HEADER HYDROLASE 15-OCT-12 4HKW TITLE CRYSTAL STRUCTURES OF MUTANT ENDO-BETA-1,4-XYLANASE II COMPLEXED WITH TITLE 2 SUBSTRATE AND PRODUCTS 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; COMPND 5 EC: 3.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA REESEI; SOURCE 3 ORGANISM_TAXID: 51453 KEYWDS XYLANASE II, XYLOPENTAOSE, INDUCED FIT MECHANISM, OXOCARBENIUM ION, KEYWDS 2 GLYCOSIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.Y.KOVALEVSKY,Q.WAN,P.LANGAN,L.COATES REVDAT 4 29-JUL-20 4HKW 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 25-DEC-19 4HKW 1 SEQADV SEQRES LINK REVDAT 2 12-FEB-14 4HKW 1 JRNL REVDAT 1 08-JAN-14 4HKW 0 JRNL AUTH Q.WAN,Q.ZHANG,S.HAMILTON-BREHM,K.WEISS,M.MUSTYAKIMOV, JRNL AUTH 2 L.COATES,P.LANGAN,D.GRAHAM,A.KOVALEVSKY JRNL TITL X-RAY CRYSTALLOGRAPHIC STUDIES OF FAMILY 11 XYLANASE JRNL TITL 2 MICHAELIS AND PRODUCT COMPLEXES: IMPLICATIONS FOR THE JRNL TITL 3 CATALYTIC MECHANISM. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 11 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24419374 JRNL DOI 10.1107/S1399004713023626 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.159 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.159 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 944 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18694 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.145 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 16432 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 248 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1778.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7135 REMARK 3 NUMBER OF RESTRAINTS : 6377 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.047 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.062 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.044 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.057 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5417 REMARK 200 MONOCHROMATOR : NONE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16432 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 0.1M CACL2, PH=8.5, 15% REMARK 280 PEG4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.21400 REMARK 290 SMTRY3 2 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 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 87 CB - CG - CD1 ANGL. DEV. = 5.4 DEGREES 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 ASP A 170 -138.09 -104.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 407 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 92 OD1 REMARK 620 2 PHE A 93 O 75.5 REMARK 620 3 HOH A1096 O 77.0 75.1 REMARK 620 4 HOH A1101 O 145.2 73.3 109.1 REMARK 620 5 HOH A1108 O 135.1 139.2 129.9 68.0 REMARK 620 6 HOH A1181 O 77.4 148.0 82.5 136.7 72.8 REMARK 620 N 1 2 3 4 5 DBREF 4HKW A 2 190 UNP P36217 XYN2_HYPJE 34 222 SEQADV 4HKW PCA A 1 UNP P36217 EXPRESSION TAG SEQRES 1 A 190 PCA THR ILE GLN PRO GLY THR GLY TYR ASN ASN GLY TYR SEQRES 2 A 190 PHE TYR SER TYR TRP ASN ASP GLY HIS GLY GLY VAL THR SEQRES 3 A 190 TYR THR ASN GLY PRO GLY GLY GLN PHE SER VAL ASN TRP SEQRES 4 A 190 SER ASN SER GLY ASN PHE VAL GLY GLY LYS GLY TRP GLN SEQRES 5 A 190 PRO GLY THR LYS