HEADER SERINE HYDROLASE 01-SEP-98 1BS9 TITLE ACETYLXYLAN ESTERASE FROM P. PURPUROGENUM REFINED AT 1.10 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACETYL XYLAN ESTERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM PURPUROGENUM; SOURCE 3 ORGANISM_TAXID: 28575 KEYWDS SERINE HYDROLASE, ESTERASE, ALPHA/BETA HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.GHOSH,M.ERMAN,M.W.SAWICKI,P.LALA,D.R.WEEKS,N.LI,W.PANGBORN, AUTHOR 2 D.J.THIEL,H.JORNVALL,J.EYZAGUIRRE REVDAT 3 16-OCT-24 1BS9 1 REMARK REVDAT 2 24-FEB-09 1BS9 1 VERSN REVDAT 1 18-MAY-99 1BS9 0 JRNL AUTH D.GHOSH,M.ERMAN,M.SAWICKI,P.LALA,D.R.WEEKS,N.LI,W.PANGBORN, JRNL AUTH 2 D.J.THIEL,H.JORNVALL,R.GUTIERREZ,J.EYZAGUIRRE JRNL TITL DETERMINATION OF A PROTEIN STRUCTURE BY IODINATION: THE JRNL TITL 2 STRUCTURE OF IODINATED ACETYLXYLAN ESTERASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 779 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10089308 JRNL DOI 10.1107/S0907444999000244 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 69.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.123 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.128 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2232 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 43972 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.111 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.116 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1946 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 38151 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1442 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1576.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1203.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14389 REMARK 3 NUMBER OF RESTRAINTS : 16950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.079 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.091 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.063 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BS9 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_1000172046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-95 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44040 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 69.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0 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 17.44300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.21250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.49150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.21250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.44300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.49150 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 VAL A 25 CG1 - CB - CG2 ANGL. DEV. = 12.1 DEGREES REMARK 500 ALA A 173 C - N - CA ANGL. DEV. = 15.6 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 14 -2.90 71.44 REMARK 500 SER A 90 -118.20 59.69 REMARK 500 ALA A 149 -117.15 -122.05 REMARK 500 CYS A 179 -164.94 -124.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: THESE THREE RESIDUES FORM THE CATALYTIC TRIAD REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 208 DBREF 1BS9 A 1 207 UNP O59893 O59893_PENPU 28 234 SEQRES 1 A 207 SER CYS PRO ALA ILE HIS VAL PHE GLY ALA ARG GLU THR SEQRES 2 A 207 THR ALA SER PRO GLY TYR GLY SER SER SER THR VAL VAL SEQRES 3 A 207 ASN GLY VAL LEU SER ALA TYR PRO GLY SER THR ALA GLU SEQRES 4 A 207 ALA ILE ASN TYR PRO ALA CYS GLY GLY GLN SER SER CYS SEQRES 5 A 207 GLY GLY ALA SER TYR SER SER SER VAL ALA GLN GLY ILE SEQRES 6 A 207 ALA ALA VAL ALA SER ALA VAL ASN SER PHE ASN SER GLN SEQRES 7 A 207 CYS PRO SER THR LYS ILE VAL LEU VAL GLY TYR SER GLN SEQRES 8 A 207 GLY GLY GLU ILE MET ASP VAL ALA LEU CYS GLY GLY GLY SEQRES 9 A 207 ASP PRO ASN GLN GLY TYR THR ASN THR ALA VAL GLN LEU SEQRES 10 A 207 SER SER SER ALA VAL ASN MET VAL LYS ALA ALA ILE PHE SEQRES 11 A 207 MET GLY ASP PRO MET PHE ARG ALA GLY LEU SER TYR GLU SEQRES 12 A 207 VAL GLY THR CYS ALA ALA GLY GLY PHE ASP GLN ARG PRO SEQRES 13 A 207 ALA GLY PHE SER CYS PRO SER ALA ALA LYS ILE LYS SER SEQRES 14 A 207 TYR CYS ASP ALA SER ASP PRO TYR CYS CYS ASN GLY SER SEQRES 15 A 207 ASN ALA ALA THR HIS GLN GLY TYR GLY SER GLU TYR GLY SEQRES 16 A 207 SER GLN ALA LEU ALA PHE VAL LYS SER LYS LEU GLY HET SO4 A 208 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *143(H2 O) HELIX 1 1 GLY A 20 ALA A 32 5 13 HELIX 2 2 SER A 50 CYS A 52 5 3 HELIX 3 3 TYR A 57 GLN A 78 1 22 HELIX 4 4 SER A 90 CYS A 101 5 12 HELIX 5 5 PRO A 106 GLN A 108 5 3 HELIX 6 6 SER A 119 MET A 124 1 6 HELIX 7 7 ALA A 164 LYS A 166 5 3 HELIX 8 8 ALA A 184 GLN A 188 1 5 HELIX 9 9 TYR A 190 LYS A 205 1 16 SHEET 1 A 5 THR A 37 ALA A 40 0 SHEET 2 A 5 ILE A 5 ALA A 10 1 N VAL A 7 O THR A 37 SHEET 3 A 5 LYS A 83 TYR A 89 1 N LYS A 83 O HIS A 6 SHEET 4 A 5 VAL A 125 MET A 131 1 N LYS A 126 O ILE A 84 SHEET 5 A 5 ILE A 167 TYR A 170 1 N LYS A 168 O ALA A 128 SSBOND 1 CYS A 2 CYS A 79 1555 1555 2.04 SSBOND 2 CYS A 46 CYS A 52 1555 1555 2.03 SSBOND 3 CYS A 101 CYS A 161 1555 1555 2.01 SSBOND 4 CYS A 147 CYS A 179 1555 1555 2.04 SSBOND 5 CYS A 171 CYS A 178 1555 1555 2.03 SITE 1 CAT 3 SER A 90 ASP A 175 HIS A 187 SITE 1 AC1 5 THR A 146 ASP A 172 ALA A 173 SER A 174 SITE 2 AC1 5 HOH A 399 CRYST1 34.886 60.983 72.425 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 0.028665 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016398 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013807 0.00000