HEADER HYDROLASE 05-JUL-01 1JJF TITLE STRUCTURAL BASIS FOR THE SUBSTRATE SPECIFICITY OF THE FERULOYL TITLE 2 ESTERASE DOMAIN OF THE CELLULOSOMAL XYLANASE Z OF CLOSTRIDIUM TITLE 3 THERMOCELLUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE Z; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 20-287; COMPND 5 SYNONYM: FERULOYL ESTERASE; XYLANASE Z; 1,4-BETA-D-XYLAN COMPND 6 XYLANOHYDROLASE Z; COMPND 7 EC: 3.2.1.8; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM; SOURCE 3 ORGANISM_TAXID: 1515; SOURCE 4 GENE: XYNZ; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS FERULOYL ESTERASE, FERULIC ACID ESTERASE, FAE_XYNZ, XYNZ, STRUCTURAL KEYWDS 2 GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, SOUTHEAST COLLABORATORY KEYWDS 3 FOR STRUCTURAL GENOMICS, SECSG, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.D.SCHUBOT,I.A.KATAEVA,D.L.BLUM,A.K.SHAH,L.G.LJUNGDAHL,J.P.ROSE, AUTHOR 2 B.C.WANG,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 4 07-FEB-24 1JJF 1 REMARK LINK REVDAT 3 24-FEB-09 1JJF 1 VERSN REVDAT 2 01-FEB-05 1JJF 1 JRNL AUTHOR KEYWDS REMARK REVDAT 1 31-OCT-01 1JJF 0 JRNL AUTH F.D.SCHUBOT,I.A.KATAEVA,D.L.BLUM,A.K.SHAH,L.G.LJUNGDAHL, JRNL AUTH 2 J.P.ROSE,B.C.WANG JRNL TITL STRUCTURAL BASIS FOR THE SUBSTRATE SPECIFICITY OF THE JRNL TITL 2 FERULOYL ESTERASE DOMAIN OF THE CELLULOSOMAL XYLANASE Z FROM JRNL TITL 3 CLOSTRIDIUM THERMOCELLUM. JRNL REF BIOCHEMISTRY V. 40 12524 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11601976 JRNL DOI 10.1021/BI011391C REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 283824.720 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 21940 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) : 0.189 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2186 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2951 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 341 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1968 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 281 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 1.87000 REMARK 3 B33 (A**2) : -1.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.16 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.670 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.350 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.560 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.460 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 79.68 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21940 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 95.3 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : 0.33000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SOLOMON REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEGMME2000, AMMONIUM SULFATE, SODIUM REMARK 280 ACETATE, GLYCEROL, PH 4.60, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 21.64650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.88850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.82600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.88850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.64650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.82600 