HEADER HYDROLASE 16-MAY-15 5A2A TITLE CRYSTAL STRUCTURE OF ANOXYBACILLUS ALPHA-AMYLASE PROVIDES INSIGHTS TITLE 2 INTO A NEW GLYCOSYL HYDROLASE SUBCLASS COMPND MOL_ID: 1; COMPND 2 MOLECULE: APO FORM OF ANOXYBACILLUS ALPHA-AMYLASES; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN A WITH TIM BARREL FOLD (RESIDUES 26 TO COMPND 5 139,187 TO 393), DOMAIN B (RESIDUES 140 TO 186), AND DOMAIN C WITH AN COMPND 6 ALL-ALPAH-BETA FOLD (RESIDUES 394 TO 475); COMPND 7 EC: 3.2.1.1; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: TRUNCATED PROTEIN WITH 23 RESIDUES AT THE N-TERMINUS COMPND 10 (1 TO 23) AND 27 RESIDUES AT THE C-TERMINUS (RESIDUES 479 TO 505) COMPND 11 REMOVED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANOXYBACILLUS SP.; SOURCE 3 ORGANISM_TAXID: 654421; SOURCE 4 STRAIN: SK3-4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 OTHER_DETAILS: ISOLATED FROM SUNGAI KLAH HOT SPRING MALAYSIA KEYWDS HYDROLASE, ANOXYBACILLUS, ALPHA-AMYLASE, CALCIUM-BINDING SITE, KEYWDS 2 GEOBACILLUS, GLYCOSYL HYDROLASE. EXPDTA X-RAY DIFFRACTION AUTHOR C.L.NG,K.P.CHAI,N.F.OTHMAN,A.H.TEH,K.L.HO,K.G.CHAN,K.M.GOH REVDAT 2 10-JAN-24 5A2A 1 REMARK LINK REVDAT 1 30-MAR-16 5A2A 0 JRNL AUTH K.P.CHAI,N.F.B.OTHMAN,A.TEH,K.L.HO,K.CHAN,M.S.SHAMSIR, JRNL AUTH 2 K.M.GOH,C.L.NG JRNL TITL CRYSTAL STRUCTURE OF ANOXYBACILLUS ALPHA-AMYLASE PROVIDES JRNL TITL 2 INSIGHTS INTO MALTOSE BINDING OF A NEW GLYCOSYL HYDROLASE JRNL TITL 3 SUBCLASS. JRNL REF SCI.REP. V. 6 23126 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 26975884 JRNL DOI 10.1038/SREP23126 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 33142 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 + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1785 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 0 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 0.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.0000 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.0000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3768 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 405 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.21000 REMARK 3 B22 (A**2) : -9.71000 REMARK 3 B33 (A**2) : 18.92000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.038 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3889 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5270 ; 2.232 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 7.253 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;35.368 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 668 ;17.401 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.595 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 545 ; 0.157 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3023 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1813 ; 1.106 ; 0.873 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2263 ; 1.680 ; 1.299 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2076 ; 1.527 ; 1.019 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.875 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.125 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 