10 20 30 40 50 60 70 80 1UD8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 28-APR-03 1UD8
TITLE CRYSTAL STRUCTURE OF AMYK38 WITH LITHIUM ION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-480; COMPND 5 SYNONYM: ALPHA-AMYLASE; COMPND 6 EC: 3.2.1.1; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SP. KSM-K38; SOURCE 3 ORGANISM_TAXID: 129736; SOURCE 4 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1423; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PHSP64
KEYWDS CALCIUM-FREE, ALKALINE, ALPHA-AMYLASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.NONAKA,M.FUJIHASHI,A.KITA,H.HAGIHARA,K.OZAKI,S.ITO,K.MIKI
REVDAT 2 24-FEB-09 1UD8 1 VERSN REVDAT 1 22-JUL-03 1UD8 0
JRNL AUTH T.NONAKA,M.FUJIHASHI,A.KITA,H.HAGIHARA,K.OZAKI, JRNL AUTH 2 S.ITO,K.MIKI JRNL TITL CRYSTAL STRUCTURE OF CALCIUM-FREE ALPHA-AMYLASE JRNL TITL 2 FROM BACILLUS SP. STRAIN KSM-K38 (AMYK38) AND ITS JRNL TITL 3 SODIUM ION BINDING SITES JRNL REF J.BIOL.CHEM. V. 278 24818 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12719434 JRNL DOI 10.1074/JBC.M212763200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.88 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2038246.490 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 17611 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) : 0.205 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 889 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.06 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2689 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 137 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3908 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.37 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.48 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) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.78 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.940 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.840 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.140 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 38.45 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CISPEP_2003.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS STRUCTURE WAS DETERMINED FROM REMARK 3 THE DATASET OF THE CRYSTAL SOAKED INTO LI+ ION CONTAINING REMARK 3 SOLUTION. HOWEVER, METAL ATOMS WERE REFINED AS SODIUM IONS.
REMARK 4 REMARK 4 1UD8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAY-03. REMARK 100 THE RCSB ID CODE IS RCSB005696.
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 : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17867 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.880 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.100 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 12.