0.016409 0.000000 0.000000 0.000000 0.016409 0.000000 0.000000 0.000000 0.007643 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) Partnership for Stem Cell Biology Partnership for Stem Cell Biology (STEMCELL) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.000 90.000 90.000 60.942 60.942 130.839 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C8 H18 N2 O2 174.241 n N-DIMETHYL-LYSINE L-peptide linking C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking Na 1 22.990 SODIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Plos One 1932-6203 7 e43761 e43761 10.1371/journal.pone.0043761 22984442 Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein. 2012 10.2210/pdb3u21/pdb pdb_00003u21 100 1 double crystal monochromator CCD 2011-06-22 MARMOSAIC 325 mm CCD double crystal MAD M x-ray 1 0.91837 1.0 0.97936 1.0 0.97915 1.0 BL9-2 SSRL 0.91837,0.97936,0.97915 SYNCHROTRON SSRL BEAMLINE BL9-2 14504.097 Nuclear factor related to kappa-B-binding protein 2 man polymer 22.990 SODIUM ION 1 syn non-polymer 18.015 water 25 nat water DNA-binding protein R kappa-B, INO80 complex subunit G no yes GLGINEISSSFFSLLLEILLLESQASLP(MSE)LEERVLDWQSSPASSLNSWFSAAPNWAELVLPALQYLAGESRAVPSS FSPFVEF(MLY)E(MLY)TQQW(MLY)LLGQSQDNE(MLY)ELAALFQLWLET(MLY)DQAFC(MLY)QENEDSS GLGINEISSSFFSLLLEILLLESQASLPMLEERVLDWQSSPASSLNSWFSAAPNWAELVLPALQYLAGESRAVPSSFSPF VEFKEKTQQWKLLGQSQDNEKELAALFQLWLETKDQAFCKQENEDSS A,B 421522 polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample BC063280, INO80G, NFRKB 9606 Homo sapiens 562 Escherichia Coli HK100 Plasmid SpeedET 1 2.09 41.26 VAPOR DIFFUSION, SITTING DROP 7.5 0.09M HEPES pH 7.5, 10% glycerol, 1.26M tri-sodium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI:Biology Partnership for Stem Cell Biology STEMCELL PSI:Biology software database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Database references Refinement description Database references Derived calculations 1 0 2011-11-02 1 1 2012-10-10 1 2 2017-11-08 1 3 2023-02-01 _software.classification _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y RCSB Y RCSB 2011-09-30 REL REL NA SODIUM ION HOH water 1. THIS CONSTRUCT (RESIDUES 370-495) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. RESIDUE NUMBERING IS BASED ON ISOFORM 1 OF UNIPROTKB ID Q6P4R8. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION. NA 500 2 NA NA 500 A HOH 501 3 HOH HOH 501 A HOH 502 3 HOH HOH 502 A HOH 503 3 HOH HOH 503 A HOH 504 3 HOH HOH 504 A HOH 505 3 HOH HOH 505 A HOH 506 3 HOH HOH 506 A HOH 507 3 HOH HOH 507 A HOH 508 3 HOH HOH 508 A HOH 509 3 HOH HOH 509 A HOH 511 3 HOH HOH 511 A HOH 523 3 HOH HOH 523 A HOH 524 3 HOH HOH 524 A HOH 525 3 HOH HOH 525 A HOH 510 3 HOH HOH 510 B HOH 512 3 HOH HOH 512 B HOH 513 3 HOH HOH 513 B HOH 514 3 HOH HOH 514 B HOH 515 3 HOH HOH 515 B HOH 516 3 HOH HOH 516 B HOH 517 3 HOH HOH 517 B HOH 518 3 HOH HOH 518 B HOH 519 3 HOH HOH 519 B HOH 520 3 HOH HOH 520 B HOH 521 3 HOH HOH 521 B HOH 522 3 HOH HOH 522 B n 1 0 A n 2 370 A n 3 371 A ILE 372 n 4 ILE 372 A ASN 373 n 5 ASN 373 A GLU 374 n 6 GLU 374 A ILE 375 n 7 ILE 375 A SER 376 n 8 SER 376 A SER 377 n 9 SER 377 A SER 378 n 10 SER 378 A PHE 379 n 11 PHE 379 A PHE 380 n 12 PHE 380 A SER 381 n 13 SER 381 A LEU 382 n 14 LEU 382 A LEU 383 n 15 LEU 383 A LEU 384 n 16 LEU 384 A GLU 385 n 17 GLU 385 A ILE 386 n 18 ILE 386 A LEU 387 n 19 LEU 387 A LEU 388 n 20 LEU 388 A LEU 389 n 21 LEU 389 A GLU 390 n 22 GLU 390 A SER 391 n 23 SER 391 A GLN 392 n 24 GLN 392 A ALA 393 n 25 ALA 393 A SER 394 n 26 SER 394 A LEU 395 n 27 LEU 395 A PRO 396 n 28 PRO 396 A MSE 397 n 29 MSE 397 A LEU 398 n 30 LEU 398 A GLU 399 n 31 GLU 399 A GLU 400 n 32 GLU 400 A ARG 401 n 33 ARG 401 A VAL 402 n 34 VAL 402 A LEU 403 n 35 LEU 403 A ASP 404 n 36 ASP 404 A TRP 405 n 37 TRP 405 A GLN 406 n 38 GLN 406 A SER 407 n 39 SER 407 A SER 408 n 40 SER 408 A PRO 409 n 41 PRO 409 A ALA 410 n 42 ALA 410 A SER 411 n 43 SER 411 A SER 412 n 44 SER 412 A LEU 413 n 45 LEU 413 A ASN 414 n 46 ASN 414 A SER 415 n 47 SER 415 A TRP 416 n 48 TRP 416 A PHE 417 n 49 PHE 417 A SER 418 n 50 SER 418 A ALA 419 n 51 ALA 419 A ALA 420 n 52 ALA 420 A PRO 421 n 53 PRO 421 A ASN 422 n 54 ASN 422 A TRP 423 n 55 TRP 423 A ALA 424 n 56 ALA 424 A GLU 425 n 57 GLU 425 A LEU 426 n 58 LEU 426 A VAL 427 n 59 VAL 427 A LEU 428 n 60 LEU 428 A PRO 429 n 61 PRO 429 A ALA 430 n 62 ALA 430 A LEU 431 n 63 LEU 431 A GLN 432 n 64 GLN 432 A TYR 433 n 65 TYR 433 A LEU 434 n 66 LEU 434 A ALA 435 n 67 ALA 435 A GLY 436 n 68 GLY 436 A GLU 437 n 69 GLU 437 A SER 438 n 70 SER 438 A ARG 439 n 71 ARG 439 A ALA 440 n 72 ALA 440 A VAL 441 n 73 VAL 441 A PRO 442 n 74 PRO 442 A SER 443 n 75 SER 443 A SER 444 n 76 SER 444 A PHE 445 n 77 PHE 445 A SER 446 n 78 SER 446 A PRO 447 n 79 PRO 447 A PHE 448 n 80 PHE 448 A VAL 449 n 81 VAL 449 A GLU 450 n 82 GLU 450 A PHE 451 n 83 PHE 451 A MLY 452 n 84 MLY 452 A GLU 453 n 85 GLU 453 A MLY 454 n 86 MLY 454 A THR 455 n 87 THR 455 A GLN 456 n 88 GLN 456 A GLN 457 n 89 GLN 457 A TRP 458 n 90 TRP 458 A MLY 459 n 91 MLY 459 A LEU 460 n 92 LEU 460 A LEU 461 n 93 LEU 461 A GLY 462 n 94 GLY 462 A n 95 463 A n 96 464 A n 97 465 A ASP 466 n 98 ASP 466 A ASN 467 n 99 ASN 467 A GLU 468 n 100 GLU 468 A MLY 469 n 101 MLY 469 A GLU 470 n 102 GLU 470 A LEU 471 n 103 LEU 471 A ALA 472 n 104 