26 A 475 REMARK 3 ORIGIN FOR THE GROUP (A): 16.5100 -6.4110 -19.5950 REMARK 3 T TENSOR REMARK 3 T11: 0.1610 T22: 0.1280 REMARK 3 T33: 0.0022 T12: 0.0029 REMARK 3 T13: -0.0057 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.5866 L22: 0.2578 REMARK 3 L33: 0.4193 L12: 0.0828 REMARK 3 L13: 0.3680 L23: -0.0768 REMARK 3 S TENSOR REMARK 3 S11: 0.0011 S12: -0.0222 S13: -0.0230 REMARK 3 S21: -0.0282 S22: 0.0064 S23: -0.0167 REMARK 3 S31: -0.0085 S32: 0.0205 S33: -0.0075 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. COMPARE TO FULL LENGTH ASKA SEQUENCES, TASKA HAS 23 REMARK 3 RESIDUES AT THE N-TERMINUS AND 27 RESIDUES AT THE C- TERMINUS REMARK 3 TRUNCATED. REMARK 4 REMARK 4 5A2A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1290063768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 MICROMAX-007 HF 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 : NULL REMARK 200 DETECTOR MANUFACTURER : RIGAKU R-AXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 19.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4E2O REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE (PH 6.5) 18% (W/V) POLYETHYLENE GLYCOL 8, 000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 30.71450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.37900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.72150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.37900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.71450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.72150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 LYS A 24 REMARK 465 THR A 25 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2234 O HOH A 2276 1.53 REMARK 500 O HOH A 2199 O HOH A 2200 1.70 REMARK 500 O HOH A 2079 O HOH A 2336 1.80 REMARK 500 OD2 ASP A 224 O HOH A 2220 1.92 REMARK 500 O HOH A 2165 O HOH A 2330 1.93 REMARK 500 OD2 ASP A 116 O HOH A 2122 1.95 REMARK 500 O HOH A 2085 O HOH A 2184 2.07 REMARK 500 N GLY A 95 O HOH A 2097 2.08 REMARK 500 O HOH A 2044 O HOH A 2083 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2082 O HOH A 2375 3544 1.85 REMARK 500 OD2 ASP A 246 NH2 ARG A 451 3554 1.89 REMARK 500 O HOH A 2112 O HOH A 2323 4545 1.99 REMARK 500 CB ASP A 50 NH2 ARG A 322 4545 2.00 REMARK 500 NE2 GLN A 437 O HOH A 2164 2554 2.15 REMARK 500 O HOH A 2141 O HOH A 2397 3554 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 75 CG TYR A 75 CD2 0.080 REMARK 500 GLU A 270 CD GLU A 270 OE2 -0.076 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 47 C - N - CA ANGL. DEV. = -10.3 DEGREES REMARK 500 LEU A 285 CB - CG - CD2 ANGL. DEV. = -11.9 DEGREES REMARK 500 LEU A 301 CB - CG - CD1 ANGL. DEV. = -12.6 DEGREES REMARK 500 ARG A 313 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU A 431 CB - CG - CD1 ANGL. DEV. = -11.0 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 PHE A 42 -76.42 -99.51 REMARK 500 GLU A 93 -176.96 -69.30 REMARK 500 TRP A 101 76.53 -117.00 REMARK 500 GLU A 109 124.58 -39.53 REMARK 500 PHE A 164 -62.16 -105.82 REMARK 500 PRO A 181 110.26 -35.27 REMARK 500 ILE A 207 161.16 -47.93 REMARK 500 HIS A 245 143.87 -171.40 REMARK 500 LEU A 301 64.91 -102.09 REMARK 500 ASP A 358 124.95 -34.65 REMARK 500 ASP A 370 144.63 -34.50 REMARK 500 GLU A 412 -110.65 43.06 REMARK 500 ASN A 422 47.56 -93.61 REMARK 500 ASP A 432 79.53 -154.68 REMARK 500 LYS A 439 -168.03 -110.27 REMARK 500 ASP A 454 52.03 70.49 REMARK 500 LYS A 474 150.14 -43.