HEADER HYDROLASE 17-MAY-15 5A2C TITLE CRYSTAL STRUCTURE OF ANOXYBACILLUS ALPHA-AMYLASE PROVIDES INSIGHTS TITLE 2 INTO A NEW GLYCOSYL HYDROLASE SUBCLASS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-AMYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRUNCATED PROTEIN, RESIDUES 24-478; COMPND 5 EC: 3.2.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CATALYTIC DOMAIN A WITH TIM BARREL FOLD (RESIDUES 26 COMPND 8 TO 139,187 TO 393), DOMAIN B (RESIDUES 140 TO 186), AND DOMAIN C WITH COMPND 9 AN ALL-ALPHA-BETA FOLD (RESIDUES 394 TO 475) 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_PLASMID: PET28A; SOURCE 9 OTHER_DETAILS: ISOLATED FROM SUNGAI KLAH HOT SPRING MALAYSIA KEYWDS HYDROLASE, CALCIUM-BINDING SITE, 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 3 10-JAN-24 5A2C 1 HETSYN REVDAT 2 29-JUL-20 5A2C 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 FORMUL LINK SITE ATOM REVDAT 1 30-MAR-16 5A2C 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) : 61.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 35690 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1861 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) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2366 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3756 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 518 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.54000 REMARK 3 B22 (A**2) : -0.63000 REMARK 3 B33 (A**2) : 1.18000 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): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.483 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3917 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3648 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5316 ; 1.821 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8409 ; 0.884 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 459 ; 6.138 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;35.821 ;24.143 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 675 ;14.061 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.418 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 557 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4398 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 950 ; 0.001 ; 0.020 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): 1809 ; 1.292 ; 1.488 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1808 ; 1.284 ; 1.487 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2262 ; 1.875 ; 2.224 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2108 ; 1.991 ; 1.750 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 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 3 A 452 REMARK 3 ORIGIN FOR THE GROUP (A): -14.5510 -6.5820 -19.9090 REMARK 3 T TENSOR REMARK 3 T11: 0.0063 T22: 0.0191 REMARK 3 T33: 0.0056 T12: 0.0045 REMARK 3 T13: -0.0024 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.7438 L22: 0.2451 REMARK 3 L33: 0.5197 L12: 0.0601 REMARK 3 L13: 0.4489 L23: -0.0500 REMARK 3 S TENSOR REMARK 3 S11: 0.0027 S12: -0.0012 S13: -0.0160 REMARK 3 S21: -0.0179 S22: 0.0098 S23: -0.0129 REMARK 3 S31: 0.0008 S32: 0.0314 S33: -0.0125 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. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U REMARK 3 VALUES WITH TLS ADDED REMARK 4 REMARK 4 5A2C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1290063802. 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) : 1.548 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 37601 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 19.