HEADER HYDROLASE 20-OCT-98 1PVX TITLE DO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ENDO-1,4-BETA-XYLANASE); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYLA; COMPND 5 EC: 3.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAECILOMYCES VARIOTII; SOURCE 3 ORGANISM_TAXID: 45996 KEYWDS THERMOPHILIC, XYLANASE, FAMILY-11 OF GLYCOSYL HYDROLASES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.RAJESHKUMAR,S.ESWARAMOORTHY,P.J.VITHAYATHIL,M.A.VISWAMITRA REVDAT 4 16-AUG-23 1PVX 1 REMARK REVDAT 3 04-OCT-17 1PVX 1 REMARK REVDAT 2 24-FEB-09 1PVX 1 VERSN REVDAT 1 20-OCT-99 1PVX 0 JRNL AUTH P.R.KUMAR,S.ESWARAMOORTHY,P.J.VITHAYATHIL,M.A.VISWAMITRA JRNL TITL THE TERTIARY STRUCTURE AT 1.59 A RESOLUTION AND THE PROPOSED JRNL TITL 2 AMINO ACID SEQUENCE OF A FAMILY-11 XYLANASE FROM THE JRNL TITL 3 THERMOPHILIC FUNGUS PAECILOMYCES VARIOTI BAINIER. JRNL REF J.MOL.BIOL. V. 295 581 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10623548 JRNL DOI 10.1006/JMBI.1999.3348 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 24200 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) : 0.191 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2394 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 : 1486 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.56 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) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.64 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.170 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE WAS REFINED USING BOTH X-PLOR AND REFMAC. A BULK REMARK 3 SOLVENT REMARK 3 CORRECTION WAS USED IN EACH CASE. REMARK 4 REMARK 4 1PVX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000007041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-97 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 4.50 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR, XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24200 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 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 (%) : 92.5 REMARK 200 DATA REDUNDANCY : 5.130 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.35800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.190 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1YNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.50 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 19.38100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.03200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.02900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.03200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.38100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.02900 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 SER A 6 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 SER A 6 CA - CB - OG ANGL. DEV. = 16.6 DEGREES REMARK 500 TYR A 14 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 TYR A 77 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 81 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 81 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 157 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 187 CD - NE - CZ ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG A 187 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 187 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 192 CB - CG - OD1 ANGL. DEV. = 6.1 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 THR A 2 125.05 -26.18 REMARK 500 TYR A 171 -136.78 -101.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 1PVX A 1 194 UNP P81536 XYNA_PAEVA 1 194 SEQRES 1 A 194 GLY 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 GLY ASP SER THR SEQRES 3 A 194 TYR THR ASN ASN SER GLY GLY THR TYR GLU ILE THR TRP SEQRES 4 A 194 GLY ASN 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 THR GLY VAL SEQRES 6 A 194 TYR GLN PRO ASN GLY THR SER TYR LEU SER 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 SER SER ASN PRO SER SER GLY SER THR ASP SEQRES 9 A 194 LEU GLY THR VAL SER CYS ASP GLY SER THR TYR THR LEU SEQRES 10 A 194 GLY GLN SER THR ARG TYR ASN ALA PRO SER ILE ASP GLY SEQRES 11 A 194 THR GLN THR PHE ASN GLN TYR TRP SER VAL ARG GLN ASP SEQRES 12 A 194 LYS ARG SER SER GLY THR VAL GLN THR GLY CYS HIS PHE SEQRES 13 A 194 ASP ALA TRP ALA SER ALA GLY LEU ASN VAL THR 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 FORMUL 2 HOH *128(H2 O) HELIX 1 1 THR A 152 SER A 161 1 10 SHEET 1 A 9 SER A 6 HIS A 10 0 SHEET 2 A 9 TYR A 13 SER A 19 -1 N TRP A 17 O SER A 6 SHEET 3 A 9 ASN A 44 TRP A 51 -1 N GLY A 50 O TYR A 14 SHEET 4 A 9 GLN A 173 TYR A 180 -1 N GLY A 179 O LEU A 45 SHEET 5 A 9 SER A 72 THR A 80 -1 N TYR A 77 O ILE A 174 SHEET 6 A 9 VAL A 85 PHE A 93 -1 N ASN A 92 O LEU A 74 SHEET 7 A 9 PHE A 134 ARG A 141 1 N ASN A 135 O GLU A 86 SHEET 8 A 9 SER A 113 ARG A 122 -1 N ARG A 122 O PHE A 134 SHEET 9 A 9 THR A 103 CYS A 110 -1 N CYS A 110 O SER A 113 SHEET 1 B 5 SER A 25 ASN A 29 0 SHEET 2 B 5 THR A 34 TRP A 39 -1 N THR A 38 O THR A 26 SHEET 3 B 5 GLY A 184 ASP A 192 -1 N ILE A 188 O TYR A 35 SHEET 4 B 5 ALA A 59 PRO A 68 -1 N GLN A 67 O TYR A 185 SHEET 5 B 5 GLY A 148 GLN A 151 -1 N VAL A 150 O ILE A 60 SHEET 1 C 2 ALA A 125 SER A 127 0 SHEET 2 C 2 GLY A 130 GLN A 132 -1 N GLN A 132 O ALA A 125 SSBOND 1 CYS A 110 CYS A 154 1555 1555 2.03 CISPEP 1 ASN A 52 PRO A 53 0 9.02 CISPEP 2 ASN A 82 PRO A 83 0 13.48 CRYST1 38.762 54.058 90.064 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 0.025798 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011103 0.00000