HEADER HYDROLASE 02-AUG-00 1FHL TITLE CRYSTAL STRUCTURE OF BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEATUS TITLE 2 AT 293K COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-1,4-GALACTANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.89 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS ACULEATUS; SOURCE 3 ORGANISM_TAXID: 5053 KEYWDS B/A BARREL, GLYCOSYL HYDROLASE, FAMILY 53, CLAN GH-A, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.RYTTERSGAARD,S.LARSEN REVDAT 4 04-OCT-17 1FHL 1 REMARK REVDAT 3 24-FEB-09 1FHL 1 VERSN REVDAT 2 17-JUN-03 1FHL 1 JRNL REVDAT 1 03-JUN-03 1FHL 0 JRNL AUTH C.RYTTERSGAARD,L.L.LEGGIO,P.M.COUTINHO,B.HENRISSAT,S.LARSEN JRNL TITL ASPERGILLUS ACULEATUS BETA-1,4-GALACTANASE: SUBSTRATE JRNL TITL 2 RECOGNITION AND RELATIONS TO OTHER GLYCOSIDE HYDROLASES IN JRNL TITL 3 CLAN GH-A JRNL REF BIOCHEMISTRY V. 41 15135 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12484750 JRNL DOI 10.1021/BI026238C REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.RYTTERSGAARD,J.POULSEN,S.CHRISTGAU,T.SANDAL,H.DALBOGE, REMARK 1 AUTH 2 S.LARSEN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF REMARK 1 TITL 2 BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEATUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 929 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444998001073 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.80 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) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15582 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1578 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 : 2598 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.384 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.25 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.734 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FHL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000011594. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-97 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : TRUNCATE REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15582 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.39200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, CALCIUM CHLORIDE, SODIUM REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.21000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.47000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.54000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.21000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.47000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.54000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.21000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.47000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.54000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.21000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.47000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.54000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 401 LIES ON A SPECIAL POSITION. 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 ASP A 17 7.29 -65.89 REMARK 500 GLN A 30 139.45 -173.18 REMARK 500 VAL A 50 -73.77 -78.56 REMARK 500 ASP A 91 111.00 -161.42 REMARK 500 LEU A 142 64.11 38.33 REMARK 500 SER A 150 78.94 -157.73 REMARK 500 ASP A 182 54.28 38.48 REMARK 500 SER A 219 127.98 168.76 REMARK 500 CYS A 253 82.94 -153.95 REMARK 500 PRO A 261 150.16 -47.