HEADER HYDROLASE 01-DEC-03 1USW TITLE CRYSTAL STRUCTURE OF FERULIC ACID ESTERASE FROM ASPERGILLUS NIGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERULOYL ESTERASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FERULIC ACID ESTERASE, FAE-III; COMPND 5 EC: 3.1.1.73; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS NIGER; SOURCE 3 ORGANISM_TAXID: 5061; SOURCE 4 STRAIN: CBS 120.49/N400; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS HYDROLASE, FERULOYL ESTERASE, DEGRADATION PLANT CELL WALLS EXPDTA X-RAY DIFFRACTION AUTHOR J.HERMOSO,J.SANZ-APARICIO,R.MOLINA,C.FAULDS REVDAT 4 13-DEC-23 1USW 1 HETSYN REVDAT 3 29-JUL-20 1USW 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 1USW 1 VERSN REVDAT 1 23-APR-04 1USW 0 JRNL AUTH J.HERMOSO,J.SANZ-APARICIO,R.MOLINA,N.JUGE,R.GONZALEZ, JRNL AUTH 2 C.FAULDS JRNL TITL THE CRYSTAL STRUCTURE OF FERULOYL ESTERASE A FROM JRNL TITL 2 ASPERGILLUS NIGER SUGGESTS EVOLUTIVE FUNCTIONAL CONVERGENCE JRNL TITL 3 IN FERULOYL ESTERASE FAMILY JRNL REF J.MOL.BIOL. V. 338 495 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15081808 JRNL DOI 10.1016/J.JMB.2004.03.003 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.97 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) (%) : 85.8 REMARK 3 NUMBER OF REFLECTIONS : 6830 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) : 0.212 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 527 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 772 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 65 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.045 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1993 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.17000 REMARK 3 B22 (A**2) : -1.22000 REMARK 3 B33 (A**2) : -3.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.87000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.29 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) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 100.5 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1USW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1290014089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 7.50 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 : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6360 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 31.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.21300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1TIB, 3TGL, 4TGL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.59000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 ALA A 26 -126.47 -105.60 REMARK 500 CYS A 29 -130.05 -39.18 REMARK 500 LYS A 59 46.84 77.52 REMARK 500 CYS A 91 92.20 -54.93 REMARK 500 ASP A 93 30.83 79.28 REMARK 500 SER A 133 -124.21 56.83 REMARK 500 SER A 147 -9.56 -54.08 REMARK 500 SER A 192 -126.42 44.05 REMARK 500 TYR A 219 -97.30 -35.00 REMARK 500 SER A 220 159.64 57.97 REMARK 500 ASN A 223 44.91 -108.15 REMARK 500 GLU A 231 -178.18 -178.13 REMARK 500 CYS A 234 -136.99 42.28 REMARK 500 GLN A 241 -80.02 -79.13 REMARK 500 VAL A 243 84.94 36.54 REMARK 500 ALA A 257 160.05 165.80 REMARK 500 CYS A 258 141.05 -16.66 REMARK 500 THR A 259 1.08 -176.