HEADER HYDROLASE 12-NOV-07 3BCF TITLE ALPHA-AMYLASE B FROM HALOTHERMOTHRIX ORENII COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA AMYLASE, CATALYTIC REGION; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMYB; COMPND 5 EC: 3.2.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOTHERMOTHRIX ORENII; SOURCE 3 ORGANISM_TAXID: 373903; SOURCE 4 STRAIN: H 168; SOURCE 5 GENE: AMYB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-19B KEYWDS ALPHA-AMYLASE, THERMOSTABLE, HALOPHILIC, N DOMAIN, RAW STARCH KEYWDS 2 BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.-C.TAN,B.N.MIJTS,K.SWAMINATHAN,B.K.C.PATEL,C.DIVNE REVDAT 4 01-NOV-23 3BCF 1 REMARK LINK REVDAT 3 18-MAY-11 3BCF 1 REMARK REVDAT 2 24-FEB-09 3BCF 1 VERSN REVDAT 1 22-APR-08 3BCF 0 JRNL AUTH T.-C.TAN,B.N.MIJTS,K.SWAMINATHAN,B.K.C.PATEL,C.DIVNE JRNL TITL CRYSTAL STRUCTURE OF THE POLYEXTREMOPHILIC ALPHA-AMYLASE JRNL TITL 2 AMYB FROM HALOTHERMOTHRIX ORENII: DETAILS OF A PRODUCTIVE JRNL TITL 3 ENZYME-SUBSTRATE COMPLEX AND AN N DOMAIN WITH A ROLE IN JRNL TITL 4 BINDING RAW STARCH JRNL REF J.MOL.BIOL. V. 378 850 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18387632 JRNL DOI 10.1016/J.JMB.2008.02.041 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 35637 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1902 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2692 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4747 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.78000 REMARK 3 B22 (A**2) : 1.97000 REMARK 3 B33 (A**2) : -1.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.255 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.865 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4903 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3167 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6645 ; 1.796 ; 1.923 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7674 ; 1.008 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 6.932 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 273 ;37.502 ;25.055 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 750 ;15.667 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.635 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 684 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5589 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1052 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1016 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3440 ; 0.206 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2375 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2468 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 283 ; 0.189 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.086 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.189 