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: MODEL OF NATIVE AMYK38 STRUCTURE REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, LITHIUM ACETATE, REMARK 280 GLYCEROL, MES-LIOH, TRIS-HCL, PH 6.7, SOAKING OF NATIVE REMARK 280 CRYSTALS, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 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: 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 TYR A 11 159.07 175.03 REMARK 500 HIS A 14 31.67 -93.73 REMARK 500 ASN A 17 56.09 -90.36 REMARK 500 ALA A 29 -72.71 -45.68 REMARK 500 LEU A 61 -7.89 -56.23 REMARK 500 LEU A 64 51.32 -91.12 REMARK 500 ASN A 124 81.81 -157.10 REMARK 500 ARG A 125 -7.58 -55.14 REMARK 500 TYR A 150 -38.80 71.21 REMARK 500 GLN A 170 78.71 51.46 REMARK 500 TYR A 193 30.40 -97.13 REMARK 500 LEU A 196 -63.75 -121.52 REMARK 500 ALA A 232 29.63 39.14 REMARK 500 ILE A 233 -0.18 -56.43 REMARK 500 ASP A 266 106.68 -165.04 REMARK 500 TRP A 279 50.17 33.45 REMARK 500 ASP A 285 76.41 -69.69 REMARK 500 PRO A 317 10.17 -65.00 REMARK 500 PRO A 331 126.92 -38.97 REMARK 500 SER A 337 44.67 -171.15 REMARK 500 ALA A 392 74.05 -67.75 REMARK 500 TYR A 399 55.08 -145.28 REMARK 500 ASP A 404 -64.60 -121.06 REMARK 500 PRO A 417 133.14 -31.82 REMARK 500 ASN A 418 15.93 43.81 REMARK 500 SER A 419 -172.60 -59.22 REMARK 500 VAL A 437 10.63 -141.50 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 NA A1001 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 OD1 REMARK 620 2 ASN A 104 OD1 172.3 REMARK 620 3 ASP A 194 O 70.3 105.9 REMARK 620 4 HIS A 235 O 81.4 91.9 88.2 REMARK 620 5 ASN A 200 OD1 95.4 89.7 73.2 161.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 300 O REMARK 620 2 TRP A 403 O 169.9 REMARK 620 3 HOH A2018 O 85.0 93.5 REMARK 620 4 ASP A 404 OD1 111.1 78.8 88.1 REMARK 620 5 TYR A 302 O 77.0 93.0 88.9 171.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1003 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 289 O REMARK 620 2 ASN A 289 OD1 88.2 REMARK 620 3 VAL A 324 O 117.3 65.3 REMARK 620 4 ASP A 325 OD1 168.5 80.4 56.0 REMARK 620 5 SER A 337 O 119.8 124.0 122.1 69.0 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1001 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1002 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1003
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UD2 RELATED DB: PDB REMARK 900 THE STRUCTURE WHICH SODIUM IONS, INSTEAD OF CALCIUM IONS, REMARK 900 ARE USED TO RETAIN THE STRUCTURE AND FUNCTION OF AMYK38. REMARK 900 RELATED ID: 1UD3 RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE N289H MUTANT OF AMYK38. REMARK 900 RELATED ID: 1UD4 RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE CALCIUM-FREE ALPHA-AMYLASE, AMYK38, REMARK 900 FROM THE CRYSTAL GROWN IN THE CACL2 CONTAINING SOLUTION. REMARK 900 RELATED ID: 1UD5 RELATED DB: PDB REMARK 900 THIS STRUCTURE WAS DETERMINED FROM THE DATASET OF THE REMARK 900 CRYSTAL SOAKED INTO RB+ ION CONTAINING SOLUTION. REMARK 900 RELATED ID: 1UD6 RELATED DB: PDB REMARK 900 THIS STRUCTURE WAS DETERMINED FROM THE DATASET OF THE REMARK 900 CRYSTAL SOAKED INTO K+ ION CONTAINING SOLUTION.