ALA 472 A ALA 473 n 105 ALA 473 A LEU 474 n 106 LEU 474 A PHE 475 n 107 PHE 475 A GLN 476 n 108 GLN 476 A LEU 477 n 109 LEU 477 A TRP 478 n 110 TRP 478 A LEU 479 n 111 LEU 479 A GLU 480 n 112 GLU 480 A THR 481 n 113 THR 481 A MLY 482 n 114 MLY 482 A ASP 483 n 115 ASP 483 A n 116 484 A n 117 485 A n 118 486 A n 119 487 A n 120 488 A n 121 489 A n 122 490 A n 123 491 A n 124 492 A n 125 493 A n 126 494 A n 127 495 A n 1 0 B LEU 370 n 2 LEU 370 B GLY 371 n 3 GLY 371 B ILE 372 n 4 ILE 372 B ASN 373 n 5 ASN 373 B GLU 374 n 6 GLU 374 B ILE 375 n 7 ILE 375 B SER 376 n 8 SER 376 B SER 377 n 9 SER 377 B SER 378 n 10 SER 378 B PHE 379 n 11 PHE 379 B PHE 380 n 12 PHE 380 B SER 381 n 13 SER 381 B LEU 382 n 14 LEU 382 B LEU 383 n 15 LEU 383 B LEU 384 n 16 LEU 384 B GLU 385 n 17 GLU 385 B ILE 386 n 18 ILE 386 B LEU 387 n 19 LEU 387 B LEU 388 n 20 LEU 388 B LEU 389 n 21 LEU 389 B GLU 390 n 22 GLU 390 B SER 391 n 23 SER 391 B GLN 392 n 24 GLN 392 B ALA 393 n 25 ALA 393 B SER 394 n 26 SER 394 B LEU 395 n 27 LEU 395 B PRO 396 n 28 PRO 396 B MSE 397 n 29 MSE 397 B LEU 398 n 30 LEU 398 B GLU 399 n 31 GLU 399 B GLU 400 n 32 GLU 400 B ARG 401 n 33 ARG 401 B VAL 402 n 34 VAL 402 B LEU 403 n 35 LEU 403 B ASP 404 n 36 ASP 404 B TRP 405 n 37 TRP 405 B GLN 406 n 38 GLN 406 B SER 407 n 39 SER 407 B SER 408 n 40 SER 408 B PRO 409 n 41 PRO 409 B ALA 410 n 42 ALA 410 B SER 411 n 43 SER 411 B SER 412 n 44 SER 412 B LEU 413 n 45 LEU 413 B ASN 414 n 46 ASN 414 B SER 415 n 47 SER 415 B TRP 416 n 48 TRP 416 B PHE 417 n 49 PHE 417 B SER 418 n 50 SER 418 B ALA 419 n 51 ALA 419 B ALA 420 n 52 ALA 420 B PRO 421 n 53 PRO 421 B ASN 422 n 54 ASN 422 B TRP 423 n 55 TRP 423 B ALA 424 n 56 ALA 424 B GLU 425 n 57 GLU 425 B LEU 426 n 58 LEU 426 B VAL 427 n 59 VAL 427 B LEU 428 n 60 LEU 428 B PRO 429 n 61 PRO 429 B ALA 430 n 62 ALA 430 B LEU 431 n 63 LEU 431 B GLN 432 n 64 GLN 432 B TYR 433 n 65 TYR 433 B LEU 434 n 66 LEU 434 B ALA 435 n 67 ALA 435 B GLY 436 n 68 GLY 436 B GLU 437 n 69 GLU 437 B SER 438 n 70 SER 438 B ARG 439 n 71 ARG 439 B n 72 440 B n 73 441 B n 74 442 B n 75 443 B SER 444 n 76 SER 444 B PHE 445 n 77 PHE 445 B SER 446 n 78 SER 446 B PRO 447 n 79 PRO 447 B PHE 448 n 80 PHE 448 B VAL 449 n 81 VAL 449 B GLU 450 n 82 GLU 450 B PHE 451 n 83 PHE 451 B MLY 452 n 84 MLY 452 B GLU 453 n 85 GLU 453 B MLY 454 n 86 MLY 454 B THR 455 n 87 THR 455 B GLN 456 n 88 GLN 456 B GLN 457 n 89 GLN 457 B TRP 458 n 90 TRP 458 B MLY 459 n 91 MLY 459 B LEU 460 n 92 LEU 460 B LEU 461 n 93 LEU 461 B n 94 462 B n 95 463 B SER 464 n 96 SER 464 B GLN 465 n 97 GLN 465 B ASP 466 n 98 ASP 466 B ASN 467 n 99 ASN 467 B GLU 468 n 100 GLU 468 B MLY 469 n 