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2014 DISTANCE = 6.93 ANGSTROMS DBREF 1USW A 1 260 UNP O42807 FAEA_ASPNG 22 281 SEQRES 1 A 260 ALA SER THR GLN GLY ILE SER GLU ASP LEU TYR ASN ARG SEQRES 2 A 260 LEU VAL GLU MET ALA THR ILE SER GLN ALA ALA TYR ALA SEQRES 3 A 260 ASP LEU CYS ASN ILE PRO SER THR ILE ILE LYS GLY GLU SEQRES 4 A 260 LYS ILE TYR ASN ALA GLN THR ASP ILE ASN GLY TRP ILE SEQRES 5 A 260 LEU ARG ASP ASP THR SER LYS GLU ILE ILE THR VAL PHE SEQRES 6 A 260 ARG GLY THR GLY SER ASP THR ASN LEU GLN LEU ASP THR SEQRES 7 A 260 ASN TYR THR LEU THR PRO PHE ASP THR LEU PRO GLN CYS SEQRES 8 A 260 ASN ASP CYS GLU VAL HIS GLY GLY TYR TYR ILE GLY TRP SEQRES 9 A 260 ILE SER VAL GLN ASP GLN VAL GLU SER LEU VAL LYS GLN SEQRES 10 A 260 GLN ALA SER GLN TYR PRO ASP TYR ALA LEU THR VAL THR SEQRES 11 A 260 GLY HIS SER LEU GLY ALA SER MET ALA ALA LEU THR ALA SEQRES 12 A 260 ALA GLN LEU SER ALA THR TYR ASP ASN VAL ARG LEU TYR SEQRES 13 A 260 THR PHE GLY GLU PRO ARG SER GLY ASN GLN ALA PHE ALA SEQRES 14 A 260 SER TYR MET ASN ASP ALA PHE GLN VAL SER SER PRO GLU SEQRES 15 A 260 THR THR GLN TYR PHE ARG VAL THR HIS SER ASN ASP GLY SEQRES 16 A 260 ILE PRO ASN LEU PRO PRO ALA ASP GLU GLY TYR ALA HIS SEQRES 17 A 260 GLY GLY VAL GLU TYR TRP SER VAL ASP PRO TYR SER ALA SEQRES 18 A 260 GLN ASN THR PHE VAL CYS THR GLY ASP GLU VAL GLN CYS SEQRES 19 A 260 CYS GLU ALA GLN GLY GLY GLN GLY VAL ASN ASP ALA HIS SEQRES 20 A 260 THR THR TYR PHE GLY MET THR SER GLY ALA CYS THR TRP MODRES 1USW ASN A 79 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET SO4 A1261 5 HET SO4 A1262 5 HET SO4 A1263 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *114(H2 O) HELIX 1 1 SER A 7 ALA A 24 1 18 HELIX 2 2 SER A 70 ASN A 79 1 10 HELIX 3 3 GLY A 98 ILE A 105 1 8 HELIX 4 4 VAL A 107 SER A 120 1 14 HELIX 5 5 SER A 133 SER A 147 1 15 HELIX 6 6 ASN A 165 PHE A 176 1 12 HELIX 7 7 PRO A 201 GLY A 205 5 5 HELIX 8 8 GLN A 233 GLY A 239 1 7 HELIX 9 9 ASN A 244 THR A 248 1 5 SHEET 1 AA 9 SER A 2 GLN A 4 0 SHEET 2 AA 9 THR A 224 CYS A 227 -1 O VAL A 226 N THR A 3 SHEET 3 AA 9 VAL A 211 SER A 215 -1 O GLU A 212 N CYS A 227 SHEET 4 AA 9 TYR A 186 HIS A 191 1 O TYR A 186 N VAL A 211 SHEET 5 AA 9 VAL A 153 PHE A 158 1 O LEU A 155 N PHE A 187 SHEET 6 AA 9 ALA A 126 HIS A 132 1 O LEU A 127 N ARG A 154 SHEET 7 AA 9 GLU A 60 PHE A 65 1 O ILE A 61 N THR A 128 SHEET 8 AA 9 ILE A 48 ASP A 55 -1 O TRP A 51 N VAL A 64 SHEET 9 AA 9 ILE A 35 ASN A 43 -1 O ILE A 36 N ARG A 54 SHEET 1 AB 2 LEU A 82 PRO A 84 0 SHEET 2 AB 2 GLU A 95 HIS A 97 -1 O VAL A 96 N THR A 83 SHEET 1 AC 2 THR A 249 TYR A 250 0 SHEET 2 AC 2 MET A 253 THR A 254 -1 O MET A 253 N TYR A 250 SSBOND 1 CYS A 29 CYS A 258 1555 1555 2.02 SSBOND 2 CYS A 91 CYS A 94 1555 1555 2.02 SSBOND 3 CYS A 227 CYS A 234 1555 1555 2.04 LINK ND2 ASN A 79 C1 NAG B 1 1555 1555 1.46 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.38 CISPEP 1 LEU A 199 PRO A 200 0 -0.77 CISPEP 2 ASP A 217 PRO A 218 0 -1.07 CRYST1 39.200 47.180 62.400 90.00 96.14 90.00 P 1 21 1 2 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 0.025510 0.000000 0.002744 0.00000 SCALE2 0.000000 0.021195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016118 0.00000