PDB Short entry for 1BLI HEADER HYDROLASE 07-JAN-98 1BLI TITLE BACILLUS LICHENIFORMIS ALPHA-AMYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-AMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUCANOTRANSFERASE, ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE; COMPND 5 EC: 3.2.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: PROTEIN PRODUCED BY NOVO NORDISK A/S, DENMARK SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 CELL_LINE: 293; SOURCE 5 ATCC: ATCC 6598; SOURCE 6 COLLECTION: ATCC 6598; SOURCE 7 GENE: AMYL; SOURCE 8 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 1423; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: 293; SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: SECRETED; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PINA9C9 KEYWDS HYDROLASE, GLYCOSYLTRANSFERASE, ALPHA-AMYLASE, STARCH DEGRADATION, KEYWDS 2 ALPHA-1, 4-GLUCAN-4-GLUCANOHYDROLASE, THERMOSTABILITY, CALCIUM, KEYWDS 3 SODIUM EXPDTA X-RAY DIFFRACTION AUTHOR M.MACHIUS,N.DECLERCK,R.HUBER,G.WIEGAND REVDAT 3 02-AUG-23 1BLI 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1BLI 1 VERSN REVDAT 1 23-MAR-99 1BLI 0 JRNL AUTH M.MACHIUS,N.DECLERCK,R.HUBER,G.WIEGAND JRNL TITL ACTIVATION OF BACILLUS LICHENIFORMIS ALPHA-AMYLASE THROUGH A JRNL TITL 2 DISORDER-->ORDER TRANSITION OF THE SUBSTRATE-BINDING SITE JRNL TITL 3 MEDIATED BY A CALCIUM-SODIUM-CALCIUM METAL TRIAD. JRNL REF STRUCTURE V. 6 281 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9551551 JRNL DOI 10.1016/S0969-2126(98)00032-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.Y.HWANG,H.K.SONG,C.CHANG,J.LEE,S.Y.LEE,K.K.KIM,S.CHOE, REMARK 1 AUTH 2 R.M.SWEET,S.W.SUH REMARK 1 TITL CRYSTAL STRUCTURE OF THERMOSTABLE ALPHA-AMYLASE FROM REMARK 1 TITL 2 BACILLUS LICHENIFORMIS REFINED AT 1.7 A RESOLUTION REMARK 1 REF MOL.CELLS V. 7 251 1997 REMARK 1 REFN ISSN 1016-8478 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.MACHIUS,G.WIEGAND,R.HUBER REMARK 1 TITL CRYSTAL STRUCTURE OF CALCIUM-DEPLETED BACILLUS LICHENIFORMIS REMARK 1 TITL 2 ALPHA-AMYLASE AT 2.2 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 246 545 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 45685 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2291 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3790 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 204 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3905 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 4.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.730 ; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : TIP3P.PARAMETER REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1BLI 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_1000171889. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-97 REMARK 200 TEMPERATURE (KELVIN) : 278 REMARK 200 PH : 7.0 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 : NI FILTER REMARK 200 OPTICS : BEAM FOCUSSING MIRROR SYSTEM REMARK 200 (MSC, USA) REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46801 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 27.