2D0G - Header Asymmetric Unit

HEADER HYDROLASE 02-AUG-05 2D0G

TITLE CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA- TITLE 2 AMYLASE 1 (TVAI) MUTANT D356N/E396Q COMPLEXED WITH P5, A TITLE 3 PULLULAN MODEL OLIGOSACCHARIDE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-AMYLASE I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TVA I; COMPND 5 EC: 3.2.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOACTINOMYCES VULGARIS; SOURCE 3 ORGANISM_TAXID: 2026; SOURCE 4 STRAIN: R-47; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562

KEYWDS ALPHA-AMYLASE, HYDROLASE

EXPDTA X-RAY DIFFRACTION

AUTHOR A.ABE,H.YOSHIDA,T.TONOZUKA,Y.SAKANO,S.KAMITORI

REVDAT 3 04-AUG-09 2D0G 1 HETATM HETNAM REVDAT 2 24-FEB-09 2D0G 1 VERSN REVDAT 1 11-JUL-06 2D0G 0

JRNL AUTH A.ABE,H.YOSHIDA,T.TONOZUKA,Y.SAKANO,S.KAMITORI JRNL TITL COMPLEXES OF THERMOACTINOMYCES VULGARIS R-47 JRNL TITL 2 ALPHA-AMYLASE 1 AND PULLULAN MODEL OLIGOSSACHARIDES JRNL TITL 3 PROVIDE NEW INSIGHT INTO THE MECHANISM FOR JRNL TITL 4 RECOGNIZING SUBSTRATES WITH ALPHA-(1,6) GLYCOSIDIC JRNL TITL 5 LINKAGES JRNL REF FEBS J. V. 272 6145 2005 JRNL REFN ISSN 1742-464X JRNL PMID 16302977 JRNL DOI 10.1111/J.1742-4658.2005.05013.X

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17376 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) : 0.150 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1899 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE : 0.2640 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 : 5038 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 217 REMARK 3 SOLVENT ATOMS : 482 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 2D0G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-05. REMARK 100 THE RCSB ID CODE IS RCSB024833.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19275 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 35.355 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3% PEG20000, 0.05M MES, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 60.44250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.34900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.44250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.34900 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 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 A2112 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 4 33.43 -143.71 REMARK 500 HIS A 14 140.50 -178.56 REMARK 500 GLN A 16 35.83 -96.09 REMARK 500 ALA A 23 78.01 -154.69 REMARK 500 SER A 67 -176.53 -178.97 REMARK 500 PRO A 140 -62.82 -18.92 REMARK 500 PHE A 143 -63.73 -95.84 REMARK 500 ASP A 224 62.78 -106.19 REMARK 500 ASP A 227 105.05 -162.57 REMARK 500 LEU A 316 68.99 -118.43 REMARK 500 TYR A 333 -24.96 -141.71 REMARK 500 ALA A 357 29.63 42.06 REMARK 500 ASN A 364 11.29 55.25 REMARK 500 THR A 405 -29.92 -146.54 REMARK 500 GLN A 410 -102.80 -129.17 REMARK 500 PHE A 420 -68.39 -138.88 REMARK 500 ASN A 435 36.27 71.79 REMARK 500 ALA A 438 104.28 -167.44 REMARK 500 TYR A 505 119.54 -26.52 REMARK 500 ASP A 516 137.09 -38.00 REMARK 500 ASP A 574 -159.65 -147.73 REMARK 500 VAL A 596 -3.28 -59.67 REMARK 500 VAL A 634 78.49 -119.00 REMARK 500 REMARK 500 REMARK: NULL

REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 2 O REMARK 620 2 ASP A 4 OD1 69.4 REMARK 620 3 ASN A 6 O 157.4 88.0 REMARK 620 4 ASP A 42 O 83.6 138.8 115.4 REMARK 620 5 ASP A 42 OD1 105.6 137.0 90.7 79.2 REMARK 620 6 ASP A 96 OD2 98.9 73.0 73.5 81.4 146.6 REMARK 620 7 HOH A2474 O 71.1 67.0 100.6 133.1 71.0 139.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 145 OD1 REMARK 620 2 ASP A 147 O 70.3 REMARK 620 3 ASN A 150 OD1 143.0 72.8 REMARK 620 4 ASP A 151 OD2 78.6 84.8 96.6 REMARK 620 5 GLY A 187 O 77.2 146.1 139.4 98.2 REMARK 620 6 ASP A 189 OD2 84.9 79.4 90.0 160.3 88.5 REMARK 620 7 HOH A2118 O 148.3 138.7 67.1 90.2 75.3 109.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 276 OD2 REMARK 620 2 ASN A 279 OD1 102.6 REMARK 620 3 PHE A 281 O 86.9 76.8 REMARK 620 4 SER A 283 O 92.7 150.1 78.6 REMARK 620 5 GLU A 288 OE1 83.7 71.9 144.4 136.0 REMARK 620 6 GLU A 288 OE2 77.8 125.3 155.2 82.7 53.6 REMARK 620 7 HOH A2263 O 175.0 82.5 94.1 82.6 98.2 99.6 REMARK 620 N 1 2 3 4 5 6

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 701 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 702 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 703 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 704 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 705 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 706 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 707 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 708 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 709 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 710 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 801 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 802 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 810 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 901 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 902 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 903 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 904 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 905 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 910 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2001 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2002 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2003 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1001

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JI1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THERMOACTINOMYCES VULGARIS R- REMARK 900 47 ALPHA-AMYLASE 1 REMARK 900 RELATED ID: 2D0F RELATED DB: PDB REMARK 900 THE SAME PROTEIN, D356N MUTANT COMPLEXED WITH P2, A REMARK 900 PULLULAN MODEL OLIGOSACCHARIDE REMARK 900 RELATED ID: 2D0H RELATED DB: PDB REMARK 900 THE SAME PROTEIN, D356N/E396Q MUTANT COMPLEXED WITH P2, A REMARK 900 PULLULAN MODEL OLIGOSACCHARIDE