101 MLY 469 B GLU 470 n 102 GLU 470 B LEU 471 n 103 LEU 471 B ALA 472 n 104 ALA 472 B ALA 473 n 105 ALA 473 B LEU 474 n 106 LEU 474 B PHE 475 n 107 PHE 475 B GLN 476 n 108 GLN 476 B LEU 477 n 109 LEU 477 B TRP 478 n 110 TRP 478 B LEU 479 n 111 LEU 479 B GLU 480 n 112 GLU 480 B THR 481 n 113 THR 481 B MLY 482 n 114 MLY 482 B ASP 483 n 115 ASP 483 B n 116 484 B n 117 485 B n 118 486 B n 119 487 B n 120 488 B n 121 489 B n 122 490 B n 123 491 B n 124 492 B n 125 493 B n 126 494 B n 127 495 B 1.0635 0.6754 -0.2069 5.4284 0.1736 4.0382 -0.0925 0.0321 0.1089 -0.0577 0.1532 -0.2375 -0.3529 0.0032 -0.0607 0.1040 -0.0072 -0.0181 0.0908 -0.0191 0.0800 refined 61.0380 45.3410 53.3450 X-RAY DIFFRACTION 3.0864 0.5889 -0.5343 2.0962 -0.3884 4.4276 0.0515 -0.2075 -0.0591 0.0171 0.1051 0.1458 0.0318 -0.5040 -0.1566 0.0991 0.0091 -0.0305 0.1636 0.0487 0.0509 refined 48.6910 30.9920 75.4320 X-RAY DIFFRACTION A 372 A 462 X-RAY DIFFRACTION 1 A 466 A 483 X-RAY DIFFRACTION 1 B 370 B 461 X-RAY DIFFRACTION 2 B 464 B 483 X-RAY DIFFRACTION 2 author_and_software_defined_assembly PISA 2 dimeric 1510 -23 11610 A ASN 373 A OD1 ASN 5 1_555 A NA 500 C NA NA 1_555 A ILE 375 A O ILE 7 1_555 91.6 A ASN 373 A OD1 ASN 5 1_555 A NA 500 C NA NA 1_555 B ASN 373 B OD1 ASN 5 1_555 171.4 A ILE 375 A O ILE 7 1_555 A NA 500 C NA NA 1_555 B ASN 373 B OD1 ASN 5 1_555 88.2 A ASN 373 A OD1 ASN 5 1_555 A NA 500 C NA NA 1_555 B ILE 375 B O ILE 7 1_555 94.2 A ILE 375 A O ILE 7 1_555 A NA 500 C NA NA 1_555 B ILE 375 B O ILE 7 1_555 102.9 B ASN 373 B OD1 ASN 5 1_555 A NA 500 C NA NA 1_555 B ILE 375 B O ILE 7 1_555 94.3 A ASN 373 A OD1 ASN 5 1_555 A NA 500 C NA NA 1_555 B HOH 521 E O HOH 1_555 94.7 A ILE 375 A O ILE 7 1_555 A NA 500 C NA NA 1_555 B HOH 521 E O HOH 1_555 164.8 B ASN 373 B OD1 ASN 5 1_555 A NA 500 C NA NA 1_555 B HOH 521 E O HOH 1_555 83.5 B ILE 375 B O ILE 7 1_555 A NA 500 C NA NA 1_555 B HOH 521 E O HOH 1_555 90.5 A MSE 397 SELENOMETHIONINE A MSE 29 MET A MLY 452 N-DIMETHYL-LYSINE A MLY 84 LYS A MLY 454 N-DIMETHYL-LYSINE A MLY 86 LYS A MLY 459 N-DIMETHYL-LYSINE A MLY 91 LYS A MLY 469 N-DIMETHYL-LYSINE A MLY 101 LYS A MLY 482 N-DIMETHYL-LYSINE A MLY 114 LYS B MSE 397 SELENOMETHIONINE B MSE 29 MET B MLY 452 N-DIMETHYL-LYSINE B MLY 84 LYS B MLY 454 N-DIMETHYL-LYSINE B MLY 86 LYS B MLY 459 N-DIMETHYL-LYSINE B MLY 91 LYS B MLY 469 N-DIMETHYL-LYSINE B MLY 101 LYS B MLY 482 N-DIMETHYL-LYSINE B MLY 114 LYS 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N ALA 393 A N ALA 25 A O TRP 458 A O TRP 90 A O MLY 459 A O MLY 91 A N GLU 450 A N GLU 82 B N ALA 393 B N ALA 25 B O TRP 458 B O TRP 90 B O MLY 459 B O MLY 91 B N GLU 450 B N