ASN LYS VAL ILE ASN PHE SER GLY SER SEQRES 6 A 190 TYR ASN PRO ASN GLY ASN SER TYR LEU SER VAL TYR GLY SEQRES 7 A 190 TRP SER ARG ASN PRO LEU ILE GLU TYR TYR ILE VAL GLU SEQRES 8 A 190 ASN PHE GLY THR TYR ASN PRO SER THR GLY ALA THR LYS SEQRES 9 A 190 LEU GLY GLU VAL THR SER ASP GLY SER VAL TYR ASP ILE SEQRES 10 A 190 TYR ARG THR GLN ARG VAL ASN GLN PRO SER ILE ILE GLY SEQRES 11 A 190 THR ALA THR PHE TYR GLN TYR TRP SER VAL ARG ARG ASN SEQRES 12 A 190 HIS ARG SER SER GLY SER VAL ASN THR ALA ASN HIS PHE SEQRES 13 A 190 ASN ALA TRP ALA GLN GLN GLY LEU THR LEU GLY THR MET SEQRES 14 A 190 ASP TYR GLN ILE VAL ALA VAL GLU GLY TYR PHE SER SER SEQRES 15 A 190 GLY SER ALA SER ILE THR VAL SER MODRES 4HKW PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HET XYS B 1 10 HET XYP B 2 9 HET XYP B 3 9 HET XYP C 1 9 HET XYP C 2 9 HET TRS A 406 8 HET CA A 407 1 HETNAM PCA PYROGLUTAMIC ACID HETNAM XYS ALPHA-D-XYLOPYRANOSE HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM CA CALCIUM ION HETSYN TRS TRIS BUFFER FORMUL 1 PCA C5 H7 N O3 FORMUL 2 XYS C5 H10 O5 FORMUL 2 XYP 4(C5 H10 O5) FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 CA CA 2+ FORMUL 6 HOH *248(H2 O) HELIX 1 1 THR A 152 GLN A 162 1 11 SHEET 1 A 9 GLY A 6 ASN A 10 0 SHEET 2 A 9 TYR A 13 ASN A 19 -1 O TYR A 13 N ASN A 10 SHEET 3 A 9 ASN A 44 TRP A 51 -1 O VAL A 46 N TRP A 18 SHEET 4 A 9 THR A 168 TYR A 179 -1 O GLN A 172 N TRP A 51 SHEET 5 A 9 SER A 72 ARG A 81 -1 N TRP A 79 O ASP A 170 SHEET 6 A 9 ILE A 85 PHE A 93 -1 O ILE A 89 N VAL A 76 SHEET 7 A 9 ALA A 132 ARG A 141 1 O SER A 139 N VAL A 90 SHEET 8 A 9 SER A 113 GLN A 125 -1 N ARG A 122 O PHE A 134 SHEET 9 A 9 LYS A 104 SER A 110 -1 N LEU A 105 O ILE A 117 SHEET 1 B 5 VAL A 25 ASN A 29 0 SHEET 2 B 5 GLN A 34 TRP A 39 -1 O SER A 36 N THR A 28 SHEET 3 B 5 SER A 182 SER A 190 -1 O GLY A 183 N TRP A 39 SHEET 4 B 5 VAL A 59 ASN A 69 -1 N ASN A 61 O SER A 190 SHEET 5 B 5 GLY A 148 ASN A 151 -1 O GLY A 148 N PHE A 62 LINK C PCA A 1 N THR A 2 1555 1555 1.32 LINK O1 TRS A 406 C1 XYP C 1 1555 1555 1.44 LINK O4 XYS B 1 C1 XYP B 2 1555 1555 1.44 LINK O4 XYP B 2 C1 XYP B 3 1555 1555 1.44 LINK O4 XYP C 1 C1 XYP C 2 1555 1555 1.43 LINK OD1 ASN A 92 CA CA A 407 1555 1555 2.46 LINK O PHE A 93 CA CA A 407 1555 1555 2.44 LINK CA CA A 407 O HOH A1096 1555 1555 2.55 LINK CA CA A 407 O HOH A1101 1555 1555 2.53 LINK CA CA A 407 O HOH A1108 1555 1555 2.39 LINK CA CA A 407 O HOH A1181 1555 1555 2.63 CISPEP 1 GLN A 52 PRO A 53 0 -3.58 CISPEP 2 ASN A 82 PRO A 83 0 1.95 CRYST1 41.879 38.428 56.315 90.00 105.93 90.00 P 1 21 1 2 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 0.023878 0.000000 0.006815 0.00000 SCALE2 0.000000 0.026023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018466 0.00000 HETATM 1 N PCA A 1 18.200 -21.830 12.266 1.00 31.48 N HETATM 2 CA PCA A 1 19.461 -21.285 12.703 1.00 25.70 C HETATM 3 CB PCA A 1 20.326 -21.370 11.436 1.00 20.63 C HETATM 4 CG PCA A 1 19.393 -21.685 10.304 1.00 31.44 C HETATM 5 CD PCA A 1 18.153 -22.219 10.970 1.00 37.58 C HETATM 6 OE PCA A 1 17.282 -22.880 10.412 1.00 43.91 O HETATM 7 C PCA A 1 19.336 -19.788 12.964 1.00 26.53 C HETATM 8 O PCA A 1 18.293 -19.229 12.555 1.00 19.68 O