DBREF 1UD8 A 1 480 UNP Q93I48 Q93I48_9BACI 22 501
SEQRES 1 A 480 ASP GLY LEU ASN GLY THR MET MET GLN TYR TYR GLU TRP SEQRES 2 A 480 HIS LEU GLU ASN ASP GLY GLN HIS TRP ASN ARG LEU HIS SEQRES 3 A 480 ASP ASP ALA ALA ALA LEU SER ASP ALA GLY ILE THR ALA SEQRES 4 A 480 ILE TRP ILE PRO PRO ALA TYR LYS GLY ASN SER GLN ALA SEQRES 5 A 480 ASP VAL GLY TYR GLY ALA TYR ASP LEU TYR ASP LEU GLY SEQRES 6 A 480 GLU PHE ASN GLN LYS GLY THR VAL ARG THR LYS TYR GLY SEQRES 7 A 480 THR LYS ALA GLN LEU GLU ARG ALA ILE GLY SER LEU LYS SEQRES 8 A 480 SER ASN ASP ILE ASN VAL TYR GLY ASP VAL VAL MET ASN SEQRES 9 A 480 HIS LYS MET GLY ALA ASP PHE THR GLU ALA VAL GLN ALA SEQRES 10 A 480 VAL GLN VAL ASN PRO THR ASN ARG TRP GLN ASP ILE SER SEQRES 11 A 480 GLY ALA TYR THR ILE ASP ALA TRP THR GLY PHE ASP PHE SEQRES 12 A 480 SER GLY ARG ASN ASN ALA TYR SER ASP PHE LYS TRP ARG SEQRES 13 A 480 TRP PHE HIS PHE ASN GLY VAL ASP TRP ASP GLN ARG TYR SEQRES 14 A 480 GLN GLU ASN HIS ILE PHE ARG PHE ALA ASN THR ASN TRP SEQRES 15 A 480 ASN TRP ARG VAL ASP GLU GLU ASN GLY ASN TYR ASP TYR SEQRES 16 A 480 LEU LEU GLY SER ASN ILE ASP PHE SER HIS PRO GLU VAL SEQRES 17 A 480 GLN ASP GLU LEU LYS ASP TRP GLY SER TRP PHE THR ASP SEQRES 18 A 480 GLU LEU ASP LEU ASP GLY TYR ARG LEU ASP ALA ILE LYS SEQRES 19 A 480 HIS ILE PRO PHE TRP TYR THR SER ASP TRP VAL ARG HIS SEQRES 20 A 480 GLN ARG ASN GLU ALA ASP GLN ASP LEU PHE VAL VAL GLY SEQRES 21 A 480 GLU TYR TRP LYS ASP ASP VAL GLY ALA LEU GLU PHE TYR SEQRES 22 A 480 LEU ASP GLU MET ASN TRP GLU MET SER LEU PHE ASP VAL SEQRES 23 A 480 PRO LEU ASN TYR ASN PHE TYR ARG ALA SER GLN GLN GLY SEQRES 24 A 480 GLY SER TYR ASP MET ARG ASN ILE LEU ARG GLY SER LEU SEQRES 25 A 480 VAL GLU ALA HIS PRO MET HIS ALA VAL THR PHE VAL ASP SEQRES 26 A 480 ASN HIS ASP THR GLN PRO GLY GLU SER LEU GLU SER TRP SEQRES 27 A 480 VAL ALA ASP TRP PHE LYS PRO LEU ALA TYR ALA THR ILE SEQRES 28 A 480 LEU THR ARG GLU GLY GLY TYR PRO ASN VAL PHE TYR GLY SEQRES 29 A 480 ASP TYR TYR GLY ILE PRO ASN ASP ASN ILE SER ALA LYS SEQRES 30 A 480 LYS ASP MET ILE ASP GLU LEU LEU ASP ALA ARG GLN ASN SEQRES 31 A 480 TYR ALA TYR GLY THR GLN HIS ASP TYR PHE ASP HIS TRP SEQRES 32 A 480 ASP VAL VAL GLY TRP THR ARG GLU GLY SER SER SER ARG SEQRES 33 A 480 PRO ASN SER GLY LEU ALA THR ILE MET SER ASN GLY PRO SEQRES 34 A 480 GLY GLY SER LYS TRP MET TYR VAL GLY ARG GLN ASN ALA SEQRES 35 A 480 GLY GLN THR TRP THR ASP LEU THR GLY ASN ASN GLY ALA SEQRES 36 A 480 SER VAL THR ILE ASN GLY ASP GLY TRP GLY GLU PHE PHE SEQRES 37 A 480 THR ASN GLY GLY SER VAL SER VAL TYR VAL ASN GLN
HET NA A1001 1 HET NA A1002 1 HET NA A1003 1
HETNAM NA SODIUM ION
FORMUL 2 NA 3(NA 1+) FORMUL 5 HOH *87(H2 O)