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 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) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 4E2O REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE TASKA-MALTODP3 NAMELY TASKA-T REMARK 280 COMPLEXES WAS CRYSTALLIZED USING THE STREAK SEEDING METHOD WITH REMARK 280 A COMMERCIALLY AVAILABLE SEEDING TOOL, HAMPTON RESEARCH, USA. REMARK 280 THE SEEDING TOOL WAS DIPPED INTO A DROP CONTAINING TASKA-APO,PDB REMARK 280 ID 5A2A, CRYSTALS AND STREAKED ON THE DROPS THAT CONSISTED OF REMARK 280 0.3 UL 6 MG/ML TASKA PROTEIN AND 0.3 UL RESERVOIR SOLUTION 0.1 M REMARK 280 CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, AND 18 % W/V REMARK 280 POLYETHYLENE GLYCOL 8,000 WITH 20 MM MALTOTRIOSE. 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 30.90800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.76600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.90800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.76600 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, B 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 MET A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 SER A 0 REMARK 465 SER A 1 REMARK 465 GLY A 2 REMARK 465 LEU A 3 REMARK 465 VAL A 4 REMARK 465 PRO A 5 REMARK 465 ARG A 6 REMARK 465 GLY A 7 REMARK 465 SER A 8 REMARK 465 HIS A 9 REMARK 465 MET A 10 REMARK 465 ALA A 11 REMARK 465 SER A 12 REMARK 465 MET A 13 REMARK 465 THR A 14 REMARK 465 GLY A 15 REMARK 465 GLY A 16 REMARK 465 GLN A 17 REMARK 465 GLN A 18 REMARK 465 MET A 19 REMARK 465 GLY A 20 REMARK 465 ARG A 21 REMARK 465 GLY A 22 REMARK 465 SER A 23 REMARK 465 LYS A 24 REMARK 465 THR A 25 REMARK 465 GLY A 476 REMARK 465 LEU A 477 REMARK 465 ASN A 478 REMARK 465 LEU A 479 REMARK 465 GLU A 480 REMARK 465 HIS A 481 REMARK 465 HIS A 482 REMARK 465 HIS A 483 REMARK 465 HIS A 484 REMARK 465 HIS A 485 REMARK 465 HIS A 486 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 CA CA A 1480 O HOH A 2451 1.64 REMARK 500 O HOH A 2319 O HOH A 2321 1.77 REMARK 500 O HOH A 2176 O HOH A 2341 1.99 REMARK 500 O HOH A 2176 O HOH A 2347 2.01 REMARK 500 O HOH A 2332 O HOH A 2451 2.05 REMARK 500 O HOH A 2448 O HOH A 2451 2.19 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 2341 O HOH A 2490 3454 1.44 REMARK 500 O HOH A 2354 O HOH A 2505 3454 1.93 REMARK 500 O HOH A 2355 O HOH A 2505 3454 2.06 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 ASP A 104 CB - CG - OD1 ANGL. DEV. = 6.2 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 -72.93 -97.59 REMARK 500 TRP A 101 73.15 -112.09 REMARK 500 PHE A 164 -71.87 -106.16 REMARK 500 LEU A 301 59.59 -95.24 REMARK 500 ASP A 358 120.42 -38.23 REMARK 500 GLU A 412 -120.52 48.92 REMARK 500 ASN A 422 46.60 -85.84 REMARK 500 ASP A 432 82.37 -154.17 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 A2123 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A2517 DISTANCE = 6.84 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 A1478 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 44 OD1 REMARK 620 2 ASN A 46 O 75.7 REMARK 620 3 ASN A 49 OD1 144.2 68.8 REMARK 620 4 ASP A 50 OD1 90.0 88.0 93.5 REMARK 620 5 GLY A 63 O 78.6 151.7 134.3 103.9 REMARK 620 6 ASP A 65 OD2 82.0 79.7 86.9 166.7 85.1 REMARK 620 7 HOH A2059 O 147.5 134.8 68.1 81.9 73.0 110.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1479 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 92 O REMARK 620 2 GLU A 109 OE1 85.8 REMARK 620 3 GLU A 109 OE2 125.6 48.0 REMARK 620 4 GLU A 110 OE2 157.9 116.0 72.6 REMARK 620 5 GLU A 110 OE1 143.9 80.5 65.2 51.0 REMARK 620 6 HOH A2089 O 78.4 89.8 75.2 96.8 134.3 REMARK 620 7 HOH A2128 O 84.1 169.4 138.6 74.0 109.6 85.2 REMARK 620 8 HOH A2129 O 74.1 100.3 131.9 103.9 75.7 149.8 79.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1477 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 139 OD1 REMARK 620 2 GLU A 173 O 152.4 REMARK 620 3 ASP A 182 OD1 75.1 117.6 REMARK 620 4 ASP A 182 OD2 123.4 78.8 51.1 REMARK 620 5 HIS A 217 O 77.8 78.8 142.9 157.6 REMARK 620 6 HOH A2200 O 72.7 132.3 77.0 78.6 118.1 REMARK 620 7 HOH A2201 O 89.2 74.9 68.2 86.4 86.7 144.0 REMARK 620 8 HOH A2249 O 121.5 68.4 135.3 91.9 80.9 71.0 142.