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.41800 REMARK 200 R SYM FOR SHELL (I) : 0.41800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: PATTERSON SEARCH REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1BPL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.90000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.80000 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 68.85000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 114.75000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.95000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 ASN A 2 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 LEU A 7 CA - CB - CG ANGL. DEV. = 14.0 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 ALA A 58 74.83 44.60 REMARK 500 LEU A 64 40.04 -89.87 REMARK 500 TYR A 150 -29.11 75.17 REMARK 500 LEU A 196 -61.95 -120.99 REMARK 500 TYR A 198 -145.80 53.34 REMARK 500 MET A 256 71.74 45.96 REMARK 500 PHE A 279 27.67 47.34 REMARK 500 SER A 337 54.95 -167.92 REMARK 500 PHE A 403 62.71 -118.38 REMARK 500 ASP A 407 -60.07 -120.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 195 0.09 SIDE CHAIN 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 A 600 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 104 OD1 REMARK 620 2 ASP A 194 O 102.2 REMARK 620 3 ASP A 194 OD1 159.2 81.3 REMARK 620 4 ASP A 200 OD1 87.3 79.1 113.5 REMARK 620 5 ASP A 200 OD2 129.6 87.3 70.7 45.6 REMARK 620 6 HIS A 235 O 81.8 91.1 77.6 163.5 148.2 REMARK 620 7 HOH A2080 O 86.2 161.3 96.9 84.6 74.6 106.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 500 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 161 OD1 REMARK 620 2 ASP A 161 OD2 50.6 REMARK 620 3 ALA A 181 O 86.5 85.8 REMARK 620 4 ASP A 183 OD1 129.9 81.7 106.7 REMARK 620 5 ASP A 202 OD1 81.9 94.9 164.2 89.0 REMARK 620 6 ASP A 204 OD2 155.9 153.4 92.5 73.3 93.8 REMARK 620 7 HOH A2079 O 73.4 123.5 84.2 153.8 82.3 82.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 800 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 161 OD2 REMARK 620 2 ASP A 183 OD2 92.1 REMARK 620 3 ASP A 194 OD2 86.0 88.1 REMARK 620 4 ASP A 200 OD2 117.4 150.0 88.6 REMARK 620 5 ILE A 201 O 112.8 84.0 159.8 89.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 700 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 300 O REMARK 620 2 TYR A 302 O 107.9 REMARK 620 3 HIS A 406 O 157.2 77.6 REMARK 620 4 ASP A 407 OD1 87.4 149.4 78.7 REMARK 620 5 ASP A 430 OD1 103.1 116.5 93.4 84.0 REMARK 620 6 ASP A 430 OD2 81.2 82.0 121.6 127.4 50.1 REMARK 620 7 HOH A2069 O 79.5 75.8 80.6 81.4 164.9 144.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CS REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: CA1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CALCIUM BINDING SITE. THIS CALCIUM BINDING SITE REMARK 800 IS CONSERVED IN ALL STRUCTURES OF ALPHA-AMYLASES AND RELATED REMARK 800 ENZYMES. REMARK 800 REMARK 800 SITE_IDENTIFIER: CA2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CALCIUM BINDING SITE. THIS CALCIUM BINDING SITE REMARK 800 IS NOT CONSERVED IN ALL STRUCTURES OF ALPHA-AMYLASES AND RELATED REMARK 800 ENZYMES. REMARK 800 REMARK 800 SITE_IDENTIFIER: NA1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: SODIUM BINDING SITE. THIS IS THE FIRST SODIUM REMARK 800 BINDING SITE OBSERVED IN AN ALPHA-AMYLASE OR RELATED ENZYME. REMARK 800 THIS SODIUM TOGETHER WITH THE CALCIUM IONS CA1 AND CA2 FORM A REMARK 800 LINEAR TRIADIC ARRAY WITH THE CALCIUM IONS 4.1 AND 4.5 A FROM REMARK 800 THE CENTRAL SODIUM ION. REMARK 800 REMARK 800 SITE_IDENTIFIER: CA3 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CALCIUM BINDING SITE. THIS CALCIUM BINDING SITE REMARK 800 LOCATED IN THE INTERFACE BETWEEN DOMAIN A AND C IS NOT CONSERVED REMARK 800 IN ALL STRUCTURES OF ALPHA-AMYLASES AND RELATED ENZYMES. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 800 DBREF 1BLI A 1 483 UNP P06278 AMY_BACLI 30 512 SEQADV 1BLI LEU A 134 UNP P06278 ARG 163 CONFLICT SEQADV 1BLI PHE A 190 UNP P06278 ASN 219 ENGINEERED MUTATION SEQADV 1BLI SER A 264 UNP P06278 GLN 293 ENGINEERED MUTATION SEQADV 1BLI TYR A 265 UNP P06278 ASN 294 ENGINEERED MUTATION SEQADV 1BLI GLY A 310 UNP P06278 SER 339 CONFLICT SEQADV 1BLI SER A 320 UNP P06278 ALA 349 CONFLICT SEQADV 1BLI ALA A 465 UNP P06278 GLU 494 CONFLICT SEQRES 1 A 483 ALA ASN LEU ASN GLY THR LEU MET GLN TYR PHE GLU TRP SEQRES 2 A 483 TYR MET PRO ASN ASP GLY GLN HIS TRP LYS ARG LEU GLN SEQRES 3 A 483 ASN ASP SER ALA TYR LEU ALA GLU HIS GLY ILE THR ALA SEQRES 4 A 483 VAL TRP ILE PRO PRO ALA TYR LYS GLY THR SER GLN ALA SEQRES 5 A 483 ASP VAL GLY TYR GLY ALA TYR ASP LEU TYR ASP LEU GLY SEQRES 6 A 483 GLU PHE HIS GLN LYS GLY THR VAL ARG THR LYS TYR GLY SEQRES 7 A 483 THR LYS GLY GLU LEU GLN SER ALA ILE LYS SER LEU HIS SEQRES 8 A 483 SER ARG ASP ILE ASN VAL TYR GLY ASP VAL VAL ILE ASN SEQRES 9 A 483 HIS LYS GLY GLY ALA ASP ALA THR GLU ASP VAL THR ALA SEQRES 10 A 483 VAL GLU VAL ASP PRO ALA ASP ARG ASN ARG VAL ILE SER SEQRES 11 A 483 GLY GLU HIS LEU ILE LYS ALA TRP THR HIS PHE HIS PHE SEQRES 12 A 483 PRO GLY ARG GLY SER THR TYR SER ASP PHE LYS TRP HIS SEQRES 13 A 483 TRP TYR HIS PHE ASP GLY THR ASP TRP ASP GLU SER ARG SEQRES 14 A 483 LYS LEU ASN ARG ILE TYR LYS PHE GLN GLY LYS ALA TRP SEQRES 15 A 483 ASP TRP GLU VAL SER ASN GLU PHE GLY ASN TYR ASP TYR SEQRES 16 A 483 LEU MET TYR ALA ASP ILE ASP TYR ASP HIS PRO ASP VAL SEQRES 17 A 483 ALA ALA GLU ILE LYS ARG TRP GLY THR TRP TYR ALA ASN SEQRES 18 A 483 GLU LEU GLN LEU ASP GLY PHE ARG LEU ASP ALA VAL LYS SEQRES 19 A 483 HIS ILE LYS PHE SER PHE LEU ARG ASP TRP VAL ASN HIS SEQRES 20 A 483 VAL ARG GLU LYS THR GLY LYS GLU MET PHE THR VAL ALA SEQRES 21 A 483 GLU TYR TRP SER TYR ASP LEU GLY ALA LEU GLU ASN TYR SEQRES 22 A 483 LEU ASN LYS THR ASN PHE ASN HIS SER VAL PHE ASP VAL SEQRES 23 A 483 PRO LEU HIS TYR GLN PHE HIS ALA ALA SER THR GLN GLY SEQRES 24 A 483 GLY GLY TYR ASP MET ARG LYS LEU LEU ASN GLY THR VAL SEQRES 25 A 483 VAL SER LYS HIS PRO LEU LYS SER VAL THR PHE VAL ASP SEQRES 26 A 483 ASN HIS ASP THR GLN PRO GLY GLN SER LEU GLU SER THR SEQRES 27 A 483 VAL GLN THR TRP PHE LYS PRO LEU ALA TYR ALA PHE ILE SEQRES 28 A 483 LEU THR ARG GLU SER GLY TYR PRO GLN VAL PHE TYR GLY SEQRES 29 A 483 ASP MET TYR GLY THR LYS GLY ASP SER GLN ARG GLU ILE SEQRES 30 A 483 PRO ALA LEU LYS HIS LYS ILE GLU PRO ILE LEU LYS ALA SEQRES 31 A 483 ARG LYS GLN TYR ALA TYR GLY ALA GLN HIS ASP TYR PHE SEQRES 32 A 483 ASP HIS HIS ASP ILE VAL GLY TRP THR ARG GLU GLY ASP SEQRES 33 A 483 SER SER VAL ALA ASN SER GLY LEU ALA ALA LEU ILE THR SEQRES 34 A 483 ASP GLY PRO GLY GLY ALA LYS ARG MET TYR VAL GLY ARG SEQRES 35 A 483 GLN ASN ALA GLY GLU THR TRP HIS ASP ILE THR GLY ASN SEQRES 36 A 483 ARG SER GLU PRO VAL VAL ILE ASN SER ALA GLY TRP GLY SEQRES 37 A 483 GLU PHE HIS VAL ASN GLY GLY SER VAL SER ILE TYR VAL SEQRES 38 A 483 GLN ARG HET CA A 500 1 HET CA A 600 1 HET CA A 700 1 HET NA A 800 1 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 2 CA 3(CA 2+) FORMUL 5 NA NA 1+ FORMUL 6 HOH *221(H2 O) HELIX 1 1 HIS A 21 GLU A 34 1 14 HELIX 2 2 LYS A 80 ARG A 93 1 14 HELIX 3 