HEADER HYDROLASE 09-AUG-94 1XYN TITLE STRUCTURAL COMPARISON OF TWO MAJOR ENDO-1,4-BETA-XYLANASES FROM TITLE 2 TRICHODREMA REESEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYNI; COMPND 5 EC: 3.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYPOCREA JECORINA; SOURCE 3 ORGANISM_TAXID: 51453; SOURCE 4 STRAIN: RUT-C30 KEYWDS XYLANASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.ROUVINEN,A.TORRONEN REVDAT 4 14-FEB-24 1XYN 1 REMARK LINK REVDAT 3 24-FEB-09 1XYN 1 VERSN REVDAT 2 01-APR-03 1XYN 1 JRNL REVDAT 1 08-AUG-95 1XYN 0 JRNL AUTH A.TORRONEN,J.ROUVINEN JRNL TITL STRUCTURAL COMPARISON OF TWO MAJOR ENDO-1,4-XYLANASES FROM JRNL TITL 2 TRICHODERMA REESEI. JRNL REF BIOCHEMISTRY V. 34 847 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7827044 JRNL DOI 10.1021/BI00003A019 REMARK 1 REMARK 1 REFERENCE 1 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 7475 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1348 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.76 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XYN 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_1000177332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7631 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.0 REMARK 200 DATA REDUNDANCY : 2.650 REMARK 200 R MERGE (I) : 0.08970 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.12500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.12500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.50500 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 2 120.68 148.74 REMARK 500 ASN A 29 79.13 -162.45 REMARK 500 PHE A 54 99.11 -165.20 REMARK 500 ASN A 71 71.49 50.20 REMARK 500 PRO A 86 85.54 -63.69 REMARK 500 ALA A 87 98.49 -49.81 REMARK 500 ASN A 157 -147.20 -111.19 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 601 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 81 OD1 REMARK 620 2 ASP A 81 OD2 46.3 REMARK 620 3 HIS A 83 NE2 74.8 80.1 REMARK 620 4 HOH A 556 O 107.2 129.3 142.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 601 DBREF 1XYN A 1 178 UNP P36218 XYN1_TRIRE 52 229 SEQRES 1 A 178 ALA SER ILE ASN TYR ASP GLN ASN TYR GLN THR GLY GLY SEQRES 2 A 178 GLN VAL SER TYR SER PRO SER ASN THR GLY PHE SER VAL SEQRES 3 A 178 ASN TRP ASN THR GLN ASP ASP PHE VAL VAL GLY VAL GLY SEQRES 4 A 178 TRP THR THR GLY SER SER ALA PRO ILE ASN PHE GLY GLY SEQRES 5 A 178 SER PHE SER VAL ASN SER GLY THR GLY LEU LEU SER VAL SEQRES 6 A 178 TYR GLY TRP SER THR ASN PRO LEU VAL GLU TYR TYR ILE SEQRES 7 A 178 MET GLU ASP ASN HIS ASN TYR PRO ALA GLN GLY THR VAL SEQRES 8 A 178 LYS GLY THR VAL THR SER ASP GLY ALA THR TYR THR ILE SEQRES 9 A 178 TRP GLU ASN THR ARG VAL ASN GLU PRO SER ILE GLN GLY SEQRES 10 A 178 THR ALA THR PHE ASN GLN TYR ILE SER VAL ARG ASN SER SEQRES 11 A 178 PRO ARG THR SER GLY THR VAL THR VAL GLN ASN HIS PHE SEQRES 12 A 178 ASN ALA TRP ALA SER LEU GLY LEU HIS LEU GLY GLN MET SEQRES 13 A 178 ASN TYR GLN VAL VAL ALA VAL GLU GLY TRP GLY GLY SER SEQRES 14 A 178 GLY SER ALA SER GLN SER VAL SER ASN HET CA A 601 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *80(H2 O) HELIX 1 1 THR A 138 LEU A 149 1 12 SHEET 1 A 8 TYR A 5 GLN A 10 0 SHEET 2 A 8 PHE A 34 TRP A 40 -1 O VAL A 35 N TYR A 9 SHEET 3 A 8 GLN A 155 TRP A 166 -1 O GLN A 159 N TRP A 40 SHEET 4 A 8 THR A 60 THR A 70 -1 N THR A 60 O TRP A 166 SHEET 5 A 8 VAL A 74 HIS A 83 -1 N VAL A 74 O SER A 69 SHEET 6 A 8 GLY A 117 ARG A 128 1 O ASN A 122 N GLU A 75 SHEET 7 A 8 ALA A 100 SER A 114 -1 O THR A 103 N VAL A 127 SHEET 8 A 8 THR A 90 SER A 97 -1 N THR A 90 O GLU A 106 SHEET 1 B 5 GLN A 14 PRO A 19 0 SHEET 2 B 5 GLY A 23 THR A 30 -1 O SER A 25 N SER A 18 SHEET 3 B 5 GLY A 168 SER A 177 -1 O GLY A 168 N THR A 30 SHEET 4 B 5 ILE A 48 VAL A 56 -1 N ASN A 49 O SER A 177 SHEET 5 B 5 GLY A 135 VAL A 137 -1 N GLY A 135 O PHE A 50 LINK OD1 ASP A 81 CA CA A 601 1555 1555 2.92 LINK OD2 ASP A 81 CA CA A 601 1555 1555 2.64 LINK NE2 HIS A 83 CA CA A 601 1555 1555 2.71 LINK O HOH A 556 CA CA A 601 1555 1555 2.93 CISPEP 1 ASN A 71 PRO A 72 0 0.30 SITE 1 AC1 3 ASP A 81 HIS A 83 HOH A 556 CRYST1 72.250 39.010 54.300 90.00 91.80 90.00 C 1 2 1 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 0.013841 0.000000 0.000435 0.00000 SCALE2 0.000000 0.025634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018425 0.00000