HEADER HYDROLASE 06-SEP-19 6KWD TITLE CRYSTAL STRUCTURE ANALYSIS OF ENDO-BETA-1,4-XYLANASE II COMPLEXED WITH TITLE 2 XYLOTRIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYLANASE 2,1,4-BETA-D-XYLAN XYLANOHYDROLASE 2,ALKALINE ENDO- COMPND 5 BETA-1,4-XYLANASE; COMPND 6 EC: 3.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA REESEI RUT C-30; SOURCE 3 ORGANISM_TAXID: 1344414; SOURCE 4 GENE: XYN2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS XYLANASE II, COMPLEX, CO-CRYSTALLIZATION, XYLOTRIOSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.LI,Q.WAN REVDAT 2 22-NOV-23 6KWD 1 REMARK REVDAT 1 30-DEC-20 6KWD 0 JRNL AUTH Z.LI,X.ZHANG,C.LI,A.KOVALEVSKY,Q.WAN JRNL TITL STUDYING THE ROLE OF A SINGLE MUTATION OF A FAMILY 11 JRNL TITL 2 GLYCOSIDE HYDROLASE USING HIGH-RESOLUTION X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF PROTEIN J. V. 39 671 2020 JRNL REFN ISSN 1572-3887 JRNL PMID 33128114 JRNL DOI 10.1007/S10930-020-09938-5 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 49040 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2484 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 32.7300 - 3.3997 0.99 2766 142 0.1745 0.1686 REMARK 3 2 3.3997 - 2.6988 0.99 2661 134 0.1542 0.1443 REMARK 3 3 2.6988 - 2.3578 1.00 2630 141 0.1403 0.1598 REMARK 3 4 2.3578 - 2.1423 1.00 2612 139 0.1376 0.1511 REMARK 3 5 2.1423 - 1.9887 1.00 2568 150 0.1282 0.1523 REMARK 3 6 1.9887 - 1.8715 1.00 2631 121 0.1297 0.1571 REMARK 3 7 1.8715 - 1.7778 1.00 2595 138 0.1251 0.1479 REMARK 3 8 1.7778 - 1.7004 1.00 2572 140 0.1241 0.1645 REMARK 3 9 1.7004 - 1.6349 1.00 2571 145 0.1262 0.1664 REMARK 3 10 1.6349 - 1.5785 1.00 2571 146 0.1276 0.1389 REMARK 3 11 1.5785 - 1.5292 1.00 2579 147 0.1294 0.1585 REMARK 3 12 1.5292 - 1.4855 1.00 2562 135 0.1493 0.2073 REMARK 3 13 1.4855 - 1.4464 1.00 2586 130 0.1535 0.1680 REMARK 3 14 1.4464 - 1.4111 1.00 2582 133 0.1682 0.2249 REMARK 3 15 1.4111 - 1.3790 1.00 2550 152 0.1752 0.1979 REMARK 3 16 1.3790 - 1.3496 1.00 2579 129 0.1820 0.2343 REMARK 3 17 1.3496 - 1.3226 1.00 2532 141 0.1904 0.2335 REMARK 3 18 1.3226 - 1.2980 0.93 2409 121 0.1962 0.2307 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.13 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 : 0.009 1607 REMARK 3 ANGLE : 1.334 2206 REMARK 3 CHIRALITY : 0.085 225 REMARK 3 PLANARITY : 0.006 288 REMARK 3 DIHEDRAL : 13.167 536 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 6KWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49040 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.298 REMARK 200 RESOLUTION RANGE LOW (A) : 32.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.170 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 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) : 0.10800 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: 2DFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, NAI, MES, PH 6.0, REMARK 280 EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.79900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.80200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.58050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.80200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.79900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.58050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO4 XYP B 1 C1 XYP B 2 1.08 REMARK 500 O HOH A 407 O HOH A 517 1.90 REMARK 500 O HOH A 327 O HOH A 328 1.92 REMARK 500 O HOH A 