0.009680 0.005588 0.000000 0.000000 0.011177 0.000000 0.000000 0.000000 0.011010 0.00000 0.00000 0.00000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 103.311 103.311 90.830 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 C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL non-polymer 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 C6 H10 N3 O2 1 156.162 y HISTIDINE L-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 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 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 To be published 0353 Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution 10.2210/pdb4qoa/pdb pdb_00004qoa 100 1 Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator PIXEL 2014-03-27 DECTRIS PILATUS 6M double crystal Si(111) MAD M x-ray 1 0.9116 1.0 0.9794 1.0 0.9793 1.0 BL12-2 SSRL 0.9116,0.9794,0.9793 SYNCHROTRON SSRL BEAMLINE BL12-2 14669.667 Putative periplasmic protein UNP residues 21-146 1 man polymer 62.068 1,2-ETHANEDIOL 2 syn non-polymer 18.015 water 17 nat water no yes GGDVITQDTKQLPLTARNFINQYFSKPHISHIKIESEILQTKKYEVLLTDRTEIDFDKKGNWLEVDCKKSAVPEALIPVP VKEYVKANFPREIITKIERGRTGVEIELGNDYSLKFNKKGKFVS(MSE)DD GGDVITQDTKQLPLTARNFINQYFSKPHISHIKIESEILQTKKYEVLLTDRTEIDFDKKGNWLEVDCKKSAVPEALIPVP VKEYVKANFPREIITKIERGRTGVEIELGNDYSLKFNKKGKFVSMDD A JCSG-417915 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 sample 8492 BACUNI_04550 411479 Bacteroides uniformis 562 Escherichia coli PB1 Plasmid SpeedET 1 4.77 74.21 VAPOR DIFFUSION, SITTING DROP 24.00% polyethylene glycol 3350, 0.16M tri-ammonium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI:Biology software database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Refinement description Database references Derived calculations 1 0 2014-07-16 1 1 2017-11-22 1 2 2023-02-01 _software.classification _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _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 2014-06-19 REL REL EDO 1,2-ETHANEDIOL HOH water THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 21-146 OF THE TARGET SEQUENCE. EDO 147 2 EDO EDO 201 A EDO 148 2 EDO EDO 202 A HOH 149 3 HOH HOH 301 A HOH 150 3 HOH HOH 302 A HOH 151 3 HOH HOH 303 A HOH 152 3 HOH HOH 304 A HOH 153 3 HOH HOH 305 A HOH 154 3 HOH HOH 306 A HOH 155 3 HOH HOH 307 A HOH 156 3 HOH HOH 308 A HOH 157 3 HOH HOH 309 A HOH 158 3 HOH HOH 310 A HOH 159 3 HOH HOH 311 A HOH 160 3 HOH HOH 312 A HOH 161 3 HOH HOH 313 A HOH 162 3 HOH HOH 314 A HOH 163 3 HOH HOH 315 A HOH 164 3 HOH HOH 316 A HOH 165 3 HOH HOH 317 A n 1 0 A GLY 21 n 2 GLY 21 A ASP 22 n 3 ASP 22 A VAL 23 n 4 VAL 23 A ILE 24 n 5 ILE 24 A THR 25 n 6 THR 25 A GLN 