DBREF 2D0G A 1 637 UNP Q60053 NEPU1_THEVU 30 666

SEQADV 2D0G ASN A 356 UNP Q60053 ASP 385 ENGINEERED SEQADV 2D0G GLN A 396 UNP Q60053 GLU 425 ENGINEERED

SEQRES 1 A 637 ALA ALA ASN ASP ASN ASN VAL GLU TRP ASN GLY LEU PHE SEQRES 2 A 637 HIS ASP GLN GLY PRO LEU PHE ASP ASN ALA PRO GLU PRO SEQRES 3 A 637 THR SER THR GLN SER VAL THR LEU LYS LEU ARG THR PHE SEQRES 4 A 637 LYS GLY ASP ILE THR SER ALA ASN ILE LYS TYR TRP ASP SEQRES 5 A 637 THR ALA ASP ASN ALA PHE HIS TRP VAL PRO MET VAL TRP SEQRES 6 A 637 ASP SER ASN ASP PRO THR GLY THR PHE ASP TYR TRP LYS SEQRES 7 A 637 GLY THR ILE PRO ALA SER PRO SER ILE LYS TYR TYR ARG SEQRES 8 A 637 PHE GLN ILE ASN ASP GLY THR SER THR ALA TRP TYR ASN SEQRES 9 A 637 GLY ASN GLY PRO SER SER THR GLU PRO ASN ALA ASP ASP SEQRES 10 A 637 PHE TYR ILE ILE PRO ASN PHE LYS THR PRO ASP TRP LEU SEQRES 11 A 637 LYS ASN GLY VAL MET TYR GLN ILE PHE PRO ASP ARG PHE SEQRES 12 A 637 TYR ASN GLY ASP SER SER ASN ASP VAL GLN THR GLY SER SEQRES 13 A 637 TYR THR TYR ASN GLY THR PRO THR GLU LYS LYS ALA TRP SEQRES 14 A 637 GLY SER SER VAL TYR ALA ASP PRO GLY TYR ASP ASN SER SEQRES 15 A 637 LEU VAL PHE PHE GLY GLY ASP LEU ALA GLY ILE ASP GLN SEQRES 16 A 637 LYS LEU GLY TYR ILE LYS LYS THR LEU GLY ALA ASN ILE SEQRES 17 A 637 LEU TYR LEU ASN PRO ILE PHE LYS ALA PRO THR ASN HIS SEQRES 18 A 637 LYS TYR ASP THR GLN ASP TYR MET ALA VAL ASP PRO ALA SEQRES 19 A 637 PHE GLY ASP ASN SER THR LEU GLN THR LEU ILE ASN ASP SEQRES 20 A 637 ILE HIS SER THR ALA ASN GLY PRO LYS GLY TYR LEU ILE SEQRES 21 A 637 LEU ASP GLY VAL PHE ASN HIS THR GLY ASP SER HIS PRO SEQRES 22 A 637 TRP PHE ASP LYS TYR ASN ASN PHE SER SER GLN GLY ALA SEQRES 23 A 637 TYR GLU SER GLN SER SER PRO TRP TYR ASN TYR TYR THR SEQRES 24 A 637 PHE TYR THR TRP PRO ASP SER TYR ALA SER PHE LEU GLY SEQRES 25 A 637 PHE ASN SER LEU PRO LYS LEU ASN TYR GLY ASN SER GLY SEQRES 26 A 637 SER ALA VAL ARG GLY VAL ILE TYR ASN ASN SER ASN SER SEQRES 27 A 637 VAL ALA LYS THR TYR LEU ASN PRO PRO TYR SER VAL ASP SEQRES 28 A 637 GLY TRP ARG LEU ASN ALA ALA GLN TYR VAL ASP ALA ASN SEQRES 29 A 637 GLY ASN ASN GLY SER ASP VAL THR ASN HIS GLN ILE TRP SEQRES 30 A 637 SER GLU PHE ARG ASN ALA VAL LYS GLY VAL ASN SER ASN SEQRES 31 A 637 ALA ALA ILE ILE GLY GLN TYR TRP GLY ASN ALA ASN PRO SEQRES 32 A 637 TRP THR ALA GLN GLY ASN GLN TRP ASP ALA ALA THR ASN SEQRES 33 A 637 PHE ASP GLY PHE THR GLN PRO VAL SER GLU TRP ILE THR SEQRES 34 A 637 GLY LYS ASP TYR GLN ASN ASN SER ALA SER ILE SER THR SEQRES 35 A 637 THR GLN PHE ASP SER TRP LEU ARG GLY THR ARG ALA ASN SEQRES 36 A 637 TYR PRO THR ASN VAL GLN GLN SER MET MET ASN PHE LEU SEQRES 37 A 637 SER ASN HIS ASP ILE THR ARG PHE ALA THR ARG SER GLY SEQRES 38 A 637 GLY ASP LEU TRP LYS THR TYR LEU ALA LEU ILE PHE GLN SEQRES 39 A 637 MET THR TYR VAL GLY THR PRO THR ILE TYR TYR GLY ASP SEQRES 40 A 637 GLU TYR GLY MET GLN GLY GLY ALA ASP PRO ASP ASN ARG SEQRES 41 A 637 ARG SER PHE ASP TRP SER GLN ALA THR PRO SER ASN SER SEQRES 42 A 637 ALA VAL ALA LEU THR GLN LYS LEU ILE THR ILE ARG ASN SEQRES 43 A 637 GLN TYR PRO ALA LEU ARG THR GLY SER PHE MET THR LEU SEQRES 44 A 637 ILE THR ASP ASP THR ASN LYS ILE TYR SER TYR GLY ARG SEQRES 45 A 637 PHE ASP ASN VAL ASN ARG ILE ALA VAL VAL LEU ASN ASN SEQRES 46 A 637 ASP SER VAL SER HIS THR VAL ASN VAL PRO VAL TRP GLN SEQRES 47 A 637 LEU SER MET PRO ASN GLY SER THR VAL THR ASP LYS ILE SEQRES 48 A 637 THR GLY HIS SER TYR THR VAL GLN ASN GLY MET VAL THR SEQRES 49 A 637 VAL ALA VAL ASP GLY HIS TYR GLY ALA VAL LEU ALA GLN