GLU 82 1 A CG ARG 439 A CG ARG 71 1 Y 1 A CD ARG 439 A CD ARG 71 1 Y 1 A NE ARG 439 A NE ARG 71 1 Y 1 A CZ ARG 439 A CZ ARG 71 1 Y 1 A NH1 ARG 439 A NH1 ARG 71 1 Y 1 A NH2 ARG 439 A NH2 ARG 71 1 Y 1 A CG MLY 454 A CG MLY 86 1 Y 1 A CD MLY 454 A CD MLY 86 1 Y 1 A CE MLY 454 A CE MLY 86 1 Y 1 A NZ MLY 454 A NZ MLY 86 1 Y 1 A CH1 MLY 454 A CH1 MLY 86 1 Y 1 A CH2 MLY 454 A CH2 MLY 86 1 Y 1 B CG1 ILE 372 B CG1 ILE 4 1 Y 1 B CG2 ILE 372 B CG2 ILE 4 1 Y 1 B CD1 ILE 372 B CD1 ILE 4 1 Y 1 B CG ARG 439 B CG ARG 71 1 Y 1 B CD ARG 439 B CD ARG 71 1 Y 1 B NE ARG 439 B NE ARG 71 1 Y 1 B CZ ARG 439 B CZ ARG 71 1 Y 1 B NH1 ARG 439 B NH1 ARG 71 1 Y 1 B NH2 ARG 439 B NH2 ARG 71 1 Y 1 B CG MLY 454 B CG MLY 86 1 Y 1 B CD MLY 454 B CD MLY 86 1 Y 1 B CE MLY 454 B CE MLY 86 1 Y 1 B NZ MLY 454 B NZ MLY 86 1 Y 1 B CH1 MLY 454 B CH1 MLY 86 1 Y 1 B CH2 MLY 454 B CH2 MLY 86 1 Y 1 B CG GLN 465 B CG GLN 97 1 Y 1 B CD GLN 465 B CD GLN 97 1 Y 1 B OE1 GLN 465 B OE1 GLN 97 1 Y 1 B NE2 GLN 465 B NE2 GLN 97 1 Y 1 B CG ASP 483 B CG ASP 115 1 Y 1 B OD1 ASP 483 B OD1 ASP 115 1 Y 1 B OD2 ASP 483 B OD2 ASP 115 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A LEU 370 A LEU 2 1 Y 1 A GLY 371 A GLY 3 1 Y 1 A GLN 463 A GLN 95 1 Y 1 A SER 464 A SER 96 1 Y 1 A GLN 465 A GLN 97 1 Y 1 A GLN 484 A GLN 116 1 Y 1 A ALA 485 A ALA 117 1 Y 1 A PHE 486 A PHE 118 1 Y 1 A CYS 487 A CYS 119 1 Y 1 A MLY 488 A MLY 120 1 Y 1 A GLN 489 A GLN 121 1 Y 1 A GLU 490 A GLU 122 1 Y 1 A ASN 491 A ASN 123 1 Y 1 A GLU 492 A GLU 124 1 Y 1 A ASP 493 A ASP 125 1 Y 1 A SER 494 A SER 126 1 Y 1 A SER 495 A SER 127 1 Y 1 B GLY 0 B GLY 1 1 Y 1 B ALA 440 B ALA 72 1 Y 1 B VAL 441 B VAL 73 1 Y 1 B PRO 442 B PRO 74 1 Y 1 B SER 443 B SER 75 1 Y 1 B GLY 462 B GLY 94 1 Y 1 B GLN 463 B GLN 95 1 Y 1 B GLN 484 B GLN 116 1 Y 1 B ALA 485 B ALA 117 1 Y 1 B PHE 486 B PHE 118 1 Y 1 B CYS 487 B CYS 119 1 Y 1 B MLY 488 B MLY 120 1 Y 1 B GLN 489 B GLN 121 1 Y 1 B GLU 490 B GLU 122 1 Y 1 B ASN 491 B ASN 123 1 Y 1 B GLU 492 B GLU 124 1 Y 1 B ASP 493 B ASP 125 1 Y 1 B SER 494 B SER 126 1 Y 1 B SER 495 B SER 127 1 Y 1 A GLU 390 75.84 -47.01 1 A SER 391 70.91 -47.25 1 A SER 444 -98.95 45.58 1 B SER 391 74.11 -58.79 1 B ASP 466 64.73 -1.97 97.070 46.2329 25.430 -0.2100 0.0000 0.0000 -0.2100 0.0000 0.4300 0.9290 0.9050 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. SODIUM ION (NA) FROM CRYSTALLIZATION CONDITION WAS MODELED. 