HELIX 1 1 GLN A 20 GLY A 36 1 17 HELIX 2 2 THR A 79 ASN A 93 1 15 HELIX 3 3 PHE A 143 ASN A 147 5 5 HELIX 4 4 ARG A 156 PHE A 158 5 3 HELIX 5 5 HIS A 205 ASP A 224 1 20 HELIX 6 6 PRO A 237 ALA A 252 1 16 HELIX 7 7 ASP A 266 ASN A 278 1 13 HELIX 8 8 ASP A 285 GLY A 299 1 15 HELIX 9 9 ASP A 303 ILE A 307 5 5 HELIX 10 10 SER A 311 HIS A 316 1 6 HELIX 11 11 PHE A 343 ARG A 354 1 12 HELIX 12 12 TYR A 363 TYR A 367 1 5 HELIX 13 13 ILE A 369 ASN A 373 5 5 HELIX 14 14 LYS A 377 TYR A 391 1 15 HELIX 15 15 GLY A 438 ALA A 442 5 5
SHEET 1 A 8 ALA A 320 VAL A 321 0 SHEET 2 A 8 SER A 282 PHE A 284 1 N LEU A 283 O VAL A 321 SHEET 3 A 8 PHE A 257 GLY A 260 1 N GLY A 260 O SER A 282 SHEET 4 A 8 GLY A 227 LEU A 230 1 N TYR A 228 O VAL A 259 SHEET 5 A 8 ASN A 96 VAL A 101 1 N GLY A 99 O ARG A 229 SHEET 6 A 8 ALA A 39 ILE A 42 1 N ILE A 40 O ASN A 96 SHEET 7 A 8 MET A 7 GLN A 9 1 N MET A 8 O TRP A 41 SHEET 8 A 8 ASN A 360 PHE A 362 1 O VAL A 361 N MET A 7 SHEET 1 B 2 LYS A 47 GLY A 48 0 SHEET 2 B 2 ALA A 58 ASP A 60 -1 O TYR A 59 N LYS A 47 SHEET 1 C 3 TYR A 133 GLY A 140 0 SHEET 2 C 3 PHE A 111 ASN A 121 -1 N VAL A 115 O ILE A 135 SHEET 3 C 3 ASN A 124 ASP A 128 -1 O GLN A 127 N ASN A 121 SHEET 1 D 6 TYR A 133 GLY A 140 0 SHEET 2 D 6 PHE A 111 ASN A 121 -1 N VAL A 115 O ILE A 135 SHEET 3 D 6 GLU A 171 PHE A 177 -1 O ARG A 176 N VAL A 118 SHEET 4 D 6 PHE A 160 ASP A 166 -1 N VAL A 163 O PHE A 175 SHEET 5 D 6 SER A 199 ILE A 201 -1 O ASN A 200 N GLY A 162 SHEET 6 D 6 HIS A 105 LYS A 106 -1 N LYS A 106 O SER A 199 SHEET 1 E 6 GLN A 396 TYR A 399 0 SHEET 2 E 6 VAL A 405 ARG A 410 -1 O THR A 409 N HIS A 397 SHEET 3 E 6 LEU A 421 SER A 426 -1 O LEU A 421 N ARG A 410 SHEET 4 E 6 SER A 473 VAL A 478 -1 O SER A 475 N ILE A 424 SHEET 5 E 6 THR A 445 ASP A 448 -1 N THR A 447 O VAL A 478 SHEET 6 E 6 SER A 456 THR A 458 -1 O VAL A 457 N TRP A 446 SHEET 1 F 2 GLY A 431 TYR A 436 0 SHEET 2 F 2 TRP A 464 THR A 469 -1 O THR A 469 N GLY A 431
LINK NA NA A1001 OD1 ASP A 194 1555 1555 2.42 LINK NA NA A1001 OD1 ASN A 104 1555 1555 2.36 LINK NA NA A1001 O ASP A 194 1555 1555 2.55 LINK NA NA A1001 O HIS A 235 1555 1555 2.31 LINK NA NA A1002 O GLY A 300 1555 1555 2.22 LINK NA NA A1002 O TRP A 403 1555 1555 2.46 LINK NA NA A1002 O HOH A2018 1555 1555 2.48 LINK NA NA A1002 OD1 ASP A 404 1555 1555 2.31 LINK NA NA A1002 O TYR A 302 1555 1555 2.45 LINK OD1 ASN A 200 NA NA A1001 1555 1555 2.61 LINK O ASN A 289 NA NA A1003 1555 1555 2.83 LINK OD1 ASN A 289 NA NA A1003 1555 1555 2.67 LINK O VAL A 324 NA NA A1003 1555 1555 2.96 LINK OD1 ASP A 325 NA NA A1003 1555 1555 2.84 LINK O SER A 337 NA NA A1003 1555 1555 2.69
CISPEP 1 TRP A 184 ARG A 185 0 -0.26
SITE 1 AC1 4 ASN A 104 ASP A 194 ASN A 200 HIS A 235 SITE 1 AC2 6 GLY A 300 TYR A 302 TRP A 403 ASP A 404 SITE 2 AC2 6 ASN A 427 HOH A2018 SITE 1 AC3 5 ASN A 289 VAL A 324 ASP A 325 SER A 337 SITE 2 AC3 5 VAL A 339
CRYST1 132.553 132.553 132.553 90.00 90.00 90.00 P 2 3 12
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 0.007544 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007544 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007544 0.00000