HET BGC A 701 11 HET GLC A 702 11 HET BGC A 703 11 HET BGC A 704 11 HET GLC A 705 11 HET GLC A 706 11 HET GLC A 707 11 HET GLC A 708 11 HET GLC A 709 11 HET GLC A 710 12 HET BGC A 801 11 HET BGC A 802 12 HET GLC A 810 12 HET GLC A 901 11 HET BGC A 902 11 HET BGC A 903 11 HET BGC A 904 11 HET BGC A 905 12 HET BGC A 910 12 HET CA A2001 1 HET CA A2002 1 HET CA A2003 1 HET MPD A1001 8

HETNAM BGC BETA-D-GLUCOSE HETNAM GLC ALPHA-D-GLUCOSE HETNAM CA CALCIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL

FORMUL 2 BGC 10(C6 H12 O6) FORMUL 2 GLC 9(C6 H12 O6) FORMUL 7 CA 3(CA 2+) FORMUL 10 MPD C6 H14 O2 FORMUL 11 HOH *474(H2 O)

HELIX 1 1 PRO A 127 GLY A 133 1 7 HELIX 2 2 PHE A 139 PHE A 143 5 5 HELIX 3 3 ASP A 147 ASP A 151 5 5 HELIX 4 4 ASP A 180 SER A 182 5 3 HELIX 5 5 ASP A 189 LYS A 196 1 8 HELIX 6 6 LYS A 196 LYS A 202 1 7 HELIX 7 7 ASP A 237 SER A 250 1 14 HELIX 8 8 TRP A 294 TYR A 298 5 5 HELIX 9 9 SER A 326 TYR A 333 1 8 HELIX 10 10 SER A 338 ASN A 345 1 8 HELIX 11 11 ALA A 357 VAL A 361 5 5 HELIX 12 12 ASP A 370 ASN A 388 1 19 HELIX 13 13 ALA A 401 THR A 405 5 5 HELIX 14 14 PHE A 420 GLY A 430 1 11 HELIX 15 15 SER A 441 ALA A 454 1 14 HELIX 16 16 PRO A 457 GLN A 462 1 6 HELIX 17 17 ARG A 475 SER A 480 1 6 HELIX 18 18 ASP A 483 MET A 495 1 13 HELIX 19 19 ASN A 532 TYR A 548 1 17 HELIX 20 20 TYR A 548 GLY A 554 1 7 HELIX 21 21 PRO A 595 SER A 600 5 6

SHEET 1 A 3 VAL A 32 PHE A 39 0 SHEET 2 A 3 PHE A 74 ILE A 81 -1 O ASP A 75 N THR A 38 SHEET 3 A 3 VAL A 64 ASN A 68 -1 N VAL A 64 O LYS A 78 SHEET 1 B 5 PHE A 58 PRO A 62 0 SHEET 2 B 5 SER A 45 ASP A 52 -1 N TYR A 50 O HIS A 59 SHEET 3 B 5 LYS A 88 ASP A 96 -1 O ASN A 95 N SER A 45 SHEET 4 B 5 SER A 99 ASN A 104 -1 O ALA A 101 N ILE A 94 SHEET 5 B 5 GLY A 107 SER A 109 -1 O GLY A 107 N ASN A 104 SHEET 1 C 4 PHE A 58 PRO A 62 0 SHEET 2 C 4 SER A 45 ASP A 52 -1 N TYR A 50 O HIS A 59 SHEET 3 C 4 LYS A 88 ASP A 96 -1 O ASN A 95 N SER A 45 SHEET 4 C 4 PHE A 118 ILE A 120 -1 O PHE A 118 N TYR A 90 SHEET 1 D 8 ALA A 413 ALA A 414 0 SHEET 2 D 8 ALA A 392 GLY A 395 1 N GLY A 395 O ALA A 413 SHEET 3 D 8 GLY A 352 LEU A 355 1 N LEU A 355 O ILE A 394 SHEET 4 D 8 TYR A 258 GLY A 263 1 N GLY A 263 O ARG A 354 SHEET 5 D 8 ILE A 208 LEU A 211 1 N LEU A 209 O ILE A 260 SHEET 6 D 8 MET A 135 ILE A 138 1 N ILE A 138 O TYR A 210 SHEET 7 D 8 THR A 500 TYR A 504 1 O ILE A 503 N GLN A 137 SHEET 8 D 8 MET A 465 PHE A 467 1 N ASN A 466 O THR A 502 SHEET 1 E 2 GLU A 165 LYS A 166 0 SHEET 2 E 2 VAL A 184 PHE A 185 1 O PHE A 185 N GLU A 165 SHEET 1 F 2 PHE A 215 LYS A 216 0 SHEET 2 F 2 ASP A 227 VAL A 231 -1 O ALA A 230 N LYS A 216 SHEET 1 G 2 PHE A 300 THR A 302 0 SHEET 2 G 2 SER A 306 TYR A 307 -1 O SER A 306 N THR A 302 SHEET 1 H 2 SER A 309 PHE A 310 0 SHEET 2 H 2 PHE A 313 PRO A 317 -1 O PHE A 313 N PHE A 310 SHEET 1 I 6 SER A 555 ASP A 562 0 SHEET 2 I 6 ILE A 567 PHE A 573 -1 O SER A 569 N LEU A 559 SHEET 3 I 6 ARG A 578 ASN A 584 -1 O LEU A 583 N TYR A 568 SHEET 4 I 6 TYR A 631 GLN A 637 -1 O TYR A 631 N ASN A 584 SHEET 5 I 6 THR A 606 ASP A 609 -1 N THR A 608 O ALA A 636 SHEET 6 I 6 SER A 615 THR A 617 -1 O TYR A 616 N VAL A 607 SHEET 1 J 2 HIS A 590 VAL A 594 0 SHEET 2 J 2 VAL A 623 VAL A 627 -1 O VAL A 625 N VAL A 592

