HEADER HYDROLASE 03-JAN-26 21XQ TITLE A NOVEL GH8 FAMILY ENDOXYLANASE BGXYN8A COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSYL HYDROLASE FAMILY 8; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS GLYCINIFERMENTANS; SOURCE 3 ORGANISM_TAXID: 1664069; SOURCE 4 GENE: AB447_216495, P8828_09935; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDOXYLANASE GH8, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,Y.LIU REVDAT 1 13-MAY-26 21XQ 0 JRNL AUTH Y.LIU,W.XIE,Y.ZHANG,S.LIANG,S.WANG,R.ZHAN,C.WANG,K.WANG JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF A NOVEL JRNL TITL 2 GLYCOSIDE HYDROLASE FAMILY 8 ENDOXYLANASE WITH JRNL TITL 3 BROAD-SPECTRUM XYLOOLIGOSACCHARIDE PRODUCTION. JRNL REF BIORESOUR TECHNOL 34780 2026 JRNL REFN ESSN 1873-2976 JRNL PMID 42086152 JRNL DOI 10.1016/J.BIORTECH.2026.134780 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.352 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.962 REMARK 3 FREE R VALUE TEST SET COUNT : 1235 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 20.0000 - 4.5604 1.00 2780 106 0.1693 0.1717 REMARK 3 2 4.5604 - 3.6266 1.00 2635 154 0.1585 0.1545 REMARK 3 3 3.6266 - 3.1702 1.00 2647 123 0.1962 0.2332 REMARK 3 4 3.1702 - 2.8813 1.00 2609 160 0.2158 0.2577 REMARK 3 5 2.8813 - 2.6753 1.00 2616 142 0.2075 0.2237 REMARK 3 6 2.6753 - 2.5178 1.00 2594 145 0.2116 0.2790 REMARK 3 7 2.5178 - 2.3920 1.00 2585 136 0.2213 0.2988 REMARK 3 8 2.3920 - 2.2880 1.00 2608 128 0.2170 0.2707 REMARK 3 9 2.2880 - 2.2100 1.00 2578 141 0.2201 0.2966 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) : 0.251 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.598 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.23 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 3261 REMARK 3 ANGLE : 0.829 4407 REMARK 3 CHIRALITY : 0.046 443 REMARK 3 PLANARITY : 0.005 574 REMARK 3 DIHEDRAL : 6.515 1896 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 21XQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1300068028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER TURBO X-RAY SOURCE REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NONIUS KAPPA CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24887 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 21.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 20.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.03700 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: MAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM CHLORIDE, HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.78667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.39333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.39333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.78667 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 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 LEU A 84 -72.53 -78.68 REMARK 500 SER A 149 -67.36 -130.73 REMARK 500 ASN A 232 48.35 -98.03 REMARK 500 ARG A 252 133.91 -35.84 REMARK 500 SER A 317 -153.26 -131.02 REMARK 500 GLU A 359 40.03 -76.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7D88 RELATED DB: PDB DBREF1 21XQ A 37 438 UNP A0A0J6ECL7_9BACI DBREF2 21XQ A A0A0J6ECL7 30 431 SEQADV 21XQ GLY A 178 UNP A0A0J6ECL GLU 171 CONFLICT SEQADV 21XQ LYS A 208 UNP A0A0J6ECL MET 201 CONFLICT SEQADV 21XQ LYS A 276 UNP A0A0J6ECL ASN 269 CONFLICT SEQADV 21XQ ILE A 369 UNP A0A0J6ECL MET 362 CONFLICT SEQADV 21XQ LEU A 437 UNP A0A0J6ECL MET 430 CONFLICT SEQRES 1 A 402 ALA VAL HIS SER LYS THR PRO ASP ILE LEU GLY THR THR SEQRES 2 A 402 GLY LYS THR ASN LEU ASN GLN ALA TYR LYS LYS TYR PHE SEQRES 3 A 402 ASP GLY LYS GLY GLY SER