26 n 7 GLN 26 A ASP 27 n 8 ASP 27 A THR 28 n 9 THR 28 A LYS 29 n 10 LYS 29 A GLN 30 n 11 GLN 30 A LEU 31 n 12 LEU 31 A PRO 32 n 13 PRO 32 A LEU 33 n 14 LEU 33 A THR 34 n 15 THR 34 A ALA 35 n 16 ALA 35 A ARG 36 n 17 ARG 36 A ASN 37 n 18 ASN 37 A PHE 38 n 19 PHE 38 A ILE 39 n 20 ILE 39 A ASN 40 n 21 ASN 40 A GLN 41 n 22 GLN 41 A TYR 42 n 23 TYR 42 A PHE 43 n 24 PHE 43 A SER 44 n 25 SER 44 A LYS 45 n 26 LYS 45 A PRO 46 n 27 PRO 46 A HIS 47 n 28 HIS 47 A ILE 48 n 29 ILE 48 A SER 49 n 30 SER 49 A HIS 50 n 31 HIS 50 A ILE 51 n 32 ILE 51 A LYS 52 n 33 LYS 52 A ILE 53 n 34 ILE 53 A GLU 54 n 35 GLU 54 A SER 55 n 36 SER 55 A GLU 56 n 37 GLU 56 A ILE 57 n 38 ILE 57 A LEU 58 n 39 LEU 58 A GLN 59 n 40 GLN 59 A THR 60 n 41 THR 60 A LYS 61 n 42 LYS 61 A LYS 62 n 43 LYS 62 A TYR 63 n 44 TYR 63 A GLU 64 n 45 GLU 64 A VAL 65 n 46 VAL 65 A LEU 66 n 47 LEU 66 A LEU 67 n 48 LEU 67 A THR 68 n 49 THR 68 A ASP 69 n 50 ASP 69 A ARG 70 n 51 ARG 70 A THR 71 n 52 THR 71 A GLU 72 n 53 GLU 72 A ILE 73 n 54 ILE 73 A ASP 74 n 55 ASP 74 A PHE 75 n 56 PHE 75 A ASP 76 n 57 ASP 76 A LYS 77 n 58 LYS 77 A LYS 78 n 59 LYS 78 A GLY 79 n 60 GLY 79 A ASN 80 n 61 ASN 80 A TRP 81 n 62 TRP 81 A LEU 82 n 63 LEU 82 A GLU 83 n 64 GLU 83 A VAL 84 n 65 VAL 84 A ASP 85 n 66 ASP 85 A CYS 86 n 67 CYS 86 A LYS 87 n 68 LYS 87 A LYS 88 n 69 LYS 88 A SER 89 n 70 SER 89 A ALA 90 n 71 ALA 90 A VAL 91 n 72 VAL 91 A PRO 92 n 73 PRO 92 A GLU 93 n 74 GLU 93 A ALA 94 n 75 ALA 94 A LEU 95 n 76 LEU 95 A ILE 96 n 77 ILE 96 A PRO 97 n 78 PRO 97 A VAL 98 n 79 VAL 98 A PRO 99 n 80 PRO 99 A VAL 100 n 81 VAL 100 A LYS 101 n 82 LYS 101 A GLU 102 n 83 GLU 102 A TYR 103 n 84 TYR 103 A VAL 104 n 85 VAL 104 A LYS 105 n 86 LYS 105 A ALA 106 n 87 ALA 106 A ASN 107 n 88 ASN 107 A PHE 108 n 89 PHE 108 A PRO 109 n 90 PRO 109 A ARG 110 n 91 ARG 110 A GLU 111 n 92 GLU 111 A ILE 112 n 93 ILE 112 A ILE 113 n 94 ILE 113 A THR 114 n 95 THR 114 A LYS 115 n 96 LYS 115 A ILE 116 n 97 ILE 116 A GLU 117 n 98 GLU 117 A ARG 118 n 99 ARG 118 A GLY 119 n 100 GLY 119 A ARG 120 n 101 ARG 120 A THR 121 n 102 THR 121 A GLY 122 n 103 GLY 122 A VAL 123 n 104 VAL 123 A GLU 124 n 105 GLU 124 A ILE 125 n 106 ILE 125 A GLU 126 n 107 GLU 126 A LEU 127 n 108 LEU 127 A GLY 128 n 109 GLY 128 A ASN 129 n 110 ASN 129 A ASP 130 n 111 ASP 130 A TYR 131 n 112 TYR 131 A SER 132 n 113 SER 132 A LEU 133 n 114 LEU 133 A LYS 134 n 115 LYS 134 A PHE 135 n 116 PHE 135 A ASN 136 n 117 ASN 136 A LYS 137 n 118 LYS 137 A LYS 138 n 119 LYS 138 A GLY 139 n 120 GLY 139 A LYS 140 n 121 LYS 140 A PHE 141 n 122 PHE 141 A VAL 142 n 123 VAL 142 A SER 143 n 124 SER 143 A MSE 144 n 125 MSE 144 A ASP 145 n 126 ASP 145 A ASP 146 n 127 