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1480 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 400 O REMARK 620 2 HOH A2332 O 83.3 REMARK 620 3 HOH A2333 O 79.7 75.5 REMARK 620 4 HOH A2334 O 143.1 63.3 77.1 REMARK 620 5 HOH A2449 O 98.9 129.5 154.9 114.1 REMARK 620 6 HOH A2450 O 90.4 146.6 71.1 108.4 83.9 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A2A 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: 5A2B 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 SIMILAR TO TASKA-APO. PDB ID 5A2A DBREF 5A2C A 24 478 UNP I1VWH9 I1VWH9_9BACI 24 478 SEQADV 5A2C MET A -10 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLY A -9 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C SER A -8 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C SER A -7 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A -6 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A -5 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A -4 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A -3 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A -2 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A -1 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C SER A 0 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C SER A 1 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLY A 2 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C LEU A 3 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C VAL A 4 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C PRO A 5 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C ARG A 6 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLY A 7 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C SER A 8 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A 9 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C MET A 10 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C ALA A 11 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C SER A 12 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C MET A 13 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C THR A 14 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLY A 15 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLY A 16 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLN A 17 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLN A 18 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C MET A 19 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLY A 20 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C ARG A 21 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLY A 22 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C SER A 23 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C LEU A 479 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C GLU A 480 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A 481 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A 482 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A 483 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A 484 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A 485 UNP I1VWH9 EXPRESSION TAG SEQADV 5A2C HIS A 486 UNP I1VWH9 EXPRESSION TAG SEQRES 1 A 497 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 497 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 497 GLY GLN GLN MET GLY ARG GLY SER LYS THR GLU ARG THR SEQRES 4 A 497 TRP GLN ASP GLU ARG ILE TYR PHE ILE MET VAL ASP ARG SEQRES 5 A 497 PHE ASN ASN GLY ASN PRO LYS ASN ASP TYR GLU VAL ASP SEQRES 6 A 497 VAL HIS ASP PRO LYS ALA TYR HIS GLY GLY ASP LEU GLN SEQRES 7 A 497 GLY ILE ILE ASP LYS LEU ASP TYR ILE LYS GLU MET GLY SEQRES 8 A 497 PHE THR ALA ILE TRP LEU THR PRO ILE PHE ALA ASN GLU SEQRES 9 A 497 LYS GLY GLY TYR HIS GLY TYR TRP ILE GLU ASP PHE TYR SEQRES 10 A 497 LYS VAL GLU GLU HIS PHE GLY THR LEU ASP ASP PHE LYS SEQRES 11 A 497 ARG LEU VAL LYS GLU