LEU PHE HIS TYR MET ARG ASP SEQRES 4 A 402 GLY SER ALA PHE ILE ALA SER THR LEU ASP ASP ASP LEU SEQRES 5 A 402 GLY ASN GLY TYR TYR SER VAL LYS THR GLU GLY MET SER SEQRES 6 A 402 TYR GLY MET MET ILE ALA LEU GLN MET ASN ASP GLU TYR SEQRES 7 A 402 LYS PHE GLN ARG LEU TRP ASP PHE VAL ARG LYS TYR MET SEQRES 8 A 402 ARG HIS THR ASP LYS ASN ASP SER LEU TYR GLY TYR HIS SEQRES 9 A 402 ARG TRP HIS MET LYS THR ASN GLY SER ASP VAL GLN THR SEQRES 10 A 402 ILE ASP GLN ASN VAL ALA SER ASP GLY GLU VAL TRP PHE SEQRES 11 A 402 ALA ALA ALA LEU MET MET ALA SER GLY ARG TRP GLY ASP SEQRES 12 A 402 LYS GLN TYR PRO TYR ASP TYR LYS ALA ARG ALA GLN ASP SEQRES 13 A 402 MET LEU ASP ALA LEU ALA GLY ASP GLY GLU TYR ALA ASN SEQRES 14 A 402 ALA SER LYS GLU SER ARG ILE PHE ILE LYS ASN GLY ASN SEQRES 15 A 402 ASP GLN ARG TYR ALA MET VAL ARG PHE GLY PRO TYR VAL SEQRES 16 A 402 ASN TRP THR ASP PRO SER TYR HIS VAL PRO ALA PHE PHE SEQRES 17 A 402 GLU LEU PHE ALA LYS SER ALA ARG SER SER GLN GLN TYR SEQRES 18 A 402 PHE TRP LYS ASP ALA ALA ASN LYS SER ARG LYS TYR LEU SEQRES 19 A 402 SER GLU THR THR PHE LYS SER VAL LEU PRO ASN GLY SER SEQRES 20 A 402 THR VAL THR ASN ALA ALA THR GLY LEU PHE PRO ASP GLU SEQRES 21 A 402 ALA GLY PHE ASP GLY VAL SER ASP ALA ALA HIS SER SER SEQRES 22 A 402 THR LYS THR ASP ARG ASN PHE SER TYR ASP ALA TRP ARG SEQRES 23 A 402 THR VAL SER HIS VAL ALA MET ASP TYR THR LEU TRP SER SEQRES 24 A 402 SER ALA ASP ASN PRO TYR ARG ALA ARG GLU GLN LYS ALA SEQRES 25 A 402 VAL ASN LYS PHE LEU THR PHE MET LYS ARG GLU ASN TYR SEQRES 26 A 402 GLY ARG THR ALA HIS GLU TYR ILE LEU ASN GLY THR ALA SEQRES 27 A 402 VAL LYS LYS GLY SER ALA MET GLY LEU ILE ALA ALA ASN SEQRES 28 A 402 ALA GLY GLY ALA THR ALA ALA SER ASN GLY SER LEU ARG SEQRES 29 A 402 THR GLY PHE ALA ASN ALA PHE ASN SER ALA TYR ILE PRO SEQRES 30 A 402 ASP ASP TYR TYR GLY SER CYS LEU TYR MET LEU ASN SER SEQRES 31 A 402 LEU ALA ALA ASN GLY LYS PHE THR MET TYR LEU PRO HELIX 1 AA1 LEU A 46 ASP A 63 1 18 HELIX 2 AA2 THR A 97 MET A 110 1 14 HELIX 3 AA3 ASP A 112 MET A 127 1 16 HELIX 4 AA4 ALA A 159 GLY A 178 1 20 HELIX 5 AA5 ASP A 185 GLY A 199 1 15 HELIX 6 AA6 ASP A 200 ALA A 204 5 5 HELIX 7 AA7 SER A 207 ARG A 211 5 5 HELIX 8 AA8 ASP A 235 HIS A 239 5 5 HELIX 9 AA9 VAL A 240 ALA A 251 1 12 HELIX 10 AB1 ARG A 252 SER A 254 5 3 HELIX 11 AB2 GLN A 255 GLU A 272 1 18 HELIX 12 AB3 ASP A 304 SER A 308 5 5 HELIX 13 AB4 THR A 310 ASN A 315 5 6 HELIX 14 AB5 ASP A 319 TRP A 321 5 3 HELIX 15 AB6 ARG A 322 TRP A 334 1 13 HELIX 16 AB7 TYR A 341 GLU A 359 1 19 HELIX 17 AB8 ALA A 380 ALA A 391 1 12 HELIX 18 AB9 THR A 392 ALA A 394 5 3 HELIX 19 AC1 ASN A 396 SER A 409 1 14 HELIX 20 AC2 ASP A 415 ASN A 430 1 16 SHEET 1 AA1 2 VAL A 38 LYS A 41 0 SHEET 2 AA1 2 THR A 434 TYR A 436 -1 O MET A 435 N SER A 40 SHEET 1 AA2 2 PHE A 70 TYR A 72 0 SHEET 2 AA2 2 ALA A 78 ILE A 80 -1 O PHE A 79 N HIS A 71 SHEET 1 AA3 4 ASP A 87 GLY A 89 0 SHEET 2 AA3 4 TYR A 92 LYS A 96 -1 O TYR A 92 N LEU A 88 SHEET 3 AA3 4 HIS A 143 THR A 146 -1 O MET A 144 N VAL A 95 SHEET 4 AA3 4 VAL A 151 ASP A 155 -1 O GLN A 152 N LYS A 145 SHEET 1 AA4 3 THR A 284 THR A 286 0 SHEET 2 AA4 3 LYS A 276 VAL A 278 -1 N SER A 277 O VAL A 285 SHEET 3 AA4 3 VAL A 302 SER A 303 1 O SER A 303 N LYS A 276 SHEET 1 AA5 2 ALA A 365 TYR A 368 0 SHEET 2 AA5 2 ALA A 374 LYS A 377 -1 O VAL A 375 N GLU A 367 CISPEP 1 TYR A 182 PRO A 183 0 1.86 CRYST1 104.935 104.935 76.180 90.00 90.00 120.00 P 32 2 1 6 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 0.009530 0.005502 0.000000 0.00000 SCALE2 0.000000 0.011004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013127 0.00000 MASTER 229 0 0 20 13 0 0 6 3177 1 0 31 END