3 TRP A 157 HIS A 159 5 3 HELIX 4 4 PRO A 206 LEU A 223 1 18 HELIX 5 5 VAL A 233 HIS A 235 5 3 HELIX 6 6 PHE A 238 THR A 252 1 15 HELIX 7 7 LEU A 267 LYS A 276 1 10 HELIX 8 8 VAL A 286 THR A 297 1 12 HELIX 9 9 MET A 304 LEU A 308 5 5 HELIX 10 10 VAL A 312 LYS A 315 1 4 HELIX 11 11 THR A 341 THR A 353 1 13 HELIX 12 12 TYR A 363 TYR A 367 1 5 HELIX 13 13 LYS A 381 GLN A 393 1 13 HELIX 14 14 ARG A 442 ASN A 444 5 3 SHEET 1 A 7 VAL A 321 PHE A 323 0 SHEET 2 A 7 TYR A 358 PHE A 362 1 N TYR A 358 O THR A 322 SHEET 3 A 7 LEU A 7 GLN A 9 1 N LEU A 7 O VAL A 361 SHEET 4 A 7 ALA A 39 ILE A 42 1 N ALA A 39 O MET A 8 SHEET 5 A 7 ASN A 96 VAL A 101 1 N ASN A 96 O VAL A 40 SHEET 6 A 7 GLY A 227 LEU A 230 1 N GLY A 227 O GLY A 99 SHEET 7 A 7 PHE A 257 ALA A 260 1 N PHE A 257 O PHE A 228 SHEET 1 B 3 TYR A 175 PHE A 177 0 SHEET 2 B 3 ALA A 111 GLU A 119 -1 N VAL A 118 O LYS A 176 SHEET 3 B 3 HIS A 133 HIS A 140 -1 N HIS A 140 O ALA A 111 SHEET 1 C 5 GLN A 399 TYR A 402 0 SHEET 2 C 5 ILE A 408 ARG A 413 -1 N THR A 412 O HIS A 400 SHEET 3 C 5 LEU A 424 THR A 429 -1 N ILE A 428 O VAL A 409 SHEET 4 C 5 VAL A 477 GLN A 482 -1 N TYR A 480 O ALA A 425 SHEET 5 C 5 TRP A 449 ASP A 451 -1 N HIS A 450 O VAL A 481 SHEET 1 D 2 GLY A 434 TYR A 439 0 SHEET 2 D 2 TRP A 467 VAL A 472 -1 N VAL A 472 O GLY A 434 LINK OD1 ASN A 104 CA CA A 600 1555 1555 2.35 LINK OD1 ASP A 161 CA CA A 500 1555 1555 2.58 LINK OD2 ASP A 161 CA CA A 500 1555 1555 2.55 LINK OD2 ASP A 161 NA NA A 800 1555 1555 2.44 LINK O ALA A 181 CA CA A 500 1555 1555 2.39 LINK OD1 ASP A 183 CA CA A 500 1555 1555 2.36 LINK OD2 ASP A 183 NA NA A 800 1555 1555 2.71 LINK O ASP A 194 CA CA A 600 1555 1555 2.36 LINK OD1 ASP A 194 CA CA A 600 1555 1555 2.41 LINK OD2 ASP A 194 NA NA A 800 1555 1555 2.47 LINK OD1 ASP A 200 CA CA A 600 1555 1555 2.42 LINK OD2 ASP A 200 CA CA A 600 1555 1555 3.05 LINK OD2 ASP A 200 NA NA A 800 1555 1555 2.43 LINK O ILE A 201 NA NA A 800 1555 1555 2.50 LINK OD1 ASP A 202 CA CA A 500 1555 1555 2.40 LINK OD2 ASP A 204 CA CA A 500 1555 1555 2.54 LINK O HIS A 235 CA CA A 600 1555 1555 2.38 LINK O GLY A 300 CA CA A 700 1555 1555 2.47 LINK O TYR A 302 CA CA A 700 1555 1555 2.28 LINK O HIS A 406 CA CA A 700 1555 1555 2.54 LINK OD1 ASP A 407 CA CA A 700 1555 1555 2.31 LINK OD1 ASP A 430 CA CA A 700 1555 1555 2.59 LINK OD2 ASP A 430 CA CA A 700 1555 1555 2.61 LINK CA CA A 500 O HOH A2079 1555 1555 2.54 LINK CA CA A 600 O HOH A2080 1555 1555 2.50 LINK CA CA A 700 O HOH A2069 1555 1555 2.81 CISPEP 1 TRP A 184 GLU A 185 0 12.07 SITE 1 CS 3 MET A 197 VAL A 233 GLY A 300 SITE 1 CA1 4 ASN A 104 ASP A 194 ASP A 200 HIS A 235 SITE 1 CA2 5 ASP A 161 ALA A 181 ASP A 183 ASP A 202 SITE 2 CA2 5 ASP A 204 SITE 1 NA1 5 ASP A 161 ASP A 183 ASP A 194 ASP A 200 SITE 2 NA1 5 ILE A 201 SITE 1 CA3 5 GLY A 300 TYR A 302 HIS A 406 ASP A 407 SITE 2 CA3 5 ASP A 430 SITE 1 AC1 6 ASP A 161 ALA A 181 ASP A 183 ASP A 202 SITE 2 AC1 6 ASP A 204 HOH A2079 SITE 1 AC2 5 ASN A 104 ASP A 194 ASP A 200 HIS A 235 SITE 2 AC2 5 HOH A2080 SITE 1 AC3 6 GLY A 300 TYR A 302 HIS A 406 ASP A 407 SITE 2 AC3 6 ASP A 430 HOH A2069 SITE 1 AC4 5 ASP A 161 ASP A 183 ASP A 194 ASP A 200 SITE 2 AC4 5 ILE A 201 CRYST1 91.300 91.300 137.700 90.00 90.00 120.00 P 61 6 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 0.010953 0.006324 0.000000 0.00000 SCALE2 0.000000 0.012647 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007262 0.00000