HEADER CELL CYCLE 02-DEC-22 8HM1 TITLE CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-LIKE PROTEIN FROM BACTEROIDES TITLE 2 FRAGILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS; SOURCE 3 ORGANISM_TAXID: 817; SOURCE 4 GENE: UBB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS UBIQUITIN-LIKE PROTEIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR M.TONG,Z.CHEN,X.GAO REVDAT 3 24-JAN-24 8HM1 1 JRNL REVDAT 2 27-DEC-23 8HM1 1 JRNL REVDAT 1 29-NOV-23 8HM1 0 JRNL AUTH K.JIANG,W.LI,M.TONG,J.XU,Z.CHEN,Y.YANG,Y.ZANG,X.JIAO,C.LIU, JRNL AUTH 2 B.LIM,X.JIANG,J.WANG,D.WU,M.WANG,S.J.LIU,F.SHAO,X.GAO JRNL TITL BACTEROIDES FRAGILIS UBIQUITIN HOMOLOGUE DRIVES INTRASPECIES JRNL TITL 2 BACTERIAL COMPETITION IN THE GUT MICROBIOME. JRNL REF NAT MICROBIOL V. 9 70 2024 JRNL REFN ESSN 2058-5276 JRNL PMID 38082149 JRNL DOI 10.1038/S41564-023-01541-5 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 36628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1876 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.8600 - 3.0300 1.00 3011 157 0.2492 0.2755 REMARK 3 2 3.0300 - 2.4100 1.00 2790 166 0.2428 0.2330 REMARK 3 3 2.4100 - 2.1000 1.00 2789 125 0.2343 0.2237 REMARK 3 4 2.1000 - 1.9100 1.00 2730 154 0.2370 0.2510 REMARK 3 5 1.9100 - 1.7700 1.00 2729 143 0.2467 0.3012 REMARK 3 6 1.7700 - 1.6700 1.00 2677 151 0.2432 0.2635 REMARK 3 7 1.6700 - 1.5900 1.00 2713 137 0.2491 0.2401 REMARK 3 8 1.5900 - 1.5200 1.00 2676 152 0.2580 0.2838 REMARK 3 9 1.5200 - 1.4600 1.00 2665 160 0.2680 0.3104 REMARK 3 10 1.4600 - 1.4100 1.00 2674 141 0.2744 0.2969 REMARK 3 11 1.4100 - 1.3600 0.98 2599 128 0.2889 0.3005 REMARK 3 12 1.3600 - 1.3200 0.93 2439 144 0.3160 0.3342 REMARK 3 13 1.3200 - 1.2900 0.84 2260 118 0.3376 0.3635 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.193 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.867 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 1285 REMARK 3 ANGLE : 1.936 1714 REMARK 3 CHIRALITY : 0.109 192 REMARK 3 PLANARITY : 0.012 218 REMARK 3 DIHEDRAL : 14.519 497 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8HM1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 1.19.2_4158 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 32.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH 3.0, 3.4 M REMARK 280 CESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 95.43000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.19000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 143.14500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.19000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.19000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.71500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.19000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.19000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 143.14500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.19000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.19000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.71500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 95.43000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: 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 VAL A 74 -58.24 -123.10 REMARK 500 ASP A 75 21.25 -146.76 REMARK 500 ASP B 75 14.77 -152.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 339 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 340 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 341 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A 342 DISTANCE = 9.96 ANGSTROMS REMARK 525 HOH B 297 DISTANCE = 6.68 ANGSTROMS DBREF 8HM1 A 1 76 UNP Q5L8M7 Q5L8M7_BACFN 1 76 DBREF 8HM1 B 1 76 UNP Q5L8M7 Q5L8M7_BACFN 1 76 SEQADV 8HM1 SER A 0 UNP Q5L8M7 EXPRESSION TAG SEQADV 8HM1 SER B 0 UNP Q5L8M7 EXPRESSION TAG SEQRES 1 A 77 SER MET GLN VAL PHE ILE LYS ASN ARG TYR GLY TRP THR SEQRES 2 A 77 ILE THR LEU GLU VAL SER PRO THR ASP THR VAL GLU ASN SEQRES 3 A 77 VAL LYS GLN LYS ILE GLN ASP LYS GLU GLY PHE PRO PRO SEQRES 4 A 77 ASP LYS ILE ARG LEU ILE TYR GLY GLY LYS GLN MET GLU SEQRES 5 A 77 ASP GLY ARG THR LEU ALA ASP TYR ASN VAL GLN LYS ASP SEQRES 6 A 77 SER THR ILE LEU ILE CYS ILE ARG ASP VAL ASP CYS SEQRES 1 B 77 SER MET GLN VAL PHE ILE LYS ASN ARG TYR GLY TRP THR SEQRES 2 B 77 ILE THR LEU GLU VAL SER PRO THR ASP THR VAL GLU ASN SEQRES 3 B 77 VAL LYS GLN LYS ILE GLN ASP LYS GLU GLY PHE PRO PRO SEQRES 4 B 77 ASP LYS ILE ARG LEU ILE TYR GLY GLY LYS GLN MET GLU SEQRES 5 B 77 ASP GLY ARG THR LEU ALA ASP TYR ASN VAL GLN LYS ASP SEQRES 6 B 77 SER THR ILE LEU ILE CYS ILE ARG ASP VAL ASP CYS HET EDO A 101 4 HET EDO A 102 4 HET EDO A 103 4 HET EDO A 104 4 HET EDO A 105 4 HET EDO A 106 4 HET EDO A 107 4 HET EDO B 101 4 HET EDO B 102 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 9(C2 H6 O2) FORMUL 12 HOH *239(H2 O) HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 HELIX 3 AA3 LEU A 56 ASN A 60 5 5 HELIX 4 AA4 THR B 22 GLY B 35 1 14 HELIX 5 AA5 PRO B 37 ASP B 39 5 3 HELIX 6 AA6 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 LYS A 6 -1 N VAL A 3 O LEU A 15 SHEET 3 AA1 5 THR A 66 ILE A 71 1 O ILE A 67 N PHE A 4 SHEET 4 AA1 5 ILE A 41 TYR A 45 -1 N ARG A 42 O CYS A 70 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N TYR A 45 SHEET 1 AA2 5 THR B 12 VAL B 17 0 SHEET 2 AA2 5 MET B 1 LYS B 6 -1 N MET B 1 O VAL B 17 SHEET 3 AA2 5 THR B 66 ILE B 71 1 O ILE B 67 N PHE B 4 SHEET 4 AA2 5 ILE B 41 TYR B 45 -1 N ARG B 42 O CYS B 70 SHEET 5 AA2 5 LYS B 48 GLN B 49 -1 O LYS B 48 N TYR B 45 SSBOND 1 CYS A 70 CYS A 76 1555 1555 2.06 SSBOND 2 CYS B 70 CYS B 76 1555 1555 2.04 CRYST1 38.380 38.380 190.860 90.00 90.00 90.00 P 43 21 2 16 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 0.026055 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005239 0.00000