HEADER CELL CYCLE 02-DEC-22 8HM2 TITLE CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-LIKE PROTEIN FROM BACTEROIDES TITLE 2 FRAGILIS C TERMINAL CYSTEINE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS; SOURCE 3 ORGANISM_TAXID: 817; SOURCE 4 GENE: UBB, BF9343_3779; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS UBIQUTIN LIKE PROTEIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR M.TONG,Z.CHEN,X.GAO REVDAT 3 24-JAN-24 8HM2 1 JRNL REVDAT 2 27-DEC-23 8HM2 1 JRNL REVDAT 1 29-NOV-23 8HM2 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. 1.34 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 30343 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1475 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 29.0700 - 2.9800 1.00 2996 127 0.2417 0.2438 REMARK 3 2 2.9800 - 2.3600 1.00 2789 159 0.2383 0.2383 REMARK 3 3 2.3600 - 2.0600 1.00 2748 128 0.2409 0.2571 REMARK 3 4 2.0600 - 1.8800 1.00 2703 136 0.2555 0.2990 REMARK 3 5 1.8800 - 1.7400 1.00 2689 145 0.2636 0.3008 REMARK 3 6 1.7400 - 1.6400 1.00 2688 141 0.2849 0.3241 REMARK 3 7 1.6400 - 1.5600 1.00 2643 147 0.2751 0.2844 REMARK 3 8 1.5600 - 1.4900 1.00 2653 132 0.2834 0.3230 REMARK 3 9 1.4900 - 1.4300 0.97 2546 134 0.2997 0.3063 REMARK 3 10 1.4300 - 1.3800 0.89 2390 117 0.3232 0.3562 REMARK 3 11 1.3800 - 1.3400 0.77 2023 109 0.3606 0.3901 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) : 0.232 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.636 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.45 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 : 0.008 1248 REMARK 3 ANGLE : 1.067 1687 REMARK 3 CHIRALITY : 0.095 192 REMARK 3 PLANARITY : 0.007 217 REMARK 3 DIHEDRAL : 13.489 487 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 8HM2 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_1300033878. 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 : 2.8 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 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30343 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 29.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 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 : NULL 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 (%): 34.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID PH 2.8, 1.6 M REMARK 280 AMMONIUM SULFATE, 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 88.59500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.26850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.26850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 132.89250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.26850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.26850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.29750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.26850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.26850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 132.89250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.26850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.26850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.29750 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 88.59500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 143 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 153 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 VAL B 74 REMARK 465 ASP B 75 REMARK 465 GLY B 76 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 ASP A 75 -158.47 -113.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HM2 A 1 76 UNP Q5L8M7 Q5L8M7_BACFN 1 76 DBREF 8HM2 B 1 76 UNP Q5L8M7 Q5L8M7_BACFN 1 76 SEQADV 8HM2 SER A 0 UNP Q5L8M7 EXPRESSION TAG SEQADV 8HM2 VAL A 70 UNP Q5L8M7 CYS 70 ENGINEERED MUTATION SEQADV 8HM2 GLY A 76 UNP Q5L8M7 CYS 76 ENGINEERED MUTATION SEQADV 8HM2 SER B 0 UNP Q5L8M7 EXPRESSION TAG SEQADV 8HM2 VAL B 70 UNP Q5L8M7 CYS 70 ENGINEERED MUTATION SEQADV 8HM2 GLY B 76 UNP Q5L8M7 CYS 76 ENGINEERED MUTATION 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 VAL ILE ARG ASP VAL ASP GLY 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 VAL ILE ARG ASP VAL ASP GLY FORMUL 3 HOH *137(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 ILE A 5 O ILE A 13 SHEET 3 AA1 5 THR A 66 ILE A 71 1 O ILE A 69 N LYS A 6 SHEET 4 AA1 5 ILE A 41 TYR A 45 -1 N ILE A 44 O LEU A 68 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 GLU B 16 0 SHEET 2 AA2 5 GLN B 2 LYS B 6 -1 N ILE B 5 O ILE B 13 SHEET 3 AA2 5 THR B 66 ILE B 71 1 O ILE B 69 N LYS B 6 SHEET 4 AA2 5 ILE B 41 TYR B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA2 5 LYS B 48 GLN B 49 -1 O LYS B 48 N TYR B 45 CRYST1 38.537 38.537 177.190 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 0.025949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005644 0.00000