0.2695 0.2305 0.2324 2.1800 35.466 662 13504 4.9000 99.7500 1.000 0.370 12.5180 0.1560 RANDOM 1 THROUGHOUT 0.000 MAD 0.2220 0.8000 0.8000 1.2000 MAXIMUM LIKELIHOOD WITH PHASES BABINET MODEL WITH MASK 2.1800 35.466 25 1758 1 0 1732 0.012 0.022 1780 0.001 0.020 1163 1.252 1.978 2425 0.866 3.000 2861 5.482 5.000 214 37.308 26.104 77 15.037 15.133 301 7.053 15.000 2 0.070 0.200 279 0.006 0.021 1922 0.001 0.020 338 2.782 3.895 1780 0.478 3.917 1163 4.176 8.643 2424 2.448 8.825 2861 6.824 17.777 594 1 A 1 1360 X-RAY DIFFRACTION MEDIUM POSITIONAL 0.230 0.500 1 A 1 1360 X-RAY DIFFRACTION MEDIUM THERMAL 2.310 2.000 0.2890 0.2520 2.2360 40 809 849 20 99.8800 41.259 2.18 35.466 3U21 13560 -3.000 0.067 1 20.780 99.800 0.796 2.180 2.260 2.4 9710 1360 1 99.900 0.624 2.260 2.350 3.1 9264 1298 1 99.800 0.506 2.350 2.450 3.8 8939 1247 1 100.000 0.365 2.450 2.580 5.3 9488 1332 1 100.000 0.248 2.580 2.750 7.9 10006 1409 1 100.000 0.152 2.750 2.960 12.2 9368 1322 1 100.000 0.101 2.960 3.250 18.1 9300 1316 1 100.000 0.047 3.250 3.720 35.2 9515 1369 1 99.900 0.029 3.720 4.680 53.2 9606 1407 1 99.900 0.024 4.680 58.9 9421 1500 1 98.300 model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package phasing Eric de La Fortelle sharp-develop@globalphasing.com http://www.globalphasing.com/sharp/ SHARP package data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package December 6, 2010 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.6.0116 data reduction XDS phasing SHELXD Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution 1 N N 1 N N 2 N N 3 N N 3 N N CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. A SER 378 A SER 10 HELX_P A LEU 389 A LEU 21 1 1 12 A LEU 395 A LEU 27 HELX_P A SER 407 A SER 39 1 2 13 A SER 408 A SER 40 HELX_P A ASN 414 A ASN 46 5 3 7 A TRP 416 A TRP 48 HELX_P A ALA 420 A ALA 52 5 4 5 A TRP 423 A TRP 55 HELX_P A GLU 425 A GLU 57 5 5 3 A LEU 426 A LEU 58 HELX_P A ALA 435 A ALA 67 1 6 10 A ASN 467 A ASN 99 HELX_P A MLY 482 A MLY 114 1 7 16 B SER 378 B SER 10 HELX_P B SER 391 B SER 23 1 8 14 B SER 394 B SER 26 HELX_P B SER 408 B SER 40 1 9 15 B PRO 409 B PRO 41 HELX_P B ASN 414 B ASN 46 5 10 6 B TRP 416 B TRP 48 HELX_P B ALA 420 B ALA 52 5 11 5 B ASN 422 B ASN 54 HELX_P B GLU 425 B GLU 57 5 12 4 B LEU 426 B LEU 58 HELX_P B ALA 435 B ALA 67 1 13 10 B ASN 467 B ASN 99 HELX_P B MLY 482 B MLY 114 1 14 16 covale 1.335 both A PRO 396 A C PRO 28 1_555 A MSE 397 A N MSE 29 1_555 covale 1.329 both A MSE 397 A C MSE 29 1_555 A LEU 398 A N LEU 30 1_555 covale 1.328 both A PHE 451 A C PHE 83 1_555 A MLY 452 A N MLY 84 1_555 covale 1.330 both A MLY 452 A C MLY 84 1_555 A GLU 453 A N GLU 85 1_555 covale 1.333 both A GLU 453 A C GLU 85 1_555 A MLY 454 A N MLY 86 1_555 covale 1.339 both A MLY 454 A C MLY 86 1_555 A THR 455 A N THR 87 1_555 covale 1.333 both A TRP 458 A C TRP 90 1_555 A MLY 459 A N MLY 91 1_555 covale 1.327 both A MLY 459 