0.014187 0.008191 0.000000 0.000000 0.016382 0.000000 0.000000 0.000000 0.016291 0.00000 0.00000 0.00000 Prag, G. Misra, S. Jones, E. Ghirlando, R. Davies, B.A. Horazdovsky, B.F. Hurley, J.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 70.487 70.487 61.384 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 C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking 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 C5 H11 N O2 117.146 y VALINE L-peptide linking US Cell(Cambridge,Mass.) CELLB5 0998 0092-8674 113 609 620 10.1016/S0092-8674(03)00364-7 12787502 Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p 2003 10.2210/pdb1mn3/pdb pdb_00001mn3 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 95.0 1 CCD 2002-07-13 SBC-2 Sagitally focused Si(111) MAD M x-ray 1 0.95645 1.0 0.97910 1.0 0.97924 1.0 19-ID APS 0.95645,0.97910,0.97924 SYNCHROTRON APS BEAMLINE 19-ID 6222.829 Vacuolar protein sorting-associated protein VPS9 Cue domain (residues 398-451) G440E 1 man polymer 18.015 water 31 nat water no yes SSLIKKIEENERKDTLNTLQN(MSE)FPD(MSE)DPSLIEDVCIAKKSRIEPCVDALLSLSE SSLIKKIEENERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLSLSE A 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 baker's yeast Saccharomyces Escherichia sample VPS9 4932 Saccharomyces cerevisiae 562 Escherichia coli BL21(DE3)-Rosetta PLASMID pHis-parallel2 1 3.54 65.21 The number of unique reflections observed include Friedel pairs VAPOR DIFFUSION, HANGING DROP 8.5 Ammonium Sulfate, Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 database_2 struct_conn struct_ref_seq_dif repository Initial release Version format compliance Derived calculations Version format compliance Database references Derived calculations 1 0 2003-06-10 1 1 2008-04-28 1 2 2011-07-13 1 3 2021-10-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details RCSB Y RCSB 2002-09-04 REL REL HOH water WAT 1 2 HOH HOH 1 A WAT 2 2 HOH HOH 2 A WAT 3 2 HOH HOH 3 A WAT 4 2 HOH HOH 4 A WAT 5 2 HOH HOH 5 A WAT 6 2 HOH HOH 6 A WAT 8 2 HOH HOH 8 A WAT 9 2 HOH HOH 9 A WAT 10 2 HOH HOH 10 A WAT 11 2 HOH HOH 11 A WAT 12 2 HOH HOH 12 A WAT 13 2 HOH HOH 13 A WAT 14 2 HOH HOH 14 A WAT 15 2 HOH HOH 15 A WAT 16 2 HOH HOH 16 A WAT 17 2 HOH HOH 17 A WAT 18 2 HOH HOH 18 A WAT 19 2 HOH HOH 19 A WAT 20 2 HOH HOH 20 A WAT 21 2 HOH HOH 21 A WAT 22 2 HOH HOH 22 A WAT 23 2 HOH HOH 23 A WAT 24 2 HOH HOH 24 A WAT 25 2 HOH HOH 25 A WAT 26 2 HOH HOH 26 A WAT 27 2 HOH HOH 27 A WAT 28 2 HOH HOH 28 A WAT 29 2 HOH HOH 29 A WAT 30 2 HOH HOH 30 A WAT 31 2 HOH HOH 31 A WAT 32 2 HOH HOH 32 A SER 398 n 1 SER 398 A SER 399 n 2 SER 399 A LEU 400 n 3 LEU 400 A ILE 401 n 4 ILE 401 A LYS 402 n 5 LYS 402 A LYS 403 n 6 LYS 403 A ILE 404 n 7 ILE 404 A GLU 405 n 8 GLU 405 A GLU 406 n 9 GLU 406 A ASN 407 n 10 ASN 407 A GLU 408 n 11 GLU 408 A ARG 409 n 12 ARG 409 A LYS 410 n 13 LYS 410 A ASP 411 n 14 ASP 411 A THR 412 n 15 THR 412 A LEU 413 