HEADER RECOMBINATION 17-OCT-07 2JWO TITLE A PHD FINGER MOTIF IN THE C-TERMINUS OF RAG2 MODULATES RECOMBINATION TITLE 2 ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: V(D)J RECOMBINATION-ACTIVATING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD FINGER MOTIF: RESIDUES 414-487; COMPND 5 SYNONYM: RAG-2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RAG2, RAG-2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-3 KEYWDS V(D)J RECOMBINATION, PHOSPHOINOSITIDE SIGNALING, RAG2, PHD DOMAIN, KEYWDS 2 DNA RECOMBINATION, DNA-BINDING, ENDONUCLEASE, HYDROLASE, NUCLEASE, KEYWDS 3 NUCLEUS, RECOMBINATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.IVANOV,S.G.HYBERTS,Z.SUN,G.WAGNER REVDAT 3 16-MAR-22 2JWO 1 REMARK SEQADV REVDAT 2 24-FEB-09 2JWO 1 VERSN REVDAT 1 06-NOV-07 2JWO 0 SPRSDE 06-NOV-07 2JWO 2A23 JRNL AUTH S.K.ELKIN,D.IVANOV,M.EWALT,C.G.FERGUSON,S.G.HYBERTS,Z.Y.SUN, JRNL AUTH 2 G.D.PRESTWICH,J.YUAN,G.WAGNER,M.A.OETTINGER,O.P.GOZANI JRNL TITL A PHD FINGER MOTIF IN THE C TERMINUS OF RAG2 MODULATES JRNL TITL 2 RECOMBINATION ACTIVITY. JRNL REF J.BIOL.CHEM. V. 280 28701 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15964836 JRNL DOI 10.1074/JBC.M504731200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JWO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000100384. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 RAG2 PHD DOMAIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D HNCO; 3D REMARK 210 1H-13C NOESY; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, XEASY REMARK 210 METHOD USED : SIMULATED ANNEALING 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: 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: 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 GLU A 412 -156.49 -97.60 REMARK 500 1 ILE A 417 -160.87 -113.75 REMARK 500 1 THR A 429 19.74 -148.98 REMARK 500 1 ASN A 439 38.38 -167.88 REMARK 500 1 ALA A 442 79.52 -68.06 REMARK 500 1 LYS A 475 83.10 -64.78 REMARK 500 1 CYS A 478 -164.59 -60.06 REMARK 500 1 GLN A 483 57.50 -149.70 REMARK 500 1 ALA A 485 -75.79 -161.83 REMARK 500 2 PHE A 413 55.00 -97.42 REMARK 500 2 ILE A 417 -160.86 -123.73 REMARK 500 2 THR A 429 19.51 -147.15 REMARK 500 2 ASN A 439 42.54 -150.10 REMARK 500 2 MET A 443 170.38 -58.05 REMARK 500 2 SER A 447 52.91 -93.73 REMARK 500 2 HIS A 448 -155.69 -94.54 REMARK 500 2 HIS A 455 161.48 -44.20 REMARK 500 2 ASP A 460 86.90 54.57 REMARK 500 2 CYS A 478 -164.53 -60.42 REMARK 500 2 ALA A 485 -76.29 -74.57 REMARK 500 2 ARG A 486 32.60 -150.58 REMARK 500 3 SER A 410 64.57 -166.35 REMARK 500 3 PHE A 413 -154.53 -132.60 REMARK 500 3 TYR A 415 -45.71 -171.89 REMARK 500 3 ILE A 417 -159.60 -114.01 REMARK 500 3 THR A 422 33.92 -149.47 REMARK 500 3 ASP A 424 44.72 -145.89 REMARK 500 3 GLU A 471 30.57 -95.06 REMARK 500 3 LYS A 475 76.23 -67.66 REMARK 500 3 GLN A 483 59.39 -159.23 REMARK 500 3 ALA A 485 -151.84 -118.83 REMARK 500 4 GLU A 412 -164.61 -129.79 REMARK 500 4 PHE A 413 -173.81 -66.28 REMARK 500 4 TYR A 415 -38.06 -170.00 REMARK 500 4 ILE A 417 -160.13 -118.87 REMARK 500 4 ASP A 424 37.74 -154.37 REMARK 500 4 ASN A 439 -36.79 -173.44 REMARK 500 4 HIS A 455 158.89 -47.42 REMARK 500 4 ASP A 460 82.42 53.89 REMARK 500 4 CYS A 478 -164.64 -72.31 REMARK 500 4 GLN A 483 -74.87 -113.16 REMARK 500 4 ILE A 484 41.48 35.19 REMARK 500 4 ALA A 485 55.65 -166.51 REMARK 500 4 ARG A 486 114.71 -163.49 REMARK 500 5 LEU A 408 94.89 -65.08 REMARK 500 5 SER A 410 92.65 -167.06 REMARK 500 5 PHE A 413 -66.00 -123.17 REMARK 500 5 TYR A 415 51.47 -113.05 REMARK 500 5 ILE A 417 -161.91 -114.70 REMARK 500 5 ASN A 439 26.31 -141.83 REMARK 500 REMARK 500 THIS ENTRY HAS 239 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 464 0.27 SIDE CHAIN REMARK 500 1 ARG A 486 