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2021 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A2093 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A2404 DISTANCE = 8.38 ANGSTROMS 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 A1481 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 44 OD1 REMARK 620 2 ASN A 46 O 71.7 REMARK 620 3 ASN A 49 OD1 149.8 78.8 REMARK 620 4 ASP A 50 OD1 89.5 86.4 94.9 REMARK 620 5 GLY A 63 O 76.7 147.0 130.7 102.5 REMARK 620 6 ASP A 65 OD2 85.3 83.5 85.2 169.7 85.0 REMARK 620 7 HOH A2042 O 145.2 140.5 64.8 81.9 72.5 107.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1482 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 92 O REMARK 620 2 GLU A 109 OE2 123.3 REMARK 620 3 GLU A 109 OE1 87.1 47.1 REMARK 620 4 GLU A 110 OE1 149.6 65.3 80.7 REMARK 620 5 GLU A 110 OE2 161.7 63.2 106.3 47.6 REMARK 620 6 HOH A2060 O 61.0 78.5 81.7 142.5 107.8 REMARK 620 7 HOH A2091 O 87.3 137.7 174.3 104.0 79.4 96.1 REMARK 620 8 HOH A2092 O 83.2 124.9 95.5 70.6 107.3 144.1 83.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1480 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 139 OD1 REMARK 620 2 GLU A 173 O 155.7 REMARK 620 3 ASP A 182 OD1 75.2 116.0 REMARK 620 4 ASP A 182 OD2 120.6 78.2 47.9 REMARK 620 5 HIS A 217 O 80.7 78.3 143.0 155.8 REMARK 620 6 HOH A2154 O 74.3 127.8 77.6 77.8 122.1 REMARK 620 7 HOH A2155 O 88.1 77.6 68.3 85.8 83.5 144.6 REMARK 620 8 HOH A2186 O 120.2 69.7 132.1 93.0 84.4 66.1 146.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1483 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 400 O REMARK 620 2 HOH A2261 O 77.3 REMARK 620 3 HOH A2341 O 155.1 112.2 REMARK 620 4 HOH A2360 O 84.5 156.3 79.1 REMARK 620 5 HOH A2361 O 86.5 78.8 73.5 85.1 REMARK 620 6 HOH A2362 O 90.1 98.0 110.3 97.2 175.8 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1478 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1479 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1480 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1482 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1483 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A2B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ANOXYBACILLUS ALPHA-AMYLASE PROVIDES INSIGHTS REMARK 900 INTO A NEW GLYCOSYL HYDROLASE SUBCLASS REMARK 900 RELATED ID: 5A2C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ANOXYBACILLUS ALPHA-AMYLASE PROVIDES INSIGHTS REMARK 900 INTO A NEW GLYCOSYL HYDROLASE SUBCLASS REMARK 999 REMARK 999 SEQUENCE REMARK 999 COMPARE TO 1VWH9 SEQUENCE, TASKA HAS 23 RESIDUES AT THE N- REMARK 999 TERMINUS AND 27 RESIDUES AT THE C-TERMINUS TRUNCATED. DBREF 5A2A A 24 477 UNP I1VWH9 I1VWH9_9BACI 24 477 SEQRES 1 A 454 LYS THR GLU ARG THR TRP GLN ASP GLU ARG ILE TYR PHE SEQRES 2 A 454 ILE MET VAL ASP ARG PHE ASN ASN GLY ASN PRO LYS ASN SEQRES 