PDB Short entry for 1FHL 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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