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 26 ; 0.255 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.204 ; 0.200 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): 2917 ; 1.066 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1197 ; 0.268 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4662 ; 1.800 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2109 ; 2.714 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1983 ; 3.990 ; 4.500 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 : 4 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 111 A 232 REMARK 3 ORIGIN FOR THE GROUP (A): 38.0549 6.2073 22.1713 REMARK 3 T TENSOR REMARK 3 T11: .0400 T22: -.1269 REMARK 3 T33: -.0326 T12: -.1036 REMARK 3 T13: -.0020 T23: -.1123 REMARK 3 L TENSOR REMARK 3 L11: 2.4070 L22: 1.9069 REMARK 3 L33: 1.1705 L12: 1.4004 REMARK 3 L13: -.8490 L23: -.7909 REMARK 3 S TENSOR REMARK 3 S11: .2460 S12: -.5533 S13: .3238 REMARK 3 S21: .3976 S22: -.2411 S23: -.0655 REMARK 3 S31: -.2631 S32: .0953 S33: -.0049 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 333 A 503 REMARK 3 ORIGIN FOR THE GROUP (A): 34.3093 -3.3712 9.4233 REMARK 3 T TENSOR REMARK 3 T11: -.0372 T22: -.1424 REMARK 3 T33: -.0259 T12: -.0195 REMARK 3 T13: -.0108 T23: -.0306 REMARK 3 L TENSOR REMARK 3 L11: 2.3936 L22: .6408 REMARK 3 L33: 1.0869 L12: .8993 REMARK 3 L13: -.6252 L23: -.1819 REMARK 3 S TENSOR REMARK 3 S11: -.0492 S12: -.0250 S13: .0683 REMARK 3 S21: -.0394 S22: .0426 S23: -.1712 REMARK 3 S31: .1263 S32: -.3108 S33: .0066 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 504 A 599 REMARK 3 ORIGIN FOR THE GROUP (A): 15.1878 -19.7790 15.0958 REMARK 3 T TENSOR REMARK 3 T11: .0093 T22: .0690 REMARK 3 T33: -.1506 T12: -.2704 REMARK 3 T13: .0386 T23: -.0118 REMARK 3 L TENSOR REMARK 3 L11: 2.6191 L22: 2.2231 REMARK 3 L33: 3.8250 L12: .0626 REMARK 3 L13: .2246 L23: -.9933 REMARK 3 S TENSOR REMARK 3 S11: -.2174 S12: .0102 S13: -.4588 REMARK 3 S21: -.1027 S22: .1728 S23: -.0082 REMARK 3 S31: .9784 S32: -.9842 S33: .0446 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 15 A 110 REMARK 3 ORIGIN FOR THE GROUP (A): .7503 -2.7851 34.5544 REMARK 3 T TENSOR REMARK 3 T11: -.2241 T22: .2660 REMARK 3 T33: -.2789 T12: -.0737 REMARK 3 T13: -.0300 T23: -.0544 REMARK 3 L TENSOR REMARK 3 L11: 4.4290 L22: 3.9552 REMARK 3 L33: 3.7745 L12: -1.6850 REMARK 3 L13: -.3152 L23: .2213 REMARK 3 S TENSOR REMARK 3 S11: .0064 S12: -.4543 S13: .0864 REMARK 3 S21: -.0489 S22: -.0714 S23: .2259 REMARK 3 S31: -.3024 S32: -.3758 S33: .0649 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 REMARK 4 REMARK 4 3BCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51305 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10600 REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30800 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1VJS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) MONOMETHYLETHER PEG 5000, REMARK 280 0.1M MES-OH, 0.2M AMMONIUM SULFATE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 113.31000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.91000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 113.31000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.91000 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 GLY A 1 REMARK 465 CYS A 2 REMARK 465 SER A 3 REMARK 465 ASN A 4 REMARK 465 ILE A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 ASP A 8 REMARK 465 VAL A 9 REMARK 465 ASN A 10 REMARK 465 ASN A 11 REMARK 465 PRO A 12 REMARK 465 ASN A 13 REMARK 465 ARG A 14 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 ALA A 237 O HOH A 791 2.14 REMARK 500 O ARG A 373 O HOH A 709 2.19 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 TRP A 363 CB TRP A 363 CG -0.109 REMARK 500 VAL A 378 CB VAL A 378 CG1 0.138 REMARK 500 GLU A 492 CG GLU A 492 CD 0.121 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 MET A 176 CG - SD - CE ANGL. DEV. = 13.3 DEGREES REMARK 500 ASP A 188 CB - CG - OD2 ANGL. DEV. = -6.7 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 ASN A 77 35.75 76.67 REMARK 500 ALA A 128 37.37 -90.21 REMARK 500 ASN A 147 68.81 -157.95 REMARK 500 TYR A 272 -41.15 79.79 REMARK 500 LEU A 315 -58.33 -122.25 REMARK 500 LEU A 535 149.10 -170.09 REMARK 500 LYS A 569 49.56 -95.31 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 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 232 OD1 REMARK 620 2 ASP A 313 O 98.4 REMARK 620 3 ASP A 313 OD1 169.7 86.9 REMARK 620 4 ASP A 319 OD1 88.1 84.1 101.4 REMARK 620 5 HIS A 354 O 83.7 86.9 87.8 166.8 REMARK 620 6 HOH A 727 O 82.9 171.5 93.2 87.6 101.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD1 REMARK 620 2 ASP A 283 OD2 54.9 REMARK 620 3 SER A 303 O 84.9 86.9 REMARK 620 4 ASP A 305 OD1 135.1 80.8 101.2 REMARK 620 5 ASP A 321 OD1 90.5 97.1 170.6 87.8 REMARK 620 6 GLU A 323 OE1 146.8 152.9 81.6 77.5 98.2 REMARK 620 7 HOH A 742 O 72.2 127.1 86.6 151.7 84.3 76.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD2 REMARK 620 2 ASP A 305 OD2 84.5 REMARK 620 3 ASP A 313 OD1 136.2 93.0 REMARK 620 4 ASP A 313 OD2 88.8 88.2 47.3 REMARK 620 5 ASP A 319 OD2 118.5 155.4 64.9 84.3 REMARK 620 6 VAL A 320 O 109.7 95.7 114.0 161.3 84.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 703 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 419 O REMARK 620 2 ALA A 517 O 75.1 REMARK 620 3 ASP A 518 OD1 146.4 77.7 REMARK 620 4 ASP A 541 OD1 76.9 118.6 134.5 REMARK 620 5 ASP A 541 OD2 120.7 98.7 82.5 54.3 REMARK 620 6 HOH A 790 O 111.4 163.2 90.3 78.2 91.