ASP 146 A 1.8469 -1.3048 -1.6263 2.0029 1.5563 2.2761 -0.1975 -0.0240 0.1807 0.2042 -0.0189 -0.3548 0.4577 -0.2557 0.2164 -0.1368 0.0861 0.0272 -0.1862 0.0637 0.0583 refined 28.7089 24.7284 28.5723 X-RAY DIFFRACTION A 21 A 146 X-RAY DIFFRACTION 1 author_and_software_defined_assembly PISA 2 dimeric 4410 -24 15110 A MSE 144 SELENOMETHIONINE A MSE 125 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 7_555 y,x,-z+2/3 crystal symmetry operation 0.0000000000 0.0000000000 60.5533333333 A N THR 25 A N THR 6 A O ILE 51 A O ILE 32 A N VAL 65 A N VAL 46 A O ILE 73 A O ILE 54 A N GLU 72 A N GLU 53 A O ASP 85 A O ASP 66 A N VAL 84 A N VAL 65 A O ILE 116 A O ILE 97 A N LYS 115 A N LYS 96 A O GLU 126 A O GLU 107 A N VAL 123 A N VAL 104 A O PHE 135 A O PHE 116 A N LYS 134 A N LYS 115 A O SER 143 A O SER 124 1 A CG LYS 45 A CG LYS 26 1 Y 1 A CD LYS 45 A CD LYS 26 1 Y 1 A CE LYS 45 A CE LYS 26 1 Y 1 A NZ LYS 45 A NZ LYS 26 1 Y 1 A CG ARG 70 A CG ARG 51 1 Y 1 A CD ARG 70 A CD ARG 51 1 Y 1 A NE ARG 70 A NE ARG 51 1 Y 1 A CZ ARG 70 A CZ ARG 51 1 Y 1 A NH1 ARG 70 A NH1 ARG 51 1 Y 1 A NH2 ARG 70 A NH2 ARG 51 1 Y 1 A CG LYS 105 A CG LYS 86 1 Y 1 A CD LYS 105 A CD LYS 86 1 Y 1 A CE LYS 105 A CE LYS 86 1 Y 1 A NZ LYS 105 A NZ LYS 86 1 Y 1 A CG LYS 138 A CG LYS 119 1 Y 1 A CD LYS 138 A CD LYS 119 1 Y 1 A CE LYS 138 A CE LYS 119 1 Y 1 A NZ LYS 138 A NZ LYS 119 1 Y 1 A CG ASP 146 A CG ASP 127 1 Y 1 A OD1 ASP 146 A OD1 ASP 127 1 Y 1 A OD2 ASP 146 A OD2 ASP 127 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A PRO 46 -96.78 52.31 1 A SER 49 -100.95 76.96 1 A HIS 50 74.84 153.68 1 A LYS 87 58.05 -95.40 1 A ALA 106 -90.19 -62.79 1 A VAL 142 -126.39 -62.86 158.890 87.8228 50.710 14.8621 0.0000 0.0000 14.8621 0.0000 -29.7241 0.9249 0.9142 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS 3.THE MAD PHASES WERE USED AS RESTRAINTS DURING THE REFINEMENT. 4. 1,2-ETHANEDIOL USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 0.2498 0.2150 0.2166 2.7500 29.823 361 7840 4.6000 99.8300 1.000 0.750 RANDOM 1 THROUGHOUT 0.000 MAD 0.535 2.7500 29.823 17 1030 8 0 1005 487 SINUSOIDAL 6.000 30 HARMONIC 2.000 142 HARMONIC 5.000 1030 HARMONIC 20.000 140 SEMIHARMONIC 5.000 1105 SEMIHARMONIC 4.000 0.009 1030 HARMONIC 2.000 1.170 1389 HARMONIC 2.000 2.490 2.270 0.2982 0.2617 0.2635 3.0700 101 2061 2162 5 4.6700 99.8300 2.75 29.823 4QOA 7860 7860 0.084 1 15.700 9.100 99.800 0.012 2.750 2.820 0.7 5000 565 1.185 1 8.800 100.000 0.012 2.820 2.900 0.7 4393 543 1.054 1 8.100 100.000 0.012 2.900 2.980 1.2 5325 537 0.667 1 9.900 99.900 0.012 2.980 3.070 1.4 5185 520 0.541 1 10.000 100.000 0.012 3.070 3.180 1.7 4835 503 0.453 1 9.600 100.000 