LINK O ALA A 2 CA CA A2001 1555 1555 2.34 LINK OD1 ASP A 4 CA CA A2001 1555 1555 2.46 LINK O ASN A 6 CA CA A2001 1555 1555 2.20 LINK O ASP A 42 CA CA A2001 1555 1555 2.42 LINK OD1 ASP A 42 CA CA A2001 1555 1555 2.29 LINK OD2 ASP A 96 CA CA A2001 1555 1555 2.51 LINK OD1 ASN A 145 CA CA A2002 1555 1555 2.80 LINK O ASP A 147 CA CA A2002 1555 1555 2.39 LINK OD1 ASN A 150 CA CA A2002 1555 1555 2.44 LINK OD2 ASP A 151 CA CA A2002 1555 1555 2.35 LINK O GLY A 187 CA CA A2002 1555 1555 2.59 LINK OD2 ASP A 189 CA CA A2002 1555 1555 2.17 LINK OD2 ASP A 276 CA CA A2003 1555 1555 2.24 LINK OD1 ASN A 279 CA CA A2003 1555 1555 2.33 LINK O PHE A 281 CA CA A2003 1555 1555 2.36 LINK O SER A 283 CA CA A2003 1555 1555 2.52 LINK OE1 GLU A 288 CA CA A2003 1555 1555 2.38 LINK OE2 GLU A 288 CA CA A2003 1555 1555 2.50 LINK C1 BGC A 701 O4 GLC A 702 1555 1555 1.40 LINK C1 GLC A 702 O6 BGC A 703 1555 1555 1.41 LINK C1 BGC A 703 O4 BGC A 704 1555 1555 1.39 LINK C1 BGC A 704 O4 GLC A 705 1555 1555 1.39 LINK C1 GLC A 705 O6 GLC A 706 1555 1555 1.39 LINK C1 GLC A 706 O4 GLC A 707 1555 1555 1.40 LINK C1 GLC A 707 O4 GLC A 708 1555 1555 1.40 LINK C1 GLC A 708 O6 GLC A 709 1555 1555 1.40 LINK C1 GLC A 709 O4 GLC A 710 1555 1555 1.40 LINK C1 BGC A 801 O4 BGC A 802 1555 1555 1.41 LINK C1 GLC A 901 O4 BGC A 902 1555 1555 1.40 LINK C1 BGC A 902 O4 BGC A 903 1555 1555 1.40 LINK C1 BGC A 903 O6 BGC A 904 1555 1555 1.40 LINK C1 BGC A 904 O4 BGC A 905 1555 1555 1.40 LINK CA CA A2001 O HOH A2474 1555 1555 2.59 LINK CA CA A2002 O HOH A2118 1555 1555 2.36 LINK CA CA A2003 O HOH A2263 1555 1555 2.44

