PDB Short entry for 1E43 HEADER HYDROLASE 27-JUN-00 1E43 TITLE NATIVE STRUCTURE OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND B. TITLE 2 LICHENIFORMIS AT 1.7A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-AMYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CHIMAERIC STRUCTURE CONSISTING OF RESIDUES 1 - 300 OF COMPND 7 B. AMYLOLIQUEFACIENS AND RESIDUES 301 - 483 OF B. LICHENIFORMIS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS AMYLOLIQUEFACIENS; SOURCE 3 ORGANISM_TAXID: 1390; SOURCE 4 EXPRESSION_SYSTEM: BACILLUS AMYLOLIQUEFACIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1390; SOURCE 6 OTHER_DETAILS: SYNTHETIC GENE KEYWDS HYDROLASE, AMYLASE, FAMILY 13 EXPDTA X-RAY DIFFRACTION AUTHOR A.M.BRZOZOWSKI,D.M.LAWSON,J.P.TURKENBURG,H.BISGAARD-FRANTZEN, AUTHOR 2 A.SVENDSEN,T.V.BORCHERT,Z.DAUTER,K.S.WILSON,G.J.DAVIES REVDAT 4 13-DEC-23 1E43 1 REMARK LINK REVDAT 3 08-MAY-19 1E43 1 REMARK REVDAT 2 24-FEB-09 1E43 1 VERSN REVDAT 1 21-JUN-01 1E43 0 JRNL AUTH A.M.BRZOZOWSKI,D.M.LAWSON,J.P.TURKENBURG, JRNL AUTH 2 H.BISGAARD-FRANTZEN,A.SVENDSEN,T.V.BORCHERT,Z.DAUTER, JRNL AUTH 3 K.S.WILSON,G.J.DAVIES JRNL TITL STRUCTURAL ANALYSIS OF A CHIMERIC BACTERIAL ALPHA-AMYLASE. JRNL TITL 2 HIGH RESOLUTION ANALYSIS OF NATIVE AND LIGAND COMPLEXES JRNL REF BIOCHEMISTRY V. 39 9099 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10924103 JRNL DOI 10.1021/BI0000317 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 51292 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2491 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3900 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 933 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.010 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.026 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.028 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.012 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.105 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.174 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.207 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.104 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.000 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 13.300; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 29.500; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.073 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.476 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.695 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.532 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1E43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1290005109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 10.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9386 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC-Q4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.08100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 13.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: 1E3X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN AT 18C USING THE REMARK 280 HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE REMARK 280 GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH REMARK 280 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN REMARK 280 CONCENTRATION WAS 30-35MG/ML., PH 10.00, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 118.25000 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 118.25000 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 1.000000 0.000000 0.000000 26.10000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.05000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.10000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.05000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 