333 O HOH A 402 1.95 REMARK 500 O HOH A 301 O HOH A 477 1.95 REMARK 500 O HOH A 305 O HOH A 487 1.98 REMARK 500 O3 XYP B 1 O HOH A 380 1.98 REMARK 500 O HOH A 314 O HOH A 490 1.99 REMARK 500 O HOH A 303 O HOH A 431 2.05 REMARK 500 O HOH A 302 O HOH A 477 2.06 REMARK 500 O HOH A 373 O HOH A 473 2.08 REMARK 500 OD1 ASN A 61 OG SER A 149 2.12 REMARK 500 N THR A 2 O HOH A 301 2.12 REMARK 500 N THR A 2 O HOH A 302 2.14 REMARK 500 O4 XYP B 2 O5 XYP B 3 2.14 REMARK 500 O HOH A 433 O HOH A 498 2.16 REMARK 500 O HOH A 459 O HOH A 495 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 383 O HOH A 415 3554 1.89 REMARK 500 O HOH A 394 O HOH A 475 3654 2.09 REMARK 500 O HOH A 467 O HOH A 506 2564 2.12 REMARK 500 O HOH A 325 O HOH A 520 3554 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 57 29.65 -142.42 REMARK 500 ASP A 170 -138.66 -99.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KWD A 2 190 UNP P36217 XYN2_HYPJR 35 223 SEQADV 6KWD ASP A 44 UNP P36217 ASN 77 ENGINEERED MUTATION SEQRES 1 A 189 THR ILE GLN PRO GLY THR GLY TYR ASN ASN GLY TYR PHE SEQRES 2 A 189 TYR SER TYR TRP ASN ASP GLY HIS GLY GLY VAL THR TYR SEQRES 3 A 189 THR ASN GLY PRO GLY GLY GLN PHE SER VAL ASN TRP SER SEQRES 4 A 189 ASN SER GLY ASP PHE VAL GLY GLY LYS GLY TRP GLN PRO SEQRES 5 A 189 GLY THR LYS ASN LYS VAL ILE ASN PHE SER GLY SER TYR SEQRES 6 A 189 ASN PRO ASN GLY ASN SER TYR LEU SER VAL TYR GLY TRP SEQRES 7 A 189 SER ARG ASN PRO LEU ILE GLU TYR TYR ILE VAL GLU ASN SEQRES 8 A 189 PHE GLY THR TYR ASN PRO SER THR GLY ALA THR LYS LEU SEQRES 9 A 189 GLY GLU VAL THR SER ASP GLY SER VAL TYR ASP ILE TYR SEQRES 10 A 189 ARG THR GLN ARG VAL ASN GLN PRO SER ILE ILE GLY THR SEQRES 11 A 189 ALA THR PHE TYR GLN TYR TRP SER VAL ARG ARG ASN HIS SEQRES 12 A 189 ARG SER SER GLY SER VAL ASN THR ALA ASN HIS PHE ASN SEQRES 13 A 189 ALA TRP ALA GLN GLN GLY LEU THR LEU GLY THR MET ASP SEQRES 14 A 189 TYR GLN ILE VAL ALA VAL GLU GLY TYR PHE SER SER GLY SEQRES 15 A 189 SER ALA SER ILE THR VAL SER HET XYP B 1 20 HET XYP B 2 18 HET XYP B 3 18 HET GOL A 201 6 HET IOD A 202 1 HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM GOL GLYCEROL HETNAM IOD IODIDE ION HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 XYP 3(C5 H10 O5) FORMUL 3 GOL C3 H8 O3 FORMUL 4 IOD I 1- FORMUL 5 HOH *229(H2 O) HELIX 1 AA1 THR A 152 GLN A 162 1 11 SHEET 1 AA1 9 GLY A 6 ASN A 10 0 SHEET 2 AA1 9 TYR A 13 ASN A 19 -1 O TYR A 13 N ASN A 10 SHEET 3 AA1 9 ASP A 44 TRP A 51 -1 O VAL A 46 N TRP A 18 SHEET 4 AA1 9 THR A 168 TYR A 179 -1 O GLN A 172 N TRP A 51 SHEET 5 AA1 9 SER A 72 ARG A 81 -1 N TYR A 77 O ILE A 173 SHEET 6 AA1 9 ILE A 85 PHE A 93 -1 O ILE A 89 N VAL A 76 SHEET 7 AA1 9 ALA A 132 ARG A 141 1 O SER A 139 N VAL A 90 SHEET 8 AA1 9 SER A 113 GLN A 125 -1 N ARG A 122 O PHE A 134 SHEET 9 AA1 9 THR A 103 SER A 110 -1 N LEU A 105 O ILE A 117 SHEET 1 AA2 5 VAL A 25 ASN A 29 0 SHEET 2 AA2 5 GLN A 34 TRP A 39 -1 O SER A 36 N THR A 28 SHEET 3 AA2 5 SER A 182 SER A 190 -1 O GLY A 183 N TRP A 39 SHEET 4 AA2 5 VAL A 59 ASN A 69 -1 N ASN A 69 O SER A 182 SHEET 5 AA2 5 GLY A 148 ASN A 151 -1 O VAL A 150 N ILE A 60 LINK O4 XYP B 1 C1 XYP B 2 1555 1555 1.43 LINK O4 XYP B 2 C1 XYP B 3 1555 1555 1.39 CISPEP 1 GLN A 52 PRO A 53 0 0.72 CISPEP 2 ASN A 82 PRO A 83 0 4.10 CRYST1 47.598 59.161 69.604 90.00 90.00 90.00 P 21 21 21 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 0.021009 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014367 0.00000