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 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 LEU A 20 REMARK 465 VAL A 21 REMARK 465 THR A 22 REMARK 465 ILE A 23 REMARK 465 SER A 24 REMARK 465 SER A 25 REMARK 465 THR A 26 REMARK 465 SER A 27 REMARK 465 ALA A 28 REMARK 465 ALA A 29 REMARK 465 GLY A 285 REMARK 465 ASN A 286 REMARK 465 THR A 287 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 PHE A 98 -111.38 -113.24 REMARK 500 SER A 148 -56.19 -129.04 REMARK 500 SER A 172 -120.16 48.51 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 PT A 288 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CTH-FAEZ RELATED DB: TARGETDB DBREF 1JJF A 20 287 UNP P10478 XYNZ_CLOTM 20 287 SEQRES 1 A 268 LEU VAL THR ILE SER SER THR SER ALA ALA SER LEU PRO SEQRES 2 A 268 THR MET PRO PRO SER GLY TYR ASP GLN VAL ARG ASN GLY SEQRES 3 A 268 VAL PRO ARG GLY GLN VAL VAL ASN ILE SER TYR PHE SER SEQRES 4 A 268 THR ALA THR ASN SER THR ARG PRO ALA ARG VAL TYR LEU SEQRES 5 A 268 PRO PRO GLY TYR SER LYS ASP LYS LYS TYR SER VAL LEU SEQRES 6 A 268 TYR LEU LEU HIS GLY ILE GLY GLY SER GLU ASN ASP TRP SEQRES 7 A 268 PHE GLU GLY GLY GLY ARG ALA ASN VAL ILE ALA ASP ASN SEQRES 8 A 268 LEU ILE ALA GLU GLY LYS ILE LYS PRO LEU ILE ILE VAL SEQRES 9 A 268 THR PRO ASN THR ASN ALA ALA GLY PRO GLY ILE ALA ASP SEQRES 10 A 268 GLY TYR GLU ASN PHE THR LYS ASP LEU LEU ASN SER LEU SEQRES 11 A 268 ILE PRO TYR ILE GLU SER ASN TYR SER VAL TYR THR ASP SEQRES 12 A 268 ARG GLU HIS ARG ALA ILE ALA GLY LEU SER MET GLY GLY SEQRES 13 A 268 GLY GLN SER PHE ASN ILE GLY LEU THR ASN LEU ASP LYS SEQRES 14 A 268 PHE ALA TYR ILE GLY PRO ILE SER ALA ALA PRO ASN THR SEQRES 15 A 268 TYR PRO ASN GLU ARG LEU PHE PRO ASP GLY GLY LYS ALA SEQRES 16 A 268 ALA ARG GLU LYS LEU LYS LEU LEU PHE ILE ALA CYS GLY SEQRES 17 A 268 THR ASN ASP SER LEU ILE GLY PHE GLY GLN ARG VAL HIS SEQRES 18 A 268 GLU TYR CYS VAL ALA ASN ASN ILE ASN HIS VAL TYR TRP SEQRES 19 A 268 LEU ILE GLN GLY GLY GLY HIS ASP PHE ASN VAL TRP LYS SEQRES 20 A 268 PRO GLY LEU TRP ASN PHE LEU GLN MET ALA ASP GLU ALA SEQRES 21 A 268 GLY LEU THR ARG ASP GLY ASN THR HET PT A 288 1 HETNAM PT PLATINUM (II) ION FORMUL 2 PT PT 2+ FORMUL 3 HOH *281(H2 O) HELIX 1 1 ARG A 103 GLU A 114 1 12 HELIX 2 2 ASP A 136 SER A 148 1 13 HELIX 3 3 SER A 148 TYR A 157 1 10 HELIX 4 4 ASP A 162 GLU A 164 5 3 HELIX 5 5 SER A 172 THR A 184 1 13 HELIX 6 6 PRO A 203 PHE A 208 1 6 HELIX 7 7 GLY A 212 LEU A 219 1 8 HELIX 8 8 LEU A 232 ASN A 246 1 15 HELIX 9 9 ASP A 261 GLY A 280 1 20 SHEET 1 A 8 GLN A 50 SER A 58 0 SHEET 2 A 8 SER A 63 LEU A 71 -1 O SER A 63 N SER A 58 SHEET 3 A 8 ILE A 121 PRO A 125 -1 O ILE A 122 N TYR A 70 SHEET 4 A 8 VAL A 83 LEU A 87 1 O LEU A 84 N VAL A 123 SHEET 5 A 8 ARG A 166 LEU A 171 1 O ALA A 167 N TYR A 85 SHEET 6 A 8 TYR A 191 ILE A 195 1 O TYR A 191 N ILE A 168 SHEET 7 A 8 LEU A 221 GLY A 227 1 O LEU A 221 N ILE A 192 SHEET 8 A 8 VAL A 251 ILE A 255 1 O VAL A 251 N ILE A 224 LINK SD MET A 173 PT PT A 288 1555 1555 2.76 CISPEP 1 LEU A 31 PRO A 32 0 0.07 SITE 1 AC1 2 ILE A 90 MET A 173 CRYST1 43.293 63.652 79.777 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 0.023098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012535 0.00000