3 A 454 ASP TYR GLU VAL ASP VAL HIS ASP PRO LYS ALA TYR HIS SEQRES 4 A 454 GLY GLY ASP LEU GLN GLY ILE ILE ASP LYS LEU ASP TYR SEQRES 5 A 454 ILE LYS GLU MET GLY PHE THR ALA ILE TRP LEU THR PRO SEQRES 6 A 454 ILE PHE ALA ASN GLU LYS GLY GLY TYR HIS GLY TYR TRP SEQRES 7 A 454 ILE GLU ASP PHE TYR LYS VAL GLU GLU HIS PHE GLY THR SEQRES 8 A 454 LEU ASP ASP PHE LYS ARG LEU VAL LYS GLU ALA HIS LYS SEQRES 9 A 454 ARG ASP MET LYS VAL ILE LEU ASP PHE VAL VAL ASN HIS SEQRES 10 A 454 THR GLY TYR ASN HIS PRO TRP LEU ASN ASP PRO ALA LYS SEQRES 11 A 454 LYS ASP TRP PHE HIS GLU LYS LYS ASP ILE PHE ASN TRP SEQRES 12 A 454 ALA ASN GLN GLN GLU VAL GLU ASN GLY TRP LEU PHE GLY SEQRES 13 A 454 LEU PRO ASP LEU ALA GLN GLU ASN PRO GLU VAL LYS THR SEQRES 14 A 454 TYR LEU PHE ASP VAL ALA LYS TRP TRP ILE GLN GLU THR SEQRES 15 A 454 ASP ILE ASP GLY TYR ARG LEU ASP THR VAL LYS HIS VAL SEQRES 16 A 454 PRO LYS TRP PHE TRP ASP GLU PHE ALA LYS GLU VAL LYS SEQRES 17 A 454 SER VAL LYS GLN ASP PHE PHE LEU LEU GLY GLU VAL TRP SEQRES 18 A 454 HIS ASP ASP PRO ARG TYR VAL ALA GLU TYR GLY LYS HIS SEQRES 19 A 454 GLY ILE ASP ALA LEU ILE ASP PHE PRO PHE TYR LYS GLU SEQRES 20 A 454 ALA SER THR ILE PHE SER ASN VAL ASP GLN SER LEU GLU SEQRES 21 A 454 PRO LEU TYR ASN VAL TRP LYS ARG ASN VAL ALA PHE TYR SEQRES 22 A 454 GLU ARG PRO TYR LEU LEU GLY THR PHE LEU ASP ASN HIS SEQRES 23 A 454 ASP THR VAL ARG PHE THR ARG LEU ALA LEU GLN ASN ARG SEQRES 24 A 454 ILE ASN PRO VAL THR ARG LEU LYS LEU GLY LEU THR TYR SEQRES 25 A 454 LEU PHE SER ALA PRO GLY ILE PRO ILE MET TYR TYR GLY SEQRES 26 A 454 THR GLU ILE ALA LEU ASP GLY GLY GLU ASP PRO ASP ASN SEQRES 27 A 454 ARG ARG LEU MET ASN PHE ARG THR ASP LYS GLU LEU ILE SEQRES 28 A 454 ASP TYR VAL THR LYS LEU GLY GLU LEU ARG ALA LYS LEU SEQRES 29 A 454 PRO SER LEU ARG ARG GLY ASP PHE GLU LEU LEU TYR GLU SEQRES 30 A 454 LYS ASP GLY MET ALA LEU PHE LYS ARG THR TYR GLU LYS SEQRES 31 A 454 GLU THR THR VAL ILE ALA ILE ASN ASN THR SER LYS THR SEQRES 32 A 454 GLN LYS VAL THR LEU ASP GLY GLU LEU GLU GLN GLY LYS SEQRES 33 A 454 GLU LEU ARG GLY LEU LEU ALA GLY ASP LEU VAL ARG SER SEQRES 34 A 454 LYS ASP GLY LYS TYR ASP ILE ILE LEU ASP ARG GLU THR SEQRES 35 A 454 ALA GLU ILE TYR VAL LEU ALA PRO LYS THR GLY LEU HET ACT A1478 4 HET ACT A1479 4 HET CA A1480 1 HET CA A1481 1 HET CA A1482 1 HET CA A1483 1 HETNAM ACT ACETATE ION HETNAM CA CALCIUM ION FORMUL 2 ACT 2(C2 H3 O2 1-) FORMUL 4 CA 4(CA 2+) FORMUL 8 HOH *405(H2 O) HELIX 1 1 THR A 28 GLU A 32 5 5 HELIX 2 2 MET A 38 ASN A 43 1 6 HELIX 3 3 ASN A 46 ASP A 50 5 5 HELIX 4 4 ASP A 65 ASP A 71 1 7 HELIX 5 5 LYS A 72 MET A 79 1 8 HELIX 6 6 THR A 114 ARG A 128 1 15 HELIX 7 7 HIS A 145 ASP A 150 5 6 HELIX 8 8 ASP A 150 TRP A 156 5 7 HELIX 9 9 ASN A 168 GLY A 175 1 8 HELIX 10 10 TRP A 176 LEU A 180 5 5 HELIX 11 11 ASN A 187 ASP A 206 1 20 HELIX 12 12 THR A 214 VAL A 218 5 5 HELIX 13 13 PRO A 219 LYS A 234 1 16 HELIX 14 14 ASP A 247 GLU A 253 1 7 HELIX 15 15 TYR A 254 HIS A 257 5 4 HELIX 16 16 ASP A 264 SER A 276 1 13 HELIX 17 17 LEU A 282 TYR A 296 1 15 HELIX 18 18 ARG A 313 ASN A 321 1 9 HELIX 19 19 ASN A 324 ALA A 339 1 16 HELIX 20 20 GLY A 348 ALA