7 SER M 32 20.95 45.20 REMARK 500 10 SER M 32 33.93 -75.30 REMARK 500 10 SER M 82 15.64 49.42 REMARK 500 11 SER M 32 25.62 42.39 REMARK 500 11 SER M 82 16.63 52.18 REMARK 500 15 SER M 32 2.29 50.27 REMARK 500 16 ARG M 31 -76.29 -73.49 REMARK 500 16 SER M 32 34.08 38.14 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 M 29 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7419 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 MGSSHHHHHHSQDPNSSSARLQVD IS NON-BIOLOGICAL SEQUENCE. DBREF 2V6Z M 25 99 UNP P56282 DPOE2_HUMAN 1 75 SEQADV 2V6Z MET M 1 UNP P56282 EXPRESSION TAG SEQADV 2V6Z GLY M 2 UNP P56282 EXPRESSION TAG SEQADV 2V6Z SER M 3 UNP P56282 EXPRESSION TAG SEQADV 2V6Z SER M 4 UNP P56282 EXPRESSION TAG SEQADV 2V6Z HIS M 5 UNP P56282 EXPRESSION TAG SEQADV 2V6Z HIS M 6 UNP P56282 EXPRESSION TAG SEQADV 2V6Z HIS M 7 UNP P56282 EXPRESSION TAG SEQADV 2V6Z HIS M 8 UNP P56282 EXPRESSION TAG SEQADV 2V6Z HIS M 9 UNP P56282 EXPRESSION TAG SEQADV 2V6Z HIS M 10 UNP P56282 EXPRESSION TAG SEQADV 2V6Z SER M 11 UNP P56282 EXPRESSION TAG SEQADV 2V6Z GLN M 12 UNP P56282 EXPRESSION TAG SEQADV 2V6Z ASP M 13 UNP P56282 EXPRESSION TAG SEQADV 2V6Z PRO M 14 UNP P56282 EXPRESSION TAG SEQADV 2V6Z ASN M 15 UNP P56282 EXPRESSION TAG SEQADV 2V6Z SER M 16 UNP P56282 EXPRESSION TAG SEQADV 2V6Z SER M 17 UNP P56282 EXPRESSION TAG SEQADV 2V6Z SER M 18 UNP P56282 EXPRESSION TAG SEQADV 2V6Z ALA M 19 UNP P56282 EXPRESSION TAG SEQADV 2V6Z ARG M 20 UNP P56282 EXPRESSION TAG SEQADV 2V6Z LEU M 21 UNP P56282 EXPRESSION TAG SEQADV 2V6Z GLN M 22 UNP P56282 EXPRESSION TAG SEQADV 2V6Z VAL M 23 UNP P56282 EXPRESSION TAG SEQADV 2V6Z ASP M 24 UNP P56282 EXPRESSION TAG SEQADV 2V6Z SER M 98 UNP P56282 CYS 74 ENGINEERED MUTATION SEQRES 1 M 99 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 M 99 PRO ASN SER SER SER ALA ARG LEU GLN VAL ASP MET ALA SEQRES 3 M 99 PRO GLU ARG LEU ARG SER ARG ALA LEU SER ALA PHE LYS SEQRES 4 M 99 LEU ARG GLY LEU LEU LEU ARG GLY GLU ALA ILE LYS TYR SEQRES 5 M 99 LEU THR GLU ALA LEU GLN SER ILE SER GLU LEU GLU LEU SEQRES 6 M 99 GLU ASP LYS LEU GLU LYS ILE ILE ASN ALA VAL GLU LYS SEQRES 7 M 99 GLN PRO LEU SER SER ASN MET ILE GLU ARG SER VAL VAL SEQRES 8 M 99 GLU ALA ALA VAL GLN GLU SER SER HELIX 1 1 ALA M 26 ARG M 41 1 16 HELIX 2 2 ARG M 46 LEU M 57 1 12 HELIX 3 3 GLU M 64 GLU M 77 1 14 HELIX 4 4 GLU M 87 SER M 99 1 13 SHEET 1 MA 2 LEU M 44 LEU M 45 0 SHEET 2 MA 2 MET M 85 ILE M 86 1 N ILE M 86 O LEU M 44 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