A C MLY 91 1_555 A LEU 460 A N LEU 92 1_555 covale 1.328 both A GLU 468 A C GLU 100 1_555 A MLY 469 A N MLY 101 1_555 covale 1.329 both A MLY 469 A C MLY 101 1_555 A GLU 470 A N GLU 102 1_555 covale 1.333 both A THR 481 A C THR 113 1_555 A MLY 482 A N MLY 114 1_555 covale 1.327 both A MLY 482 A C MLY 114 1_555 A ASP 483 A N ASP 115 1_555 covale 1.331 both B PRO 396 B C PRO 28 1_555 B MSE 397 B N MSE 29 1_555 covale 1.335 both B MSE 397 B C MSE 29 1_555 B LEU 398 B N LEU 30 1_555 covale 1.327 both B PHE 451 B C PHE 83 1_555 B MLY 452 B N MLY 84 1_555 covale 1.321 both B MLY 452 B C MLY 84 1_555 B GLU 453 B N GLU 85 1_555 covale 1.334 both B GLU 453 B C GLU 85 1_555 B MLY 454 B N MLY 86 1_555 covale 1.332 both B MLY 454 B C MLY 86 1_555 B THR 455 B N THR 87 1_555 covale 1.337 both B TRP 458 B C TRP 90 1_555 B MLY 459 B N MLY 91 1_555 covale 1.325 both B MLY 459 B C MLY 91 1_555 B LEU 460 B N LEU 92 1_555 covale 1.323 both B GLU 468 B C GLU 100 1_555 B MLY 469 B N MLY 101 1_555 covale 1.320 both B MLY 469 B C MLY 101 1_555 B GLU 470 B N GLU 102 1_555 covale 1.332 both B THR 481 B C THR 113 1_555 B MLY 482 B N MLY 114 1_555 covale 1.331 both B MLY 482 B C MLY 114 1_555 B ASP 483 B N ASP 115 1_555 metalc 2.395 A ASN 373 A OD1 ASN 5 1_555 A NA 500 C NA NA 1_555 metalc 2.373 A ILE 375 A O ILE 7 1_555 A NA 500 C NA NA 1_555 metalc 2.285 A NA 500 C NA NA 1_555 B ASN 373 B OD1 ASN 5 1_555 metalc 2.334 A NA 500 C NA NA 1_555 B ILE 375 B O ILE 7 1_555 metalc 2.273 A NA 500 C NA NA 1_555 B HOH 521 E O HOH 1_555 Transcription regulation, DNA BINDING DNA/RNA-binding 3-helical bundle, winged-HTH domain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, Transcription regulation, DNA BINDING PROTEIN, DNA BINDING, Partnership for Stem Cell Biology, STEMCELL A B A 372 A 437 4 B 372 B 437 4 A 445 A 483 4 B 445 B 483 4 NFRKB_HUMAN UNP 1 370 Q6P4R8 LGINEISSSFFSLLLEILLLESQASLPMLEERVLDWQSSPASSLNSWFSAAPNWAELVLPALQYLAGESRAVPSSFSPFV EFKEKTQQWKLLGQSQDNEKELAALFQLWLETKDQAFCKQENEDSS 370 495 3U21 370 495 Q6P4R8 A 1 2 127 370 495 3U21 370 495 Q6P4R8 B 1 2 127 1 expression tag GLY 0 3U21 A Q6P4R8 UNP 1 2 expression tag GLY 0 3U21 B Q6P4R8 UNP 1 3 3 anti-parallel anti-parallel anti-parallel anti-parallel A GLN 392 A GLN 24 A SER 394 A SER 26 A GLN 457 A GLN 89 A LEU 460 A LEU 92 A VAL 449 A VAL 81 A MLY 452 A MLY 84 B GLN 392 B GLN 24 B ALA 393 B ALA 25 B GLN 457 B GLN 89 B LEU 460 B LEU 92 B VAL 449 B VAL 81 B MLY 452 B MLY 84 BINDING SITE FOR RESIDUE NA A 500 A NA 500 Software 5 A ASN 373 A ASN 5 5 1_555 A ILE 375 A ILE 7 5 1_555 B ASN 373 B ASN 5 5 1_555 B ILE 375 B ILE 7 5 1_555 B HOH 521 E HOH 5 1_555 96 P 43 21 2