n 16 LEU 413 A ASN 414 n 17 ASN 414 A THR 415 n 18 THR 415 A LEU 416 n 19 LEU 416 A GLN 417 n 20 GLN 417 A ASN 418 n 21 ASN 418 A MSE 419 n 22 MSE 419 A PHE 420 n 23 PHE 420 A PRO 421 n 24 PRO 421 A ASP 422 n 25 ASP 422 A MSE 423 n 26 MSE 423 A ASP 424 n 27 ASP 424 A PRO 425 n 28 PRO 425 A SER 426 n 29 SER 426 A LEU 427 n 30 LEU 427 A ILE 428 n 31 ILE 428 A GLU 429 n 32 GLU 429 A ASP 430 n 33 ASP 430 A VAL 431 n 34 VAL 431 A CYS 432 n 35 CYS 432 A ILE 433 n 36 ILE 433 A ALA 434 n 37 ALA 434 A LYS 435 n 38 LYS 435 A LYS 436 n 39 LYS 436 A SER 437 n 40 SER 437 A ARG 438 n 41 ARG 438 A ILE 439 n 42 ILE 439 A GLU 440 n 43 GLU 440 A PRO 441 n 44 PRO 441 A CYS 442 n 45 CYS 442 A VAL 443 n 46 VAL 443 A ASP 444 n 47 ASP 444 A ALA 445 n 48 ALA 445 A LEU 446 n 49 LEU 446 A LEU 447 n 50 LEU 447 A SER 448 n 51 SER 448 A LEU 449 n 52 LEU 449 A SER 450 n 53 SER 450 A GLU 451 n 54 GLU 451 A author_defined_assembly 1 monomeric software_defined_assembly PISA,PQS 2 dimeric 1740 -22 7490 A MSE 419 SELENOMETHIONINE A MSE 22 MET A MSE 423 SELENOMETHIONINE A MSE 26 MET 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 0.5000000000 0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 12_565 x,x-y+1,-z+5/6 crystal symmetry operation -35.2435000000 61.0435326366 51.1533333333 1 A A O O HOH HOH 19 19 1.21 1_555 9_555 1 A A O O HOH HOH 29 29 1.40 1_555 10_666 1 A A O O HOH HOH 10 10 1.66 1_555 12_565 PROTEIN_REP.PARAM PROTEIN.TOP WATER_REP.PARAM WATER.TOP 42.2 0.34 5.75 0.00 0.34 0.00 -0.68 0.266 0.010 0.244 2.3 43.29 763 7562 7325 10.4 96.6 RANDOM 1 RESTRAINED THROUGHOUT 0.0 MAD Engh & Huber FLAT MODEL 39.9679 0.3658 0.39 0.31 5.00 0.38 2.3 43.29 31 456 0 0 425 0.006 1.1 18.4 0.86 1.74 1.50 2.89 2.00 3.25 2.00 4.36 2.50 0.363 0.038 0.302 2.44 91 1043 1043 6 8.0 88.6 2.3 50.0 1MN3 7562 7325 -3.0 0.079 1 39.5 24.5 99.8 0.418 2.3 2.38 6.8 415 1 100.0 data reduction DENZO data scaling SCALEPACK phasing SOLVE model building RESOLVE refinement CNS 1.1 phasing RESOLVE Cue domain of yeast Vps9p 1 N N 2 N N A SER 398 A SER 1 HELX_P A PHE 420 A PHE 23 1 1 23 A ASP 424 A ASP 27 HELX_P A ILE 433 A ILE 36 1 2 10 A ARG 438 A ARG 41 HELX_P A GLU 451 A GLU 54 1 3 14 disulf 2.706 A CYS 432 A SG CYS 35 1_555 A CYS 442 A SG CYS 45 12_565 covale 1.330 both A ASN 418 A C ASN 21 1_555 A MSE 419 A N MSE 22 1_555 covale 1.334 both A MSE 419 A C MSE 22 1_555 A PHE 420 A N PHE 23 1_555 covale 1.327 both A ASP 422 A C ASP 25 1_555 A MSE 423 A N MSE 26 1_555 covale 1.326 both A MSE 423 A C MSE 26 1_555 A ASP 424 A N ASP 27 1_555 PROTEIN TRANSPORT Ubiquitin, PROTEIN TRANSPORT VPS9_YEAST UNP 1 398 P54787 SSLIKKIEENERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIGPCVDALLSLSE 398 451 1MN3 398 451 P54787 A 1 1 54 1 MET modified residue MSE 419 1MN3 A P54787 UNP 419 22 1 MET modified residue MSE 423 1MN3 A P54787 UNP 423 26 1 GLY engineered mutation GLU 440 1MN3 A P54787 UNP 440 43 179 P 65 2 2