HEADER HYDROLASE 28-FEB-06 2DFC TITLE XYLANASE II FROM TRICODERMA REESEI AT 293K 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: HYPOCREA JECORINA; SOURCE 3 ORGANISM_TAXID: 51453 KEYWDS BENT BETA SHEET, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.HARATA,T.AKIBA REVDAT 4 25-OCT-23 2DFC 1 REMARK REVDAT 3 25-DEC-19 2DFC 1 SEQADV SEQRES LINK REVDAT 2 24-FEB-09 2DFC 1 VERSN REVDAT 1 11-JUL-06 2DFC 0 JRNL AUTH N.WATANABE,T.AKIBA,R.KANAI,K.HARATA JRNL TITL STRUCTURE OF AN ORTHORHOMBIC FORM OF XYLANASE II FROM JRNL TITL 2 TRICHODERMA REESEI AND ANALYSIS OF THERMAL DISPLACEMENT. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 62 784 2006 JRNL REFN ISSN 0907-4449 JRNL PMID 16790934 JRNL DOI 10.1107/S0907444906017379 REMARK 2 REMARK 2 RESOLUTION. 1.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.106 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.122 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3354 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 67625 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)) : 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)) : NULL 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 : 1 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.035 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.098 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.099 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: NULL 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 2DFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000025351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.15 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : TRUNCATE, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67093 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04600 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) : 1.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.39200 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1ENX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M AMMONIUM SULFATE, 0.1M BICINE, REMARK 280 0.15M SODIUM IODIDE, 1.6% PROTEIN, PH 9.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 24.77500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.77500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.01500 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 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 TRP A 39 CG - CD1 - NE1 ANGL. DEV. = -7.8 DEGREES REMARK 500 TRP A 39 CD1 - NE1 - CE2 ANGL. DEV. = 12.2 DEGREES REMARK 500 TRP A 39 NE1 - CE2 - CD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 GLY A 101 C - N - CA ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR A 137 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 HIS A 155 CG - ND1 - CE1 ANGL. DEV. = 7.1 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 -144.30 -104.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 191 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DFB RELATED DB: PDB DBREF 2DFC A 1 190 UNP P36217 XYN2_TRIRE 33 222 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 2DFC PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HET IOD A 191 1 HETNAM PCA PYROGLUTAMIC ACID HETNAM IOD IODIDE ION FORMUL 1 PCA C5 H7 N O3 FORMUL 2 IOD I 1- FORMUL 3 HOH *208(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 GLY A 50 N PHE A 14 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 TYR A 77 O ILE A 173 SHEET 6 A 9 ILE A 85 PHE A 93 -1 O TYR A 87 N GLY A 78 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 THR A 103 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 ASN A 38 N THR A 26 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 69 O SER A 182 SHEET 5 B 5 GLY A 148 ASN A 151 -1 O VAL A 150 N ILE A 60 LINK C PCA A 1 N THR A 2 1555 1555 1.33 CISPEP 1 GLN A 52 PRO A 53 0 -1.59 CISPEP 2 ASN A 82 PRO A 83 0 8.38 SITE 1 AC1 2 ASN A 82 SER A 146 CRYST1 49.550 60.030 70.500 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 0.020182 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014184 0.00000 HETATM 1 N PCA A 1 29.904 42.860 -10.799 1.00 34.45 N ANISOU 1 N PCA A 1 3573 4683 4835 -1169 -1199 1433 N HETATM 2 CA PCA A 1 29.837 44.278 -11.026 1.00 36.15 C ANISOU 2 CA PCA A 1 2687 4972 6076 -1382 -762 2252 C HETATM 3 CB PCA A 1 30.860 44.487 -12.140 1.00 46.39 C ANISOU 3 CB PCA A 1 3117 6563 7945 -553 496 3145 C HETATM 4 CG PCA A 1 31.555 43.181 -12.368 1.00 48.48 C ANISOU 4 CG PCA A 1 4291 6982 7147 -35 330 2574 C HETATM 5 CD PCA A 1 30.853 42.191 -11.483 1.00 43.18 C ANISOU 5 CD PCA A 1 3774 5925 6709 -489 -360 1797 C HETATM 6 OE PCA A 1 31.049 40.977 -11.509 1.00 56.25 O ANISOU 6 OE PCA A 1 5377 5826 10171 -1110 2836 456 O HETATM 7 C PCA A 1 28.487 44.735 -11.561 1.00 33.07 C ANISOU 7 C PCA A 1 2598 4909 5056 -1254 -725 1459 C HETATM 8 O PCA A 1 27.728 43.878 -12.084 1.00 30.05 O ANISOU 8 O PCA A 1 2790 4712 3915 -1307 -83 1263 O