ALA HIS LYS ARG ASP MET LYS VAL SEQRES 12 A 497 ILE LEU ASP PHE VAL VAL ASN HIS THR GLY TYR ASN HIS SEQRES 13 A 497 PRO TRP LEU ASN ASP PRO ALA LYS LYS ASP TRP PHE HIS SEQRES 14 A 497 GLU LYS LYS ASP ILE PHE ASN TRP ALA ASN GLN GLN GLU SEQRES 15 A 497 VAL GLU ASN GLY TRP LEU PHE GLY LEU PRO ASP LEU ALA SEQRES 16 A 497 GLN GLU ASN PRO GLU VAL LYS THR TYR LEU PHE ASP VAL SEQRES 17 A 497 ALA LYS TRP TRP ILE GLN GLU THR ASP ILE ASP GLY TYR SEQRES 18 A 497 ARG LEU ASP THR VAL LYS HIS VAL PRO LYS TRP PHE TRP SEQRES 19 A 497 ASP GLU PHE ALA LYS GLU VAL LYS SER VAL LYS GLN ASP SEQRES 20 A 497 PHE PHE LEU LEU GLY GLU VAL TRP HIS ASP ASP PRO ARG SEQRES 21 A 497 TYR VAL ALA GLU TYR GLY LYS HIS GLY ILE ASP ALA LEU SEQRES 22 A 497 ILE ASP PHE PRO PHE TYR LYS GLU ALA SER THR ILE PHE SEQRES 23 A 497 SER ASN VAL ASP GLN SER LEU GLU PRO LEU TYR ASN VAL SEQRES 24 A 497 TRP LYS ARG ASN VAL ALA PHE TYR GLU ARG PRO TYR LEU SEQRES 25 A 497 LEU GLY THR PHE LEU ASP ASN HIS ASP THR VAL ARG PHE SEQRES 26 A 497 THR ARG LEU ALA LEU GLN ASN ARG ILE ASN PRO VAL THR SEQRES 27 A 497 ARG LEU LYS LEU GLY LEU THR TYR LEU PHE SER ALA PRO SEQRES 28 A 497 GLY ILE PRO ILE MET TYR TYR GLY THR GLU ILE ALA LEU SEQRES 29 A 497 ASP GLY GLY GLU ASP PRO ASP ASN ARG ARG LEU MET ASN SEQRES 30 A 497 PHE ARG THR ASP LYS GLU LEU ILE ASP TYR VAL THR LYS SEQRES 31 A 497 LEU GLY GLU LEU ARG ALA LYS LEU PRO SER LEU ARG ARG SEQRES 32 A 497 GLY ASP PHE GLU LEU LEU TYR GLU LYS ASP GLY MET ALA SEQRES 33 A 497 LEU PHE LYS ARG THR TYR GLU LYS GLU THR THR VAL ILE SEQRES 34 A 497 ALA ILE ASN ASN THR SER LYS THR GLN LYS VAL THR LEU SEQRES 35 A 497 ASP GLY GLU LEU GLU GLN GLY LYS GLU LEU ARG GLY LEU SEQRES 36 A 497 LEU ALA GLY ASP LEU VAL ARG SER LYS ASP GLY LYS TYR SEQRES 37 A 497 ASP ILE ILE LEU ASP ARG GLU THR ALA GLU ILE TYR VAL SEQRES 38 A 497 LEU ALA PRO LYS THR GLY LEU ASN LEU GLU HIS HIS HIS SEQRES 39 A 497 HIS HIS HIS HET GLC B 1 12 HET GLC B 2 11 HET CA A1477 1 HET CA A1478 1 HET CA A1479 1 HET CA A1480 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 2(C6 H12 O6) FORMUL 3 CA 4(CA 2+) FORMUL 7 HOH *518(H2 O) HELIX 1 1 THR A 28 GLU A 32 5 5 HELIX 2 2 MET A 38 PHE A 42 5 5 HELIX 3 3 ASN A 46 ASP A 50 5 5 HELIX 4 4 ASP A 65 LYS A 72 1 8 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 O4 GLC B 1 C1 GLC B 2 1555 1555 1.44 LINK OD1 ASN A 44 CA CA A1478 1555 1555 2.41 LINK O ASN A 46 CA CA A1478 1555 1555 2.51 LINK OD1 ASN A 49 CA CA A1478 1555 1555 2.44 LINK OD1 ASP A 50 CA CA A1478 1555 1555 2.27 LINK O GLY A 63 CA CA A1478 1555 1555 2.51 LINK OD2 ASP A 65 CA CA A1478 1555 1555 2.32 LINK O ASN A 92 CA CA A1479 1555 1555 2.37 LINK OE1 GLU A 109 CA CA A1479 1555 1555 2.48 LINK OE2 GLU A 109 CA CA A1479 1555 1555 2.98 LINK OE2 GLU A 110 CA CA A1479 1555 1555 2.50 LINK OE1 GLU A 110 CA CA A1479 1555 1555 2.45 LINK OD1 ASN A 139 CA CA A1477 1555 1555 2.40 LINK O GLU A 173 CA CA A1477 1555 1555 2.47 LINK OD1 ASP A 182 CA CA A1477 1555 1555 2.54 LINK OD2 ASP A 182 CA CA A1477 1555 1555 2.50 LINK O HIS A 217 CA CA A1477 1555 1555 2.52 LINK O GLU A 400 CA CA A1480 1555 1555 2.22 LINK CA CA A1477 O HOH A2200 1555 1555 2.45 LINK CA CA A1477 O HOH A2201 1555 1555 2.54 LINK CA CA A1477 O HOH A2249 1555 1555 2.52 LINK CA CA A1478 O HOH A2059 1555 1555 2.40 LINK CA CA A1479 O HOH A2089 1555 1555 2.52 LINK CA CA A1479 O HOH A2128 1555 1555 2.44 LINK CA CA A1479 O HOH A2129 1555 1555 2.35 LINK CA CA A1480 O HOH A2332 1555 1555 2.60 LINK CA CA A1480 O HOH A2333 1555 1555 2.55 LINK CA CA A1480 O HOH A2334 1555 1555 2.33 LINK CA CA A1480 O HOH A2449 1555 1555 2.40 LINK CA CA A1480 O HOH A2450 1555 1555 2.09 CISPEP 1 ASP A 358 PRO A 359 0 10.18 CRYST1 61.816 63.532 122.970 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 0.016177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015740 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008132 0.00000