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 705 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 527 O REMARK 620 2 VAL A 530 O 76.7 REMARK 620 3 ASP A 533 OD1 102.9 91.3 REMARK 620 4 HOH A 959 O 168.3 111.5 85.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 705 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BC9 RELATED DB: PDB REMARK 900 ALPHA-AMYLASE B IN COMPLEX WITH ACARBOSE REMARK 900 RELATED ID: 3BCD RELATED DB: PDB REMARK 900 ALPHA-AMYLASE B IN COMPLEX WITH MALTOTETRAOSE AND ALPHA-CYCLODEXTRIN DBREF 3BCF A 1 599 UNP Q2ADF2 Q2ADF2_9FIRM 25 623 SEQRES 1 A 599 GLY CYS SER ASN ILE SER GLU ASP VAL ASN ASN PRO ASN SEQRES 2 A 599 ARG SER LEU PHE LEU ILE GLU SER GLU PRO SER THR GLY SEQRES 3 A 599 ALA SER VAL SER LYS ASN LEU THR GLU ILE ILE LEU ILE SEQRES 4 A 599 PHE SER ASN ASP ILE ASN LYS VAL SER GLN LEU ALA LEU SEQRES 5 A 599 THR ASP LEU ILE THR ASP SER ASP ILE GLN GLY ILE ASP SEQRES 6 A 599 TYR ASN ILE GLU GLY ASN LYS VAL ILE ILE ASN ASN PHE SEQRES 7 A 599 SER LEU GLU PRO THR CYS ASN TYR ARG LEU SER TYR GLU SEQRES 8 A 599 VAL ILE ASP ILE TYR ASP ASN HIS LEU GLN GLY TYR ILE SEQRES 9 A 599 GLU PHE LEU VAL ASN GLN SER ASN TYR PRO GLN ILE PRO SEQRES 10 A 599 ASP GLN GLU VAL ASN HIS THR ILE LEU GLN ALA PHE TYR SEQRES 11 A 599 TRP GLU MET ASN THR GLY GLU TYR ALA THR GLU HIS PRO SEQRES 12 A 599 GLU GLU ALA ASN LEU TRP ASN LEU LEU ALA GLU ARG ALA SEQRES 13 A 599 PRO GLU LEU ALA GLU ALA GLY PHE THR ALA VAL TRP LEU SEQRES 14 A 599 PRO PRO ALA ASN LYS GLY MET ALA GLY ILE HIS ASP VAL SEQRES 15 A 599 GLY TYR GLY THR TYR ASP LEU TRP ASP LEU GLY GLU PHE SEQRES 16 A 599 ASP GLN LYS GLY THR VAL ARG THR LYS TYR GLY THR LYS SEQRES 17 A 599 GLY GLU LEU GLU ASN ALA ILE ASP ALA LEU HIS ASN ASN SEQRES 18 A 599 ASP ILE LYS VAL TYR PHE ASP ALA VAL LEU ASN HIS ARG SEQRES 19 A 599 MET GLY ALA ASP TYR ALA GLU THR VAL LEU LEU ASP GLU SEQRES 20 A 599 ASN SER ARG ASP LYS PRO GLY GLN TYR ILE LYS ALA TRP SEQRES 21 A 599 THR GLY PHE ASN PHE PRO GLY ARG ASN GLY GLU TYR SER SEQRES 22 A 599 ASN PHE THR TRP ASN GLY GLN CYS PHE ASP GLY THR ASP SEQRES 23 A 599 TRP ASP ASP TYR SER LYS GLU SER GLY LYS TYR LEU PHE SEQRES 24 A 599 ASP GLU LYS SER TRP ASP TRP THR TYR ASN TRP ASP GLU SEQRES 25 A 599 ASP TYR LEU MET GLY ALA ASP VAL ASP TYR GLU ASN GLU SEQRES 26 A 599 ALA VAL GLN ASN ASP VAL ILE ASP TRP GLY GLN TRP ILE SEQRES 27 A 599 ILE ASN ASN ILE ASP PHE ASP GLY PHE ARG LEU ASP ALA SEQRES 28 A 599 VAL LYS HIS ILE ASP TYR ARG PHE ILE ASP LYS TRP MET SEQRES 29 A 599 SER ALA VAL GLN ASN SER SER ASN ARG ASP VAL PHE PHE SEQRES 30 A 599 VAL GLY GLU ALA TRP VAL GLU ASP VAL ASP ASP LEU LYS SEQRES 31 A 599 GLY PHE LEU ASP THR VAL GLY ASN PRO ASP LEU ARG VAL SEQRES 32 A 599 PHE ASP PHE PRO LEU