118.25000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.10000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.05000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 118.25000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.10000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.05000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 214 CD CE NZ REMARK 480 ARG A 442 CG CD NE CZ NH1 NH2 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 NE ARG A 442 O HOH A 2871 1.27 REMARK 500 CD ARG A 442 O HOH A 2871 1.32 REMARK 500 CD LYS A 214 O HOH A 2580 1.57 REMARK 500 NH2 ARG A 442 O HOH A 2870 1.99 REMARK 500 NZ LYS A 214 O HOH A 2579 2.00 REMARK 500 CE LYS A 214 O HOH A 2579 2.02 REMARK 500 NZ LYS A 214 O HOH A 2578 2.11 REMARK 500 CE LYS A 214 O HOH A 2580 2.11 REMARK 500 CG ARG A 442 O HOH A 2871 2.14 REMARK 500 O HOH A 2274 O HOH A 2594 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 2072 O HOH A 2724 5555 1.97 REMARK 500 O HOH A 2305 O HOH A 2650 5455 2.11 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 LYS A 214 CG LYS A 214 CD 0.922 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 PHE A 9 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 LEU A 47 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 TYR A 131 CA - CB - CG ANGL. DEV. = 12.5 DEGREES REMARK 500 ASP A 162 CB - CG - OD2 ANGL. DEV. = -10.3 DEGREES REMARK 500 ARG A 167 CD - NE - CZ ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 167 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 167 NE - CZ - NH2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 176 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR A 193 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 TYR A 219 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 PHE A 238 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 PHE A 238 CB - CG - CD1 ANGL. DEV. = 4.6 DEGREES REMARK 500 TYR A 358 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 437 CA - CB - CG ANGL. DEV. = 21.1 DEGREES REMARK 500 ARG A 437 CD - NE - CZ ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 437 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 437 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 442 CD - NE - CZ ANGL. DEV. = 12.9 DEGREES REMARK 500 ASP A 451 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 483 CG - CD - NE ANGL. DEV. = 15.0 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 9 165.44 179.41 REMARK 500 ASN A 122 87.01 -158.20 REMARK 500 TYR A 148 -35.98 73.62 REMARK 500 LEU A 196 -57.78 -122.35 REMARK 500 TYR A 198 -146.07 51.69 REMARK 500 SER A 337 62.05 -171.43 REMARK 500 ARG A 375 38.53 -142.53 REMARK 500 ASP A 407 -54.40 -120.94 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 A2008 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A2013 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A2014 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A2023 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH A2029 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A2031 DISTANCE = 9.00 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A2049 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A2050 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A2055 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A2086 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A2087 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A2139 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2149 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A2203 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH A2376 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A2489 DISTANCE = 6.10 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 A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 102 OD1 REMARK 620 2 ASP A 194 O 99.8 REMARK 620 3 ASP A 194 OD1 163.3 84.6 REMARK 620 4 ASP A 200 OD1 90.8 78.4 105.9 REMARK 620 5 ASP A 200 OD2 128.8 89.2 66.9 41.7 REMARK 620 6 HIS A 235 O 82.6 90.1 81.3 165.5 148.2 REMARK 620 7 HOH A2341 O 83.8 159.5 97.8 81.4 73.3 110.