HEADER HYDROLASE 01-SEP-98 2AXE TITLE IODINATED COMPLEX OF ACETYL XYLAN ESTERASE AT 1.80 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 HYDROLASE, IODOTYROSINES, ESTERASE 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 4 20-NOV-24 2AXE 1 REMARK REVDAT 3 21-DEC-22 2AXE 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2AXE 1 VERSN REVDAT 1 18-MAY-99 2AXE 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 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) : 0.173 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.177 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 763 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 15003 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.149 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.152 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 594 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1540.2 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1182.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6189 REMARK 3 NUMBER OF RESTRAINTS : 6009 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.057 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL 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: C-I BONDS WERE NOT RESTRAINED REMARK 4 REMARK 4 2AXE 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_1000177787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 6.0 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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 (%): 22.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 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 17.45000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.26900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.63900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.26900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.45000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.63900 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 378 O HOH A 388 2.02 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 -3.26 72.44 REMARK 500 SER A 90 -119.23 56.99 REMARK 500 ALA A 149 -113.25 -123.89 REMARK 500 CYS A 179 -163.97 -125.32 REMARK 500 SER A 182 24.18 -143.43 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 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 209 DBREF 2AXE A 1 207 UNP O59893 O59893_PENPU 28 234 SEQADV 2AXE TYI A 33 UNP O59893 TYR 60 MODIFIED RESIDUE SEQADV 2AXE TYI A 177 UNP O59893 TYR 204 MODIFIED RESIDUE 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 TYI 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 TYI 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 MODRES 2AXE TYI A 33 TYR 3,5-DIIODOTYROSINE MODRES 2AXE TYI A 177 TYR 3,5-DIIODOTYROSINE HET TYI A 33 14 HET TYI A 177 14 HET SO4 A 209 5 HETNAM TYI 3,5-DIIODOTYROSINE HETNAM SO4 SULFATE ION FORMUL 1 TYI 2(C9 H9 I2 N O3) FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *91(H2 O) HELIX 1 1 GLY A 20 SER A 31 5 12 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 2.03 SSBOND 2 CYS A 46 CYS A 52 1555 1555 2.03 SSBOND 3 CYS A 101 CYS A 161 1555 1555 2.03 SSBOND 4 CYS A 147 CYS A 179 1555 1555 2.05 SSBOND 5 CYS A 171 CYS A 178 1555 1555 2.03 LINK C ALA A 32 N TYI A 33 1555 1555 1.32 LINK C TYI A 33 N PRO A 34 1555 1555 1.33 LINK C PRO A 176 N TYI A 177 1555 1555 1.33 LINK C TYI A 177 N CYS A 178 1555 1555 1.33 SITE 1 CAT 3 SER A 90 ASP A 175 HIS A 187 SITE 1 AC1 4 THR A 146 ASP A 172 ALA A 173 SER A 174 CRYST1 34.900 61.278 72.538 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 0.028653 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013786 0.00000