CISPEP 1 TRP A 303 PRO A 304 0 0.52 CISPEP 2 PRO A 346 PRO A 347 0 -0.95 CISPEP 3 ASP A 516 PRO A 517 0 -1.95

SITE 1 AC1 3 THR A 529 GLC A 702 HOH A2471 SITE 1 AC2 6 THR A 606 BGC A 701 BGC A 703 HOH A2159 SITE 2 AC2 6 HOH A2200 HOH A2471 SITE 1 AC3 8 TYR A 174 ALA A 515 ASP A 516 PRO A 517 SITE 2 AC3 8 ASP A 518 GLC A 702 BGC A 704 HOH A2438 SITE 1 AC4 7 GLN A 547 ASN A 577 GLN A 637 BGC A 703 SITE 2 AC4 7 GLC A 705 HOH A2198 HOH A2244 SITE 1 AC5 9 PRO A 549 VAL A 576 ASN A 577 BGC A 704 SITE 2 AC5 9 GLC A 706 HOH A2116 HOH A2308 HOH A2309 SITE 3 AC5 9 HOH A2340 SITE 1 AC6 6 SER A 182 ASP A 516 GLC A 705 GLC A 707 SITE 2 AC6 6 HOH A2176 HOH A2308 SITE 1 AC7 7 HIS A 221 TYR A 223 ASP A 516 ARG A 520 SITE 2 AC7 7 GLC A 706 GLC A 708 HOH A2376 SITE 1 AC8 10 TYR A 223 HIS A 267 PHE A 310 ARG A 354 SITE 2 AC8 10 ASN A 356 GLN A 396 HIS A 471 ASP A 472 SITE 3 AC8 10 GLC A 707 GLC A 709 SITE 1 AC9 7 PHE A 310 TYR A 360 GLN A 396 TRP A 398 SITE 2 AC9 7 GLC A 708 GLC A 710 HOH A2254 SITE 1 BC1 4 TRP A 398 GLN A 434 ASP A 472 GLC A 709 SITE 1 BC2 7 ALA A 115 ASP A 116 ASP A 117 TYR A 119 SITE 2 BC2 7 ASN A 402 BGC A 802 HOH A2084 SITE 1 BC3 5 PHE A 58 TYR A 89 ARG A 91 ASP A 117 SITE 2 BC3 5 BGC A 801 SITE 1 BC4 2 ASP A 418 TRP A 448 SITE 1 BC5 4 ASP A 66 SER A 67 BGC A 902 HOH A2337 SITE 1 BC6 4 TRP A 65 ASP A 66 GLC A 901 BGC A 903 SITE 1 BC7 3 BGC A 902 BGC A 904 HOH A2172 SITE 1 BC8 9 GLY A 41 ILE A 43 TRP A 65 ASP A 75 SITE 2 BC8 9 BGC A 903 BGC A 905 HOH A2184 HOH A2241 SITE 3 BC8 9 HOH A2364 SITE 1 BC9 5 LYS A 40 TRP A 65 ASN A 68 ASP A 75 SITE 2 BC9 5 BGC A 904 SITE 1 CC1 4 ASP A 483 TRP A 485 GLY A 629 HIS A 630 SITE 1 CC2 6 ALA A 2 ASP A 4 ASN A 6 ASP A 42 SITE 2 CC2 6 ASP A 96 HOH A2474 SITE 1 CC3 7 ASN A 145 ASP A 147 ASN A 150 ASP A 151 SITE 2 CC3 7 GLY A 187 ASP A 189 HOH A2118 SITE 1 CC4 6 ASP A 276 ASN A 279 PHE A 281 SER A 283 SITE 2 CC4 6 GLU A 288 HOH A2263 SITE 1 CC5 4 ASP A 446 LEU A 559 THR A 561 HOH A2058

CRYST1 120.885 50.698 108.007 90.00 103.43 90.00 C 1 2 1 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 0.008272 0.000000 0.001975 0.00000

SCALE2 0.000000 0.019725 0.000000 0.00000

SCALE3 0.000000 0.000000 0.009519 0.00000