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FOB RELATED DB: PDB REMARK 900 SAME STRUCTURE AT 100K, WITH CALCIUM IN THE ACTIVE SITE DBREF 1FHL A 1 334 UNP P48842 GANA_ASPAC 17 350 SEQRES 1 A 334 ALA LEU THR TYR ARG GLY ALA ASP ILE SER SER LEU LEU SEQRES 2 A 334 LEU LEU GLU ASP GLU GLY TYR SER TYR LYS ASN LEU ASN SEQRES 3 A 334 GLY GLN THR GLN ALA LEU GLU THR ILE LEU ALA ASP ALA SEQRES 4 A 334 GLY ILE ASN SER ILE ARG GLN ARG VAL TRP VAL ASN PRO SEQRES 5 A 334 SER ASP GLY SER TYR ASP LEU ASP TYR ASN LEU GLU LEU SEQRES 6 A 334 ALA LYS ARG VAL LYS ALA ALA GLY MET SER LEU TYR LEU SEQRES 7 A 334 ASP LEU HIS LEU SER ASP THR TRP ALA ASP PRO SER ASP SEQRES 8 A 334 GLN THR THR PRO SER GLY TRP SER THR THR ASP LEU GLY SEQRES 9 A 334 THR LEU LYS TRP GLN LEU TYR ASN TYR THR LEU GLU VAL SEQRES 10 A 334 CYS ASN THR PHE ALA GLU ASN ASP ILE ASP ILE GLU ILE SEQRES 11 A 334 ILE SER ILE GLY ASN GLU ILE ARG ALA GLY LEU LEU TRP SEQRES 12 A 334 PRO LEU GLY GLU THR SER SER TYR SER ASN ILE GLY ALA SEQRES 13 A 334 LEU LEU HIS SER GLY ALA TRP GLY VAL LYS ASP SER ASN SEQRES 14 A 334 LEU ALA THR THR PRO LYS ILE MET ILE HIS LEU ASP ASP SEQRES 15 A 334 GLY TRP SER TRP ASP GLN GLN ASN TYR PHE TYR GLU THR SEQRES 16 A 334 VAL LEU ALA THR GLY GLU LEU LEU SER THR ASP PHE ASP SEQRES 17 A 334 TYR PHE GLY VAL SER TYR TYR PRO PHE TYR SER ALA SER SEQRES 18 A 334 ALA THR LEU ALA SER LEU LYS THR SER LEU ALA ASN LEU SEQRES 19 A 334 GLN SER THR TYR ASP LYS PRO VAL VAL VAL VAL GLU THR SEQRES 20 A 334 ASN TRP PRO VAL SER CYS PRO ASN PRO ALA TYR ALA PHE SEQRES 21 A 334 PRO SER ASP LEU SER SER ILE PRO PHE SER VAL ALA GLY SEQRES 22 A 334 GLN GLN GLU PHE LEU GLU LYS LEU ALA ALA VAL VAL GLU SEQRES 23 A 334 ALA THR THR ASP GLY LEU GLY VAL TYR TYR TRP GLU PRO SEQRES 24 A 334 ALA TRP ILE GLY ASN ALA GLY LEU GLY SER SER CYS ALA SEQRES 25 A 334 ASP ASN LEU MET VAL ASP TYR THR THR ASP GLU VAL TYR SEQRES 26 A 334 GLU SER ILE GLU THR LEU GLY GLU LEU FORMUL 2 HOH *59(H2 O) HELIX 1 1 SER A 11 ASP A 17 1 7 HELIX 2 2 ALA A 31 GLY A 40 1 10 HELIX 3 3 ASP A 58 ALA A 72 1 15 HELIX 4 4 ASP A 102 ASN A 124 1 23 HELIX 5 5 GLU A 136 GLY A 140 5 5 HELIX 6 6 SER A 150 ASP A 167 1 18 HELIX 7 7 SER A 185 THR A 199 1 15 HELIX 8 8 LEU A 203 PHE A 207 5 5 HELIX 9 9 THR A 223 ASP A 239 1 17 HELIX 10 10 PRO A 261 SER A 265 5 5 HELIX 11 11 SER A 270 THR A 288 1 19 HELIX 12 12 GLU A 326 GLY A 332 1 7 SHEET 1 A 9 TYR A 4 ASP A 8 0 SHEET 2 A 9 SER A 43 VAL A 48 1 O SER A 43 N ALA A 7 SHEET 3 A 9 SER A 75 LEU A 80 1 O SER A 75 N ILE A 44 SHEET 4 A 9 ILE A 130 ILE A 133 1 O ILE A 130 N LEU A 78 SHEET 5 A 9 LYS A 175 LEU A 180 1 O LYS A 175 N ILE A 131 SHEET 6 A 9 TYR A 209 SER A 213 1 N TYR A 209 O ILE A 176 SHEET 7 A 9 VAL A 242 GLU A 246 1 O VAL A 243 N VAL A 212 SHEET 8 A 9 GLY A 291 TRP A 297 1 N LEU A 292 O VAL A 242 SHEET 9 A 9 TYR A 4 ASP A 8 1 N TYR A 4 O LEU A 292 SSBOND 1 CYS A 253 CYS A 311 1555 1555 2.03 CISPEP 1 TRP A 143 PRO A 144 0 0.47 CRYST1 60.420 88.940 129.080 90.00 90.00 90.00 I 2 2 2 8 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 0.016551 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007747 0.00000 MASTER 264 0 0 12 9 0 0 6 0 0 0 26 END