ARG SER PHE PHE VAL ASP MET LEU SEQRES 33 A 599 ASN GLY ALA TYR MET ALA ASP LEU ARG ASN ALA GLY LEU SEQRES 34 A 599 VAL ASN SER PRO GLY TYR GLU ASN ARG ALA VAL THR PHE SEQRES 35 A 599 VAL ASP ASN HIS ASP THR ASP ARG ASP GLU GLY SER TYR SEQRES 36 A 599 THR VAL SER ILE TYR SER ARG LYS TYR GLN ALA TYR ALA SEQRES 37 A 599 TYR ILE LEU THR ARG ALA GLU GLY VAL PRO THR VAL TYR SEQRES 38 A 599 TRP LYS ASP TYR TYR ILE TRP GLU MET LYS GLU GLY LEU SEQRES 39 A 599 ASP LYS LEU LEU THR ALA ARG ARG TYR TYR ALA TYR GLY SEQRES 40 A 599 PRO GLY TYR GLU VAL ASP ASN ASN ASP ALA ASP ILE TYR SEQRES 41 A 599 SER TYR VAL ARG SER GLY PHE PRO ASP VAL ALA GLY ASP SEQRES 42 A 599 GLY LEU VAL LEU MET ILE SER ASP GLY THR SER GLY ASN SEQRES 43 A 599 VAL ALA GLY LYS TRP ILE ASN SER ARG GLN PRO ASP THR SEQRES 44 A 599 GLU PHE TYR ASP LEU THR GLY HIS ILE LYS GLU HIS VAL SEQRES 45 A 599 THR THR ASP SER GLU GLY TYR GLY ASN PHE LYS VAL ILE SEQRES 46 A 599 LYS SER GLU ASP LYS GLY TRP SER ILE TRP VAL PRO VAL SEQRES 47 A 599 GLU HET CA A 701 1 HET CA A 702 1 HET CA A 703 1 HET NA A 704 1 HET CA A 705 1 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 2 CA 4(CA 2+) FORMUL 5 NA NA 1+ FORMUL 7 HOH *256(H2 O) HELIX 1 1 THR A 135 HIS A 142 1 8 HELIX 2 2 PRO A 143 ALA A 146 5 4 HELIX 3 3 ASN A 147 GLY A 163 1 17 HELIX 4 4 ALA A 177 ASP A 181 5 5 HELIX 5 5 THR A 207 ASN A 221 1 15 HELIX 6 6 ASN A 278 GLN A 280 5 3 HELIX 7 7 ASN A 324 ASN A 341 1 18 HELIX 8 8 ALA A 351 ILE A 355 5 5 HELIX 9 9 ASP A 356 SER A 371 1 16 HELIX 10 10 ASP A 385 GLY A 397 1 13 HELIX 11 11 ASP A 405 MET A 415 1 11 HELIX 12 12 LEU A 416 GLY A 418 5 3 HELIX 13 13 TYR A 420 ASN A 426 5 7 HELIX 14 14 GLY A 428 SER A 432 5 5 HELIX 15 15 TYR A 435 ASN A 437 5 3 HELIX 16 16 ARG A 462 ARG A 473 1 12 HELIX 17 17 TRP A 482 ILE A 487 1 6 HELIX 18 18 MET A 490 TYR A 504 1 15 SHEET 1 A 4 LEU A 18 GLU A 22 0 SHEET 2 A 4 GLU A 35 PHE A 40 -1 O ILE A 37 N GLU A 22 SHEET 3 A 4 LYS A 72 ASN A 76 -1 O ILE A 75 N ILE A 36 SHEET 4 A 4 ASP A 65 GLU A 69 -1 N ASP A 65 O ASN A 76 SHEET 1 B 5 SER A 28 VAL A 29 0 SHEET 2 B 5 HIS A 99 VAL A 108 1 O LEU A 107 N VAL A 29 SHEET 3 B 5 ASN A 85 ASP A 94 -1 N TYR A 86 O PHE A 106 SHEET 4 B 5 ILE A 44 ASP A 54 -1 N THR A 53 O ARG A 87 SHEET 5 B 5 SER A 59 ASP A 60 -1 O SER A 59 N ASP A 54 SHEET 1 C 9 ILE A 125 GLN A 127 0 SHEET 2 C 9 ALA A 166 TRP A 168 1 O TRP A 168 N LEU A 126 SHEET 3 C 9 LYS A 224 ALA A 229 1 O TYR A 226 N VAL A 167 SHEET 4 C 9 GLY A 346 LEU A 349 1 O ARG A 348 N PHE A 227 SHEET 5 C 9 PHE A 376 GLY A 379 1 O VAL A 378 N LEU A 349 SHEET 6 C 9 LEU A 401 PHE A 404 1 O ARG A 402 N GLY A 379 SHEET 7 C 9 ALA A 439 THR A 441 1 O VAL A 440 N VAL A 403 SHEET 8 C 9 VAL A 477 TYR A 481 1 O THR A 479 N THR A 441 SHEET 9 C 9 ILE A 125 GLN A 127 