HEADER HYDROLASE 14-JUL-98 1BK1 TITLE ENDO-1,4-BETA-XYLANASE C COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-B-XYLANASE C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYLANASE; COMPND 5 EC: 3.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS KAWACHII; SOURCE 3 ORGANISM_TAXID: 40384; SOURCE 4 STRAIN: IFO 4308; SOURCE 5 CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 6 GENE: XYNC; SOURCE 7 EXPRESSION_SYSTEM: ASPERGILLUS KAWACHII; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 40384; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: IFO 4308; SOURCE 10 EXPRESSION_SYSTEM_CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PUAMD3; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PUAMXC1; SOURCE 14 EXPRESSION_SYSTEM_GENE: XYNC KEYWDS HYDROLASE, XYLAN DEGRADATION, GLYCOSIDASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FUSHINOBU,K.ITO,M.KONNO,T.WAKAGI,H.MATSUZAWA REVDAT 7 30-OCT-24 1BK1 1 REMARK REVDAT 6 02-AUG-23 1BK1 1 SEQADV REVDAT 5 24-FEB-09 1BK1 1 VERSN REVDAT 4 01-APR-03 1BK1 1 JRNL REVDAT 3 26-MAR-99 1BK1 1 JRNL REVDAT 2 16-FEB-99 1BK1 3 REMARK HETATM DBREF SEQADV REVDAT 2 2 3 JRNL REVDAT 1 13-JAN-99 1BK1 0 JRNL AUTH S.FUSHINOBU,K.ITO,M.KONNO,T.WAKAGI,H.MATSUZAWA JRNL TITL CRYSTALLOGRAPHIC AND MUTATIONAL ANALYSES OF AN EXTREMELY JRNL TITL 2 ACIDOPHILIC AND ACID-STABLE XYLANASE: BIASED DISTRIBUTION OF JRNL TITL 3 ACIDIC RESIDUES AND IMPORTANCE OF ASP37 FOR CATALYSIS AT LOW JRNL TITL 4 PH. JRNL REF PROTEIN ENG. V. 11 1121 1998 JRNL REFN ISSN 0269-2139 JRNL PMID 9930661 JRNL DOI 10.1093/PROTEIN/11.12.1121 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.ITO,H.OGASAWARA,T.SUGIMOTO,T.ISHIKAWA REMARK 1 TITL PURIFICATION AND PROPERTIES OF ACID STABLE XYLANASES FROM REMARK 1 TITL 2 ASPERGILLUS KAWACHII REMARK 1 REF BIOSCI.BIOTECHNOL.BIOCHEM. V. 56 547 1992 REMARK 1 REFN ISSN 0916-8451 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.ITO,K.IWASHITA,K.IWANO REMARK 1 TITL CLONING AND SEQUENCING OF THE XYNC GENE ENCODING ACID REMARK 1 TITL 2 XYLANASE OF ASPERGILLUS KAWACHII REMARK 1 REF BIOSCI.BIOTECHNOL.BIOCHEM. V. 56 1338 1992 REMARK 1 REFN ISSN 0916-8451 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 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) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.9 REMARK 3 NUMBER OF REFLECTIONS : 12530 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.260 REMARK 3 FREE R VALUE TEST SET COUNT : 637 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1031 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.68 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 67 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1394 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.10 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) : 0.27 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BK1 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_1000171848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15428 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 34.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39700 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: TRICHODERMA REESEI XYNI, PDB ENTRY 1XYN REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING THE WEISSENBERG METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 56.64550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.03250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.03250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 84.96825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.03250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.03250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.32275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.03250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.03250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.96825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.03250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.03250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.32275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.64550 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1 REMARK 465 SER A 184 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 TRP A 30 47.04 -144.56 REMARK 500 ALA A 60 30.95 -143.41 REMARK 500 ILE A 121 4.92 -64.82 REMARK 500 ASN A 163 -143.55 -97.56 REMARK 500 TRP A 172 13.16 -140.82 REMARK 500 SER A 173 144.09 -171.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AS REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: GLU 79 AND GLU 170 REFER TO THE CATALYTIC ACIDIC REMARK 800 RESIDUES. DBREF 1BK1 A 1 184 UNP P33557 XYN3_ASPKA 28 211 SEQADV 1BK1 GLY A 15 UNP P33557 ALA 42 CONFLICT SEQADV 1BK1 THR A 53 UNP P33557 SER 80 CONFLICT SEQRES 1 A 184 SER ALA GLY ILE ASN TYR VAL GLN ASN TYR ASN GLY ASN SEQRES 2 A 184 LEU GLY ASP PHE THR TYR ASP GLU SER ALA GLY THR PHE SEQRES 3 A 184 SER MET TYR TRP GLU ASP GLY VAL SER SER ASP PHE VAL SEQRES 4 A 184 VAL GLY LEU GLY TRP THR THR GLY SER SER ASN ALA ILE SEQRES 5 A 184 THR TYR SER ALA GLU TYR SER ALA SER GLY SER SER SER SEQRES 6 A 184 TYR LEU ALA VAL TYR GLY TRP VAL ASN TYR PRO GLN ALA SEQRES 7 A 184 GLU TYR TYR ILE VAL GLU ASP TYR GLY ASP TYR ASN PRO SEQRES 8 A 184 CYS SER SER ALA THR SER LEU GLY THR VAL TYR SER ASP SEQRES 9 A 184 GLY SER THR TYR GLN VAL CYS THR ASP THR ARG THR ASN SEQRES 10 A 184 GLU PRO SER ILE THR GLY THR SER THR PHE THR GLN TYR SEQRES 11 A 184 PHE SER VAL ARG GLU SER THR ARG THR SER GLY THR VAL SEQRES 12 A 184 THR VAL ALA ASN HIS PHE ASN PHE TRP ALA GLN HIS GLY SEQRES 13 A 184 PHE GLY ASN SER ASP PHE ASN TYR GLN VAL MET ALA VAL SEQRES 14 A 184 GLU ALA TRP SER GLY ALA GLY SER ALA SER VAL THR ILE SEQRES 15 A 184 SER SER FORMUL 2 HOH *111(H2 O) HELIX 1 1 GLY A 12 LEU A 14 5 3 HELIX 2 2 GLU A 21 ALA A 23 5 3 HELIX 3 3 VAL A 145 HIS A 155 1 11 SHEET 1 A 8 TYR A 6 TYR A 10 0 SHEET 2 A 8 PHE A 38 TRP A 44 -1 N GLY A 43 O TYR A 6 SHEET 3 A 8 GLN A 165 ALA A 171 -1 N ALA A 171 O PHE A 38 SHEET 4 A 8 SER A 65 VAL A 73 -1 N TYR A 70 O VAL A 166 SHEET 5 A 8 ALA A 78 TYR A 86 -1 N ASP A 85 O LEU A 67 SHEET 6 A 8 PHE A 127 ARG A 134 1 N THR A 128 O GLU A 79 SHEET 7 A 8 SER A 106 ARG A 115 -1 N ARG A 115 O PHE A 127 SHEET 8 A 8 THR A 96 SER A 103 -1 N SER A 103 O SER A 106 SHEET 1 B 5 ASP A 16 ASP A 20 0 SHEET 2 B 5 THR A 25 TRP A 30 -1 N TYR A 29 O ASP A 16 SHEET 3 B 5 GLY A 176 SER A 183 -1 N VAL A 180 O PHE A 26 SHEET 4 B 5 ILE A 52 SER A 59 -1 N SER A 59 O SER A 177 SHEET 5 B 5 SER A 140 VAL A 143 -1 N VAL A 143 O ILE A 52 SHEET 1 C 2 GLU A 118 SER A 120 0 SHEET 2 C 2 GLY A 123 SER A 125 -1 N SER A 125 O GLU A 118 SSBOND 1 CYS A 92 CYS A 111 1555 1555 2.02 CISPEP 1 TYR A 75 PRO A 76 0 -0.97 SITE 1 AS 2 GLU A 79 GLU A 170 CRYST1 62.065 62.065 113.291 90.00 90.00 90.00 P 43 21 2 8 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 0.016112 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008827 0.00000