0.29 SIDE CHAIN REMARK 500 2 ARG A 464 0.31 SIDE CHAIN REMARK 500 2 ARG A 486 0.23 SIDE CHAIN REMARK 500 3 ARG A 464 0.21 SIDE CHAIN REMARK 500 3 ARG A 486 0.31 SIDE CHAIN REMARK 500 4 ARG A 464 0.23 SIDE CHAIN REMARK 500 4 ARG A 486 0.24 SIDE CHAIN REMARK 500 5 ARG A 464 0.30 SIDE CHAIN REMARK 500 5 ARG A 486 0.21 SIDE CHAIN REMARK 500 6 ARG A 464 0.23 SIDE CHAIN REMARK 500 6 ARG A 486 0.23 SIDE CHAIN REMARK 500 7 ARG A 464 0.24 SIDE CHAIN REMARK 500 7 ARG A 486 0.23 SIDE CHAIN REMARK 500 8 ARG A 464 0.23 SIDE CHAIN REMARK 500 8 ARG A 486 0.21 SIDE CHAIN REMARK 500 9 ARG A 464 0.22 SIDE CHAIN REMARK 500 9 ARG A 486 0.31 SIDE CHAIN REMARK 500 10 ARG A 464 0.23 SIDE CHAIN REMARK 500 10 ARG A 486 0.27 SIDE CHAIN REMARK 500 11 ARG A 464 0.25 SIDE CHAIN REMARK 500 11 ARG A 486 0.24 SIDE CHAIN REMARK 500 12 ARG A 464 0.24 SIDE CHAIN REMARK 500 12 ARG A 486 0.23 SIDE CHAIN REMARK 500 13 ARG A 464 0.24 SIDE CHAIN REMARK 500 13 ARG A 486 0.23 SIDE CHAIN REMARK 500 14 ARG A 464 0.24 SIDE CHAIN REMARK 500 14 ARG A 486 0.22 SIDE CHAIN REMARK 500 15 ARG A 464 0.24 SIDE CHAIN REMARK 500 15 ARG A 486 0.28 SIDE CHAIN REMARK 500 16 ARG A 464 0.23 SIDE CHAIN REMARK 500 16 ARG A 486 0.28 SIDE CHAIN REMARK 500 17 ARG A 464 0.32 SIDE CHAIN REMARK 500 17 ARG A 486 0.28 SIDE CHAIN REMARK 500 18 ARG A 464 0.28 SIDE CHAIN REMARK 500 18 ARG A 486 0.30 SIDE CHAIN REMARK 500 19 ARG A 464 0.32 SIDE CHAIN REMARK 500 19 ARG A 486 0.21 SIDE CHAIN REMARK 500 20 ARG A 464 0.29 SIDE CHAIN REMARK 500 20 ARG A 486 0.22 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 488 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 419 SG REMARK 620 2 CYS A 423 SG 107.8 REMARK 620 3 HIS A 455 ND1 114.6 106.9 REMARK 620 4 CYS A 458 SG 105.5 108.7 113.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 489 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 446 SG REMARK 620 2 HIS A 452 NE2 113.7 REMARK 620 3 CYS A 478 SG 114.1 111.4 REMARK 620 4 HIS A 481 ND1 115.2 112.2 87.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 488 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 489 DBREF 2JWO A 414 487 UNP P21784 RAG2_MOUSE 414 487 SEQADV 2JWO GLY A 406 UNP P21784 EXPRESSION TAG SEQADV 2JWO PRO A 407 UNP P21784 EXPRESSION TAG SEQADV 2JWO LEU A 408 UNP P21784 EXPRESSION TAG SEQADV 2JWO GLY A 409 UNP P21784 EXPRESSION TAG SEQADV 2JWO SER A 410 UNP P21784 EXPRESSION TAG SEQADV 2JWO PRO A 411 UNP P21784 EXPRESSION TAG SEQADV 2JWO GLU A 412 UNP P21784 EXPRESSION TAG SEQADV 2JWO PHE A 413 UNP P21784 EXPRESSION TAG SEQRES 1 A 82 GLY PRO LEU GLY SER PRO GLU PHE GLY TYR TRP ILE THR SEQRES 2 A 82 CYS CYS PRO THR CYS ASP VAL ASP ILE ASN THR TRP VAL SEQRES 3 A 82 PRO PHE TYR SER THR GLU LEU ASN LYS PRO ALA MET ILE SEQRES 4 A 82 TYR CYS SER HIS GLY ASP GLY HIS TRP VAL HIS ALA GLN SEQRES 5 A 82 CYS MET ASP LEU GLU GLU ARG THR LEU ILE HIS LEU SER SEQRES 6 A 82 GLU GLY SER ASN LYS TYR TYR CYS ASN GLU HIS VAL GLN SEQRES 7 A 82 ILE ALA ARG ALA HET ZN A 488 1 HET ZN A 489 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ALA A 456 ASP A 460 5 5 HELIX 2 2 GLU A 462 SER A 470 1 9 SHEET 1 A 2 ILE A 444 TYR A 445 0 SHEET 2 A 2 TRP A 453 VAL A 454 -1 O VAL A 454 N ILE A 444 LINK SG CYS A 419 ZN ZN A 488 1555 1555 2.35 LINK SG CYS A 423 ZN ZN A 488 1555 1555 2.35 LINK SG CYS A 446 ZN ZN A 489 1555 1555 2.35 LINK NE2 HIS A 452 ZN ZN A 489 1555 1555 2.04 LINK ND1 HIS A 455 ZN ZN A 488 1555 1555 2.06 LINK SG CYS A 458 ZN ZN A 488 1555 1555 2.35 LINK SG CYS A 478 ZN ZN A 489 1555 1555 2.34 LINK ND1 HIS A 481 ZN ZN A 489 1555 1555 2.04 SITE 1 AC1 5 CYS A 419 CYS A 423 VAL A 425 HIS A 455 SITE 2 AC1 5 CYS A 458 SITE 1 AC2 4 CYS A 446 HIS A 452 CYS A 478 HIS A 481 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