1 N GLN A 127 O VAL A 480 SHEET 1 D 2 LYS A 174 GLY A 175 0 SHEET 2 D 2 THR A 186 ASP A 188 -1 O TYR A 187 N LYS A 174 SHEET 1 E 4 HIS A 233 ARG A 234 0 SHEET 2 E 4 ALA A 318 VAL A 320 -1 O ALA A 318 N ARG A 234 SHEET 3 E 4 PHE A 282 ASP A 288 -1 N ASP A 283 O ASP A 319 SHEET 4 E 4 GLU A 293 LEU A 298 -1 O TYR A 297 N THR A 285 SHEET 1 F 2 TYR A 239 LEU A 244 0 SHEET 2 F 2 TYR A 256 GLY A 262 -1 O GLY A 262 N TYR A 239 SHEET 1 G 6 GLY A 509 GLU A 511 0 SHEET 2 G 6 ILE A 519 ARG A 524 -1 O VAL A 523 N TYR A 510 SHEET 3 G 6 LEU A 535 SER A 540 -1 O LEU A 535 N ARG A 524 SHEET 4 G 6 TRP A 592 PRO A 597 -1 O TRP A 595 N VAL A 536 SHEET 5 G 6 GLU A 560 ASP A 563 -1 N TYR A 562 O VAL A 596 SHEET 6 G 6 HIS A 571 THR A 573 -1 O VAL A 572 N PHE A 561 SHEET 1 H 2 VAL A 547 ASN A 553 0 SHEET 2 H 2 TYR A 579 ILE A 585 -1 O VAL A 584 N ALA A 548 LINK OD1 ASN A 232 CA CA A 702 1555 1555 2.25 LINK OD1 ASP A 283 CA CA A 701 1555 1555 2.39 LINK OD2 ASP A 283 CA CA A 701 1555 1555 2.45 LINK OD2 ASP A 283 NA NA A 704 1555 1555 2.26 LINK O SER A 303 CA CA A 701 1555 1555 2.30 LINK OD1 ASP A 305 CA CA A 701 1555 1555 2.34 LINK OD2 ASP A 305 NA NA A 704 1555 1555 2.30 LINK O ASP A 313 CA CA A 702 1555 1555 2.27 LINK OD1 ASP A 313 CA CA A 702 1555 1555 2.26 LINK OD1 ASP A 313 NA NA A 704 1555 1555 2.99 LINK OD2 ASP A 313 NA NA A 704 1555 1555 2.27 LINK OD1 ASP A 319 CA CA A 702 1555 1555 2.36 LINK OD2 ASP A 319 NA NA A 704 1555 1555 2.29 LINK O VAL A 320 NA NA A 704 1555 1555 2.30 LINK OD1 ASP A 321 CA CA A 701 1555 1555 2.34 LINK OE1 GLU A 323 CA CA A 701 1555 1555 2.31 LINK O HIS A 354 CA CA A 702 1555 1555 2.39 LINK O ALA A 419 CA CA A 703 1555 1555 2.35 LINK O ALA A 517 CA CA A 703 1555 1555 2.28 LINK OD1 ASP A 518 CA CA A 703 1555 1555 2.33 LINK O PHE A 527 CA CA A 705 1555 1555 2.32 LINK O VAL A 530 CA CA A 705 1555 1555 2.37 LINK OD1 ASP A 533 CA CA A 705 1555 1555 2.28 LINK OD1 ASP A 541 CA CA A 703 1555 1555 2.35 LINK OD2 ASP A 541 CA CA A 703 1555 1555 2.39 LINK CA CA A 701 O HOH A 742 1555 1555 2.37 LINK CA CA A 702 O HOH A 727 1555 1555 2.35 LINK CA CA A 703 O HOH A 790 1555 1555 2.23 LINK CA CA A 705 O HOH A 959 1555 1555 2.31 CISPEP 1 GLU A 22 PRO A 23 0 7.69 SITE 1 AC1 6 ASP A 283 SER A 303 ASP A 305 ASP A 321 SITE 2 AC1 6 GLU A 323 HOH A 742 SITE 1 AC2 5 ASN A 232 ASP A 313 ASP A 319 HIS A 354 SITE 2 AC2 5 HOH A 727 SITE 1 AC3 6 ASN A 77 ALA A 419 ALA A 517 ASP A 518 SITE 2 AC3 6 ASP A 541 HOH A 790 SITE 1 AC4 4 ASP A 283 ASP A 305 ASP A 313 ASP A 319 SITE 1 AC5 3 PHE A 527 ASP A 533 HOH A 959 CRYST1 226.620 77.820 50.330 90.00 99.38 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.004413 0.000000 0.000729 0.00000 SCALE2 0.000000 0.012850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020138 0.00000