0.012 3.180 3.290 2.9 4615 497 0.261 1 9.300 100.000 0.012 3.290 3.410 3.5 4208 466 0.213 1 9.000 99.900 0.012 3.410 3.550 4.7 3691 467 0.156 1 7.900 99.700 0.012 3.550 3.710 6.4 4175 441 0.116 1 9.500 100.000 0.012 3.710 3.890 7.3 4105 423 0.100 1 9.700 100.000 0.012 3.890 4.100 8.8 3904 411 0.078 1 9.500 99.800 0.012 4.100 4.350 10.0 3492 382 0.061 1 9.100 100.000 0.012 4.350 4.650 11.6 3005 364 0.051 1 8.300 100.000 0.012 4.650 5.020 12.7 3135 340 0.050 1 9.200 100.000 0.012 5.020 5.500 11.3 3058 322 0.056 1 9.500 100.000 0.012 5.500 6.150 10.0 2688 291 0.064 1 9.200 99.700 0.012 6.150 7.100 11.4 1962 263 0.056 1 7.500 99.900 0.012 7.100 8.700 14.9 2094 231 0.040 1 9.100 100.000 0.012 8.700 12.300 16.6 1487 179 0.034 1 8.300 99.400 0.012 12.300 29.823 17.7 796 115 0.033 1 6.900 93.100 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 Phil Evans pre@mrc-lmb.cam.ac.uk SCALA package 3.3.20 refinement Gerard Bricogne buster-develop@GlobalPhasing.com http://www.globalphasing.com/buster/ BUSTER-TNT program 2.10.0 data reduction MOSFLM phasing SHELXD refinement BUSTER 2.10.0 Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution 1 N N 2 N N 2 N N 3 N N A ASP 27 A ASP 8 HELX_P A LEU 31 A LEU 12 5 1 5 A PRO 32 A PRO 13 HELX_P A PHE 43 A PHE 24 1 2 12 A PRO 92 A PRO 73 HELX_P A ILE 96 A ILE 77 5 3 5 A PRO 97 A PRO 78 HELX_P A PHE 108 A PHE 89 1 4 12 covale 1.343 both A SER 143 A C SER 124 1_555 A MSE 144 A N MSE 125 1_555 covale 1.352 both A MSE 144 A C MSE 125 1_555 A ASP 145 A N ASP 126 1_555 STRUCTURAL GENOMICS, UNKNOWN FUNCTION Two copies of DUF2874 domain (PF11396), BLIP-like fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION A7VAB9_BACUN UNP 1 21 A7VAB9 GDVITQDTKQLPLTARNFINQYFSKPHISHIKIESEILQTKKYEVLLTDRTEIDFDKKGNWLEVDCKKSAVPEALIPVPV KEYVKANFPREIITKIERGRTGVEIELGNDYSLKFNKKGKFVSMDD 21 146 4QOA 21 146 A7VAB9 A 1 2 127 1 expression tag GLY 0 4QOA A A7VAB9 UNP 1 2 7 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A VAL 23 A VAL 4 A THR 25 A THR 6 A ILE 51 A ILE 32 A ILE 53 A ILE 34 A LYS 61 A LYS 42 A LEU 66 A LEU 47 A GLU 72 A GLU 53 A ASP 76 A ASP 57 A TRP 81 A TRP 62 A ASP 85 A ASP 66 A ILE 113 A ILE 94 A ARG 118 A ARG 99 A GLY 122 A GLY 103 A LEU 127 A LEU 108 A SER 132 A SER 113 A ASN 136 A ASN 117 A PHE 141 A PHE 122 A ASP 145 A ASP 126 BINDING SITE FOR RESIDUE EDO A 201 A EDO 201 Software 5 BINDING SITE FOR RESIDUE EDO A 202 A EDO 202 Software 4 A PRO 32 A PRO 13 5 1_555 A LEU 33 A LEU 14 5 1_555 A THR 34 A THR 15 5 1_555 A ARG 36 A ARG 17 5 10_666 A EDO 202 C EDO 5 10_666 A THR 28 A THR 9 4 1_555 A ARG 36 A ARG 17 4 1_555 A EDO 201 B EDO 4 10_666 A HOH 309 D HOH 4 1_555 179 P 65 2 2