HEADER HYDROLASE 22-AUG-96 1YNA TITLE ENDO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYNA; COMPND 5 EC: 3.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOMYCES LANUGINOSUS; SOURCE 3 ORGANISM_TAXID: 5541; SOURCE 4 STRAIN: TSIKLINSKY; SOURCE 5 ATCC: DSM 5826 KEYWDS HYDROLASE, XYLANASE EXPDTA X-RAY DIFFRACTION AUTHOR K.GRUBER,C.KRATKY REVDAT 5 25-DEC-19 1YNA 1 SEQRES LINK REVDAT 4 07-MAR-18 1YNA 1 REMARK REVDAT 3 24-FEB-09 1YNA 1 VERSN REVDAT 2 09-JUL-99 1YNA 1 JRNL REVDAT 1 12-FEB-97 1YNA 0 JRNL AUTH K.GRUBER,G.KLINTSCHAR,M.HAYN,A.SCHLACHER,W.STEINER,C.KRATKY JRNL TITL THERMOPHILIC XYLANASE FROM THERMOMYCES LANUGINOSUS: JRNL TITL 2 HIGH-RESOLUTION X-RAY STRUCTURE AND MODELING STUDIES. JRNL REF BIOCHEMISTRY V. 37 13475 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9753433 JRNL DOI 10.1021/BI980864L REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.SCHLACHER,K.HOLZMANN,M.HAYN,W.STEINER,H.SCHWAB REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF ENDO-1,4-BETA-XYLANASE II REMARK 1 TITL 2 FROM TRICHODERMA REESEI: TWO CONFORMATIONAL STATES IN THE REMARK 1 TITL 3 ACTIVE SITE REMARK 1 REF J.BIOTECHNOL. V. 49 211 1996 REMARK 1 REFN ISSN 0168-1656 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.TORRONEN,A.HARKKI,J.ROUVINEN REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF ENDO-1,4-BETA-XYLANASE II REMARK 1 TITL 2 FROM TRICHODERMA REESEI: TWO CONFORMATIONAL STATES IN THE REMARK 1 TITL 3 ACTIVE SITE REMARK 1 REF EMBO J. V. 13 2493 1994 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-93 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.9 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.193 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 26211 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.155 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)) : 19452 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1512 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1650.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6598 REMARK 3 NUMBER OF RESTRAINTS : 6091 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 1.400 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: BABINET'S PRINCIPLE (SWAT) REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YNA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-95 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CCP4, XDS REMARK 200 DATA SCALING SOFTWARE : XDS, CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26211 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 25.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 30.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXL-93, X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5-10% PEG-4000, PH 4.0, T=4 DEG C, REMARK 280 TEMPERATURE 277K 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 26.28500 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 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 TYR A 171 -138.45 -100.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 81 0.08 SIDE CHAIN REMARK 500 ARG A 116 0.12 SIDE CHAIN REMARK 500 ARG A 122 0.20 SIDE CHAIN REMARK 500 ARG A 161 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1YNA A 2 194 UNP O43097 XYNA_THELA 33 225 SEQRES 1 A 194 PCA THR THR PRO ASN SER GLU GLY TRP HIS ASP GLY TYR SEQRES 2 A 194 TYR TYR SER TRP TRP SER ASP GLY GLY ALA GLN ALA THR SEQRES 3 A 194 TYR THR ASN LEU GLU GLY GLY THR TYR GLU ILE SER TRP SEQRES 4 A 194 GLY ASP GLY GLY ASN LEU VAL GLY GLY LYS GLY TRP ASN SEQRES 5 A 194 PRO GLY LEU ASN ALA ARG ALA ILE HIS PHE GLU GLY VAL SEQRES 6 A 194 TYR GLN PRO ASN GLY ASN SER TYR LEU ALA VAL TYR GLY SEQRES 7 A 194 TRP THR ARG ASN PRO LEU VAL GLU TYR TYR ILE VAL GLU SEQRES 8 A 194 ASN PHE GLY THR TYR ASP PRO SER SER GLY ALA THR ASP SEQRES 9 A 194 LEU GLY THR VAL GLU CYS ASP GLY SER ILE TYR ARG LEU SEQRES 10 A 194 GLY LYS THR THR ARG VAL ASN ALA PRO SER ILE ASP GLY SEQRES 11 A 194 THR GLN THR PHE ASP GLN TYR TRP SER VAL ARG GLN ASP SEQRES 12 A 194 LYS ARG THR SER GLY THR VAL GLN THR GLY CYS HIS PHE SEQRES 13 A 194 ASP ALA TRP ALA ARG ALA GLY LEU ASN VAL ASN GLY ASP SEQRES 14 A 194 HIS TYR TYR GLN ILE VAL ALA THR GLU GLY TYR PHE SER SEQRES 15 A 194 SER GLY TYR ALA ARG ILE THR VAL ALA ASP VAL GLY MODRES 1YNA PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 FORMUL 2 HOH *138(H2 O) HELIX 1 1 GLY A 153 ALA A 162 1 10 SHEET 1 A 5 ALA A 25 LEU A 30 0 SHEET 2 A 5 TYR A 35 TRP A 39 -1 N SER A 38 O THR A 26 SHEET 3 A 5 SER A 183 ALA A 191 -1 N ILE A 188 O TYR A 35 SHEET 4 A 5 ALA A 59 GLN A 67 -1 N HIS A 61 O ALA A 191 SHEET 5 A 5 GLY A 148 GLN A 151 -1 N VAL A 150 O ILE A 60 SHEET 1 B 9 SER A 6 HIS A 10 0 SHEET 2 B 9 TYR A 13 SER A 19 -1 N TRP A 17 O SER A 6 SHEET 3 B 9 ASN A 44 TRP A 51 -1 N GLY A 50 O TYR A 14 SHEET 4 B 9 TYR A 172 TYR A 180 -1 N GLY A 179 O LEU A 45 SHEET 5 B 9 SER A 72 THR A 80 -1 N TYR A 77 O ILE A 174 SHEET 6 B 9 VAL A 85 GLY A 94 -1 N ASN A 92 O LEU A 74 SHEET 7 B 9 PHE A 134 GLN A 142 1 N ASP A 135 O GLU A 86 SHEET 8 B 9 SER A 113 ARG A 122 -1 N ARG A 122 O PHE A 134 SHEET 9 B 9 THR A 103 CYS A 110 -1 N CYS A 110 O SER A 113 SSBOND 1 CYS A 110 CYS A 154 1555 1555 2.03 LINK C PCA A 1 N THR A 2 1555 1555 1.34 CISPEP 1 ASN A 52 PRO A 53 0 6.67 CISPEP 2 ASN A 82 PRO A 83 0 2.68 CRYST1 40.960 52.570 50.470 90.00 100.43 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 0.024414 0.000000 0.004494 0.00000 SCALE2 0.000000 0.019022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020147 0.00000 HETATM 1 N PCA A 1 -17.564 4.471 29.286 1.00 61.06 N HETATM 2 CA PCA A 1 -16.876 3.328 29.863 1.00 57.40 C HETATM 3 CB PCA A 1 -18.014 2.278 29.801 1.00 60.21 C HETATM 4 CG PCA A 1 -19.305 3.108 30.000 1.00 62.17 C HETATM 5 CD PCA A 1 -18.905 4.391 29.332 1.00 63.25 C HETATM 6 OE PCA A 1 -19.697 5.218 28.909 1.00 70.21 O HETATM 7 C PCA A 1 -15.719 2.929 28.980 1.00 49.53 C HETATM 8 O PCA A 1 -15.290 3.731 28.166 1.00 55.15 O