PDB Short entry for 2K6G HEADER DNA BINDING PROTEIN 09-JUL-08 2K6G TITLE SOLUTION STRUCTURE OF THE DNA BINDING BRCT DOMAIN FROM THE LARGE TITLE 2 SUBUNIT OF HUMAN REPLICATION FACTOR C COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION FACTOR C SUBUNIT 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BRCT DOMAIN; COMPND 5 SYNONYM: ACTIVATOR 1 SUBUNIT 1, REPLICATION FACTOR C LARGE SUBUNIT, COMPND 6 RF-C 140 KDA SUBUNIT, ACTIVATOR 1 140 KDA SUBUNIT, A1 140 KDA COMPND 7 SUBUNIT, ACTIVATOR 1 LARGE SUBUNIT, DNA-BINDING PROTEIN PO-GA; 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: RFC1, RFC140; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET20B KEYWDS PROTEIN, BRCT, DNA BINDING, REPLICATION FACTOR C, ACTIVATOR, KEYWDS 2 ALTERNATIVE SPLICING, ATP-BINDING, DNA REPLICATION, DNA-BINDING, KEYWDS 3 METAL-BINDING, NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 4 POLYMORPHISM, TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC, ZINC- KEYWDS 5 FINGER, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 24 AUTHOR M.KOBAYASHI,G.SIEGAL,E.AB,A.M.J.J.BONVIN REVDAT 2 16-MAR-22 2K6G 1 REMARK SEQADV REVDAT 1 22-SEP-09 2K6G 0 JRNL AUTH M.KOBAYASHI,E.AB,A.M.J.J.BONVIN,G.SIEGAL JRNL TITL SOLUTION STRUCTURE OF THE DNA BOUND BRCT DOMAIN FROM HUMAN JRNL TITL 2 REPLICATION FACTOR C P140 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RECOORD SCRIPTS USING CNS REMARK 4 REMARK 4 2K6G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100735. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-15N; U-13C] RFC P140 REMARK 210 BRCT REGION, 0.5 MM SELF - REMARK 210 ANNEALING HAIRPIN - DSDNA, 20 MM REMARK 210 TRIS-HCL, 5 MM NACL, 1 MM DTT, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCA; 3D REMARK 210 HNCACB; CCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 2D 1H-1H REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 180 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 24 REMARK 210 CONFORMERS, SELECTION CRITERIA : BB CONFORMATION Z-SCORE (WHATIF) 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: 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 15 PRO A 391 C - N - CA ANGL. DEV. = 10.9 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 PRO A 391 98.69 -64.40 REMARK 500 1 SER A 396 -43.31 -131.16 REMARK 500 1 ILE A 399 93.13 57.47 REMARK 500 1 LEU A 418 -157.24 -82.00 REMARK 500 1 SER A 420 99.63 -161.17 REMARK 500 1 ASN A 446 -45.87 70.56 REMARK 500 2 LYS A 397 -30.61 -150.02 REMARK 500 2 ILE A 399 81.80 75.00 REMARK 500 2 LEU A 418 -152.03 -90.03 REMARK 500 2 ASN A 446 -34.26 71.92 REMARK 500 3 THR A 377 92.03 66.40 REMARK 500 3 PRO A 391 96.79 -65.38 REMARK 500 3 GLU A 398 -152.98 -126.82 REMARK 500 3 ASN A 446 -29.92 69.67 REMARK 500 3 ASP A 471 -167.17 -113.84 REMARK 500 4 ARG A 376 95.49 66.15 REMARK 500 4 ALA A 393 33.25 -97.90 REMARK 500 4 GLU A 398 -75.88 -56.33 REMARK 500 4 ILE A 399 97.51 67.54 REMARK 500 4 ALA A 403 109.82 -58.47 REMARK 500 4 ASN A 446 -47.42 86.67 REMARK 500 5 ASN A 378 179.15 66.24 REMARK 500 5 GLU A 389 -164.68 -116.96 REMARK 500 5 GLU A 398 -75.41 -75.09 REMARK 500 5 ILE A 399 98.11 66.35 REMARK 500 5 ASN A 446 -24.06 68.60 REMARK 500 6 GLU A 389 74.20 51.98 REMARK 500 6 GLU A 398 -147.61 -96.58 REMARK 500 6 GLU A 419 37.41 -96.95 REMARK 500 6 SER A 420 -162.85 -165.51 REMARK 500 6 ASN A 446 -61.84 69.36 REMARK 500 7 ALA A 393 31.65 -95.20 REMARK 500 7 SER A 396 -36.70 -158.84 REMARK 500 7 ILE A 399 79.85 56.54 REMARK 500 7 ASN A 446 -45.20 71.53 REMARK 500 8 ARG A 388 -58.42 60.28 REMARK 500 8 ILE A 399 101.28 62.70 REMARK 500 8 GLU A 419 51.22 -98.75 REMARK 500 8 SER A 420 -163.17 -177.16 REMARK 500 8 ASN A 446 -45.26 74.74 REMARK 500 8 ASP A 453 106.52 65.96 REMARK 500 9 GLU A 398 -163.48 -118.93 REMARK 500 9 SER A 420 -165.64 -177.21 REMARK 500 9 LYS A 443 44.08 -84.63 REMARK 500 9 LYS A 444 16.71 -162.48 REMARK 500 9 ASN A 446 -42.91 82.59 REMARK 500 10 ASN A 378 -72.78 -143.95 REMARK 500 10 ARG A 388 31.83 -90.76 REMARK 500 10 GLU A 389 -69.83 73.43 REMARK 500 10 ILE A 399 101.22 63.27 REMARK 500 REMARK 500 THIS ENTRY HAS 154 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 12 ARG A 383 0.10 SIDE CHAIN REMARK 500 14 ARG A 423 0.10 SIDE CHAIN REMARK 500 23 ARG A 388 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5041 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFS OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN REMARK 900 RELATED ID: 2EUB RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE BRCT DOMAIN FROM HUMAN REPLICATION FACTOR REMARK 900 C LARGE SUBUNIT 1 DBREF 2K6G A 375 480 UNP P35251 RFC1_HUMAN 375 480 SEQADV 2K6G ASN A 481 UNP P35251 EXPRESSION TAG SEQADV 2K6G LEU A 482 UNP P35251 EXPRESSION TAG SEQADV 2K6G GLU A 483 UNP P35251 EXPRESSION TAG SEQRES 1 A 109 LYS ARG THR ASN TYR GLN ALA TYR ARG SER TYR LEU ASN SEQRES 2 A 109 ARG GLU GLY PRO LYS ALA LEU GLY SER LYS GLU ILE PRO SEQRES 3 A 109 LYS GLY ALA GLU ASN CYS LEU GLU GLY LEU ILE PHE VAL SEQRES 4 A 109 ILE THR GLY VAL LEU GLU SER ILE GLU ARG ASP GLU ALA SEQRES 5 A 109 LYS SER LEU ILE GLU ARG TYR GLY GLY LYS VAL THR GLY SEQRES 6 A 109 ASN VAL SER LYS LYS THR ASN TYR LEU VAL MET GLY ARG SEQRES 7 A 109 ASP SER GLY GLN SER LYS SER ASP LYS ALA ALA ALA LEU SEQRES 8 A 109 GLY THR LYS ILE ILE ASP GLU ASP GLY LEU LEU ASN LEU SEQRES 9 A 109 ILE ARG ASN LEU GLU HELIX 1 1 GLN A 380 GLU A 389 1 10 HELIX 2 2 GLU A 422 TYR A 433 1 12 HELIX 3 3 GLY A 455 GLY A 466 1 12 HELIX 4 4 ASP A 471 LEU A 482 1 12 SHEET 1 A 4 LYS A 436 VAL A 437 0 SHEET 2 A 4 ILE A 411 THR A 415 1 N PHE A 412 O LYS A 436 SHEET 3 A 4 TYR A 447 MET A 450 1 O VAL A 449 N VAL A 413 SHEET 4 A 4 LYS A 468 ILE A 470 1 O ILE A 470 N LEU A 448 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