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 159 OD2 REMARK 620 2 ASP A 159 OD1 52.8 REMARK 620 3 ALA A 181 O 93.1 80.7 REMARK 620 4 ASP A 183 OD1 79.3 131.0 115.1 REMARK 620 5 ASP A 202 OD1 89.8 84.3 158.6 86.3 REMARK 620 6 ASP A 204 OD2 154.0 153.3 93.7 75.1 93.0 REMARK 620 7 HOH A2559 O 127.4 74.9 82.5 148.8 79.0 78.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 159 OD2 REMARK 620 2 ASP A 183 OD2 87.6 REMARK 620 3 ASP A 194 OD2 85.4 93.1 REMARK 620 4 ASP A 200 OD2 113.1 159.3 88.2 REMARK 620 5 VAL A 201 O 107.7 86.4 166.8 87.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 300 O REMARK 620 2 TYR A 302 O 105.5 REMARK 620 3 HIS A 406 O 162.2 77.0 REMARK 620 4 ASP A 407 OD1 91.1 152.5 80.7 REMARK 620 5 ASP A 430 OD1 102.2 116.4 92.0 80.0 REMARK 620 6 ASP A 430 OD2 79.9 76.8 117.5 128.6 53.6 REMARK 620 7 HOH A2701 O 72.7 80.9 90.6 83.5 162.6 138.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 444 OD1 REMARK 620 2 GLU A 447 OE1 86.4 REMARK 620 3 GLU A 447 OE2 93.9 53.0 REMARK 620 4 HOH A2853 O 76.4 75.9 128.6 REMARK 620 5 HOH A2854 O 93.0 149.6 156.9 74.4 REMARK 620 6 HOH A2875 O 69.0 126.4 81.0 135.9 80.9 REMARK 620 7 HOH A2879 O 130.7 124.8 81.3 141.9 77.5 61.8 REMARK 620 8 HOH A2929 O 155.8 74.5 86.5 84.5 96.1 134.7 73.4 REMARK 620 N 1 2 3 4 5 6 7 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VJS RELATED DB: PDB REMARK 900 STRUCTURE OF ALPHA-AMYLASE PRECURSOR REMARK 900 RELATED ID: 1BPL RELATED DB: PDB REMARK 900 GLYCOSYLTRANSFERASE REMARK 900 RELATED ID: 1BLI RELATED DB: PDB REMARK 900 BACILLUS LICHENIFORMIS ALPHA-AMYLASE REMARK 900 RELATED ID: 1E3Z RELATED DB: PDB REMARK 900 ACARBOSE COMPLEX OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND REMARK 900 B. LICHENIFORMIS AT 1.93A REMARK 900 RELATED ID: 1E40 RELATED DB: PDB REMARK 900 TRIS/MALTOTRIOSE COMPLEX OF CHIMAERIC AMYLASE FROM B. REMARK 900 AMYLOLIQUEFACIENS AND B. LICHENIFORMIS AT 2.2A REMARK 900 RELATED ID: 1E3X RELATED DB: PDB REMARK 900 NATIVE STRUCTURE OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND REMARK 900 B. LICHENIFORMIS AT 1.92A DBREF 1E43 A 1 300 UNP P00692 AMY_BACAM 32 331 DBREF 1E43 A 301 483 UNP P06278 AMY_BACLI 330 512 SEQRES 1 A 483 VAL ASN GLY THR LEU MET GLN TYR PHE GLU TRP TYR THR SEQRES 2 A 483 PRO ASN ASP GLY GLN HIS TRP LYS ARG LEU GLN ASN ASP SEQRES 3 A 483 ALA GLU HIS LEU SER ASP ILE GLY ILE THR ALA VAL TRP SEQRES 4 A 483 ILE PRO PRO ALA TYR LYS GLY LEU SER GLN SER ASP ASN SEQRES 5 A 483 GLY TYR GLY PRO TYR ASP LEU TYR ASP LEU GLY GLU PHE SEQRES 6 A 483 GLN GLN LYS GLY THR VAL ARG THR LYS TYR GLY THR LYS SEQRES 7 A 483 SER GLU LEU GLN ASP ALA ILE GLY SER LEU HIS SER ARG SEQRES 8 A 483 ASN VAL GLN VAL TYR GLY ASP VAL VAL LEU ASN HIS LYS SEQRES 9 A 483 ALA GLY ALA ASP ALA THR GLU ASP VAL THR ALA VAL GLU SEQRES 10 A 483 VAL ASN PRO ALA ASN ARG ASN GLN GLU THR SER GLU GLU SEQRES 11 A 483 TYR GLN ILE LYS ALA TRP THR ASP PHE ARG PHE PRO GLY SEQRES 12 A 483 ARG GLY ASN THR TYR SER ASP PHE LYS TRP HIS TRP TYR SEQRES 13 A 483 HIS PHE ASP GLY ALA ASP TRP ASP GLU SER ARG LYS ILE SEQRES 14 A 483 SER ARG ILE PHE LYS PHE ARG GLY GLU GLY LYS ALA TRP SEQRES 15 A 483 ASP TRP GLU VAL SER SER GLU ASN GLY ASN TYR ASP TYR SEQRES 16 A 483 LEU MET TYR ALA ASP VAL ASP TYR ASP HIS PRO ASP VAL SEQRES 17 A 483 VAL ALA GLU THR LYS LYS TRP GLY ILE TRP TYR ALA ASN SEQRES 18 A 483 GLU LEU SER LEU ASP GLY PHE ARG ILE ASP ALA ALA LYS SEQRES 19 A 483 HIS ILE LYS PHE SER PHE LEU ARG ASP TRP VAL GLN ALA SEQRES 20 A 483 VAL ARG GLN ALA THR GLY LYS GLU MET PHE THR VAL ALA SEQRES 21 A 483 GLU TYR TRP GLN ASN ASN ALA GLY LYS LEU GLU ASN TYR SEQRES 22 A 483 LEU ASN LYