HEADER HYDROLASE 09-SEP-23 8U46 TITLE CRYSTAL STRUCTURE OF BACTEROIDES THETAIOTAOMICRON VPI-5482 TITLE 2 ENDOGLYCOSIDASE BT1285 D161A-E163A INACTIVE VERSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON VPI-5482; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 GENE: BT_1285; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS ENDOGLYCOSIDASE, ARTIFICIAL LECTIN, HIGH MANNOSE SPECIFIC, KEYWDS 2 BACTEROIDES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.E.SASTRE,N.SULTANA,E.J.SUNDBERG REVDAT 2 26-JUN-24 8U46 1 JRNL REVDAT 1 29-MAY-24 8U46 0 JRNL AUTH D.E.SASTRE,N.SULTANA,M.V A S NAVARRO,M.HULICIAK,J.DU, JRNL AUTH 2 J.O.CIFUENTE,M.FLOWERS,X.LIU,P.LOLLAR,B.TRASTOY,M.E.GUERIN, JRNL AUTH 3 E.J.SUNDBERG JRNL TITL HUMAN GUT MICROBES EXPRESS FUNCTIONALLY DISTINCT JRNL TITL 2 ENDOGLYCOSIDASES TO METABOLIZE THE SAME N-GLYCAN SUBSTRATE. JRNL REF NAT COMMUN V. 15 5123 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38879612 JRNL DOI 10.1038/S41467-024-48802-3 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 14781 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 743 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 49.7700 - 3.5900 0.98 2927 153 0.1442 0.1656 REMARK 3 2 3.5900 - 2.8500 0.99 2859 155 0.1610 0.2287 REMARK 3 3 2.8500 - 2.4900 0.99 2794 143 0.1760 0.2462 REMARK 3 4 2.4900 - 2.2600 0.99 2761 148 0.1787 0.2513 REMARK 3 5 2.2600 - 2.1000 0.96 2697 144 0.1839 0.2587 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2052 REMARK 3 ANGLE : 0.838 2796 REMARK 3 CHIRALITY : 0.057 301 REMARK 3 PLANARITY : 0.005 367 REMARK 3 DIHEDRAL : 12.448 287 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 8U46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000277312. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14793 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 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 : 0.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% W/V PEG 1000, 12.5% W/V PEG REMARK 280 3350, 12.5% V/V MPD 0.03 M OF EACH DIVALENT CATION 0.1 M MOPS/ REMARK 280 HEPES-NA PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 35.15450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.23300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.15450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.23300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 MET A 25 REMARK 465 PRO A 26 REMARK 465 VAL A 27 REMARK 465 ASN A 28 REMARK 465 GLN A 29 REMARK 465 SER A 30 REMARK 465 ASP A 31 REMARK 465 ASN A 32 REMARK 465 ASN A 33 REMARK 465 GLN A 34 REMARK 465 SER A 35 REMARK 465 GLU A 36 REMARK 465 VAL A 37 REMARK 465 VAL A 38 REMARK 465 THR A 39 REMARK 465 ARG A 40 REMARK 465 SER A 41 REMARK 465 ALA A 42 REMARK 465 THR A 43 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 52 CG CD OE1 OE2 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 ILE A 108 -55.43 -120.69 REMARK 500 ASP A 125 43.51 -149.91 REMARK 500 PHE A 231 49.76 30.65 REMARK 500 ASP A 273 47.92 73.55 REMARK 500 SER A 293 -158.99 -144.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 8U46 A 25 306 UNP Q8A889 Q8A889_BACTN 25 306 SEQADV 8U46 ALA A 161 UNP Q8A889 ASP 161 ENGINEERED MUTATION SEQADV 8U46 ALA A 163 UNP Q8A889 GLU 163 ENGINEERED MUTATION SEQRES 1 A 282 MET PRO VAL ASN GLN SER ASP ASN ASN GLN SER GLU VAL SEQRES 2 A 282 VAL THR ARG SER ALA THR GLY ILE LYS ASN ILE VAL TYR SEQRES 3 A 282 ILE GLU VAL ASN ASP ILE ASN PRO LEU ASN ALA GLY SER SEQRES 4 A 282 TYR ILE MET ASP ASP ALA PRO PHE PHE ASP TYR VAL ILE SEQRES 5 A 282 LEU PHE ALA ALA ASN ILE ARG GLY VAL GLY SER ASP ALA SEQRES 6 A 282 THR LEU TYR ASN ASN PRO ASN VAL GLN TYR ILE LEU ASP SEQRES 7 A 282 HIS LYS ASP THR LEU ILE LYS PRO LEU GLN ASP LYS GLY SEQRES 8 A 282 ILE LYS VAL LEU LEU GLY LEU LEU GLY ASP HIS THR GLY SEQRES 9 A 282 LEU GLY PHE ALA ASN MET ASN SER ALA GLN THR GLU GLN SEQRES 10 A 282 PHE ALA THR ALA VAL ALA ASN ALA VAL SER GLN TYR GLY SEQRES 11 A 282 LEU ASP GLY VAL ASP PHE ALA ASP ALA TRP ALA GLU TYR SEQRES 12 A 282 GLY ARG ASN GLY TYR PRO SER GLY SER THR GLY SER PHE SEQRES 13 A 282 SER ASN LEU ILE THR ALA LEU HIS ASN LYS MET PRO GLY SEQRES 14 A 282 LYS THR ILE THR VAL PHE ASN TYR GLY TYR THR SER GLU SEQRES 15 A 282 LEU THR GLY VAL ASN SER TYR ILE ASP TYR GLY ILE TYR SEQRES 16 A 282 ALA PHE PHE ASN SER PRO SER TRP SER THR GLY PHE GLY SEQRES 17 A 282 MET PRO ASN SER LYS PHE ALA PRO TYR THR ILE ASN LEU SEQRES 18 A 282 ASN SER ALA PRO SER ALA ALA SER ALA GLN LEU TYR SER SEQRES 19 A 282 GLY GLN VAL ALA SER LYS GLY TYR GLY ALA ILE GLY TYR SEQRES 20 A 282 TYR ASP LEU ARG ALA ASN ASN ILE VAL SER VAL LEU ASN SEQRES 21 A 282 GLY VAL ALA LYS GLY ALA PHE LYS SER THR CYS THR TYR SEQRES 22 A 282 ASP GLY ASN SER TYR PRO LYS ASN TYR FORMUL 2 HOH *168(H2 O) HELIX 1 AA1 ASN A 57 GLY A 62 5 6 HELIX 2 AA2 ASN A 94 HIS A 103 1 10 HELIX 3 AA3 HIS A 103 ILE A 108 1 6 HELIX 4 AA4 ILE A 108 LYS A 114 1 7 HELIX 5 AA5 ASN A 135 GLY A 154 1 20 HELIX 6 AA6 GLY A 168 TYR A 172 5 5 HELIX 7 AA7 GLY A 178 MET A 191 1 14 HELIX 8 AA8 GLY A 202A ILE A 214 5 13 HELIX 9 AA9 PRO A 234 SER A 236 5 3 HELIX 10 AB1 SER A 250 LYS A 264 1 15 HELIX 11 AB2 ILE A 279 LYS A 292 1 14 SHEET 1 AA1 7 ASP A 88 TYR A 92 0 SHEET 2 AA1 7 TYR A 74 VAL A 85 -1 N ASN A 81 O TYR A 92 SHEET 3 AA1 7 LYS A 117 GLY A 124 1 O LEU A 119 N LEU A 77 SHEET 4 AA1 7 GLY A 157 ALA A 161 1 O ALA A 161 N LEU A 122 SHEET 5 AA1 7 THR A 195 ASN A 200 1 O PHE A 199 N PHE A 160 SHEET 6 AA1 7 TYR A 216 TYR A 219 1 O ILE A 218 N ASN A 200 SHEET 7 AA1 7 PHE A 238 ALA A 239 1 O ALA A 239 N TYR A 219 SHEET 1 AA2 5 ASP A 88 TYR A 92 0 SHEET 2 AA2 5 TYR A 74 VAL A 85 -1 N ASN A 81 O TYR A 92 SHEET 3 AA2 5 LYS A 46 GLU A 52 1 N VAL A 49 O TYR A 74 SHEET 4 AA2 5 ALA A 268 TYR A 272 1 O TYR A 271 N TYR A 50 SHEET 5 AA2 5 THR A 242 ASN A 244 1 N ILE A 243 O TYR A 272 SHEET 1 AA3 3 ALA A 69 PRO A 70 0 SHEET 2 AA3 3 TYR A 64 MET A 66 -1 N MET A 66 O ALA A 69 SHEET 3 AA3 3 THR A 296 TYR A 297 -1 O THR A 296 N ILE A 65 CISPEP 1 PHE A 78 ALA A 79 0 6.69 CRYST1 70.309 70.466 50.051 90.00 90.00 90.00 P 21 21 2 4 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 0.014223 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019980 0.00000