A 352 5 5 HELIX 21 21 LYS A 371 LEU A 387 1 17 HELIX 22 22 LEU A 387 GLY A 393 1 7 SHEET 1 AA 9 ILE A 34 ILE A 37 0 SHEET 2 AA 9 ALA A 83 LEU A 86 1 O ALA A 83 N TYR A 35 SHEET 3 AA 9 LYS A 131 PHE A 136 1 O LYS A 131 N ILE A 84 SHEET 4 AA 9 GLY A 209 LEU A 212 1 O GLY A 209 N LEU A 134 SHEET 5 AA 9 PHE A 238 GLY A 241 1 O PHE A 238 N TYR A 210 SHEET 6 AA 9 ALA A 261 ILE A 263 1 O ALA A 261 N GLY A 241 SHEET 7 AA 9 LEU A 302 THR A 304 1 N GLY A 303 O LEU A 262 SHEET 8 AA 9 ILE A 342 TYR A 346 1 O ILE A 342 N THR A 304 SHEET 9 AA 9 ILE A 34 ILE A 37 1 O ILE A 34 N MET A 345 SHEET 1 AB 2 PHE A 90 ASN A 92 0 SHEET 2 AB 2 ILE A 102 VAL A 108 -1 N GLU A 103 O ALA A 91 SHEET 1 AC 6 GLU A 396 LYS A 401 0 SHEET 2 AC 6 MET A 404 TYR A 411 -1 O MET A 404 N LYS A 401 SHEET 3 AC 6 GLU A 414 ASN A 421 -1 O GLU A 414 N TYR A 411 SHEET 4 AC 6 ALA A 466 PRO A 473 -1 O GLU A 467 N ALA A 419 SHEET 5 AC 6 LYS A 439 GLY A 443 -1 O GLU A 440 N ALA A 472 SHEET 6 AC 6 LEU A 449 ARG A 451 -1 O VAL A 450 N LEU A 441 SHEET 1 AD 2 GLN A 427 ASP A 432 0 SHEET 2 AD 2 LYS A 456 LEU A 461 -1 O TYR A 457 N LEU A 431 LINK OD1 ASN A 44 CA CA A1481 1555 1555 2.61 LINK O ASN A 46 CA CA A1481 1555 1555 2.58 LINK OD1 ASN A 49 CA CA A1481 1555 1555 2.44 LINK OD1 ASP A 50 CA CA A1481 1555 1555 2.17 LINK O GLY A 63 CA CA A1481 1555 1555 2.56 LINK OD2 ASP A 65 CA CA A1481 1555 1555 2.25 LINK O ASN A 92 CA CA A1482 1555 1555 2.37 LINK OE2 GLU A 109 CA CA A1482 1555 1555 2.88 LINK OE1 GLU A 109 CA CA A1482 1555 1555 2.41 LINK OE1 GLU A 110 CA CA A1482 1555 1555 2.57 LINK OE2 GLU A 110 CA CA A1482 1555 1555 2.80 LINK OD1 ASN A 139 CA CA A1480 1555 1555 2.38 LINK O GLU A 173 CA CA A1480 1555 1555 2.46 LINK OD1 ASP A 182 CA CA A1480 1555 1555 2.72 LINK OD2 ASP A 182 CA CA A1480 1555 1555 2.61 LINK O HIS A 217 CA CA A1480 1555 1555 2.42 LINK O GLU A 400 CA CA A1483 1555 1555 2.28 LINK CA CA A1480 O HOH A2154 1555 1555 2.63 LINK CA CA A1480 O HOH A2155 1555 1555 2.60 LINK CA CA A1480 O HOH A2186 1555 1555 2.47 LINK CA CA A1481 O HOH A2042 1555 1555 2.48 LINK CA CA A1482 O HOH A2060 1555 1555 2.81 LINK CA CA A1482 O HOH A2091 1555 1555 2.53 LINK CA CA A1482 O HOH A2092 1555 1555 2.32 LINK CA CA A1483 O HOH A2261 1555 1555 2.52 LINK CA CA A1483 O HOH A2341 1555 3554 2.81 LINK CA CA A1483 O HOH A2360 1555 1555 2.53 LINK CA CA A1483 O HOH A2361 1555 1555 2.46 LINK CA CA A1483 O HOH A2362 1555 1555 2.29 CISPEP 1 ASP A 358 PRO A 359 0 9.95 SITE 1 AC1 4 ASP A 358 ARG A 362 ACT A1479 HOH A2299 SITE 1 AC2 7 TYR A 100 HIS A 140 ASP A 213 ACT A1478 SITE 2 AC2 7 HOH A2208 HOH A2210 HOH A2403 SITE 1 AC3 7 ASN A 139 GLU A 173 ASP A 182 HIS A 217 SITE 2 AC3 7 HOH A2154 HOH A2155 HOH A2186 SITE 1 AC4 7 ASN A 44 ASN A 46 ASN A 49 ASP A 50 SITE 2 AC4 7 GLY A 63 ASP A 65 HOH A2042 SITE 1 AC5 6 ASN A 92 GLU A 109 GLU A 110 HOH A2060 SITE 2 AC5 6 HOH A2091 HOH A2092 SITE 1 AC6 6 GLU A 400 HOH A2261 HOH A2341 HOH A2360 SITE 2 AC6 6 HOH A2361 HOH A2362 CRYST1 61.429 63.443 122.758 90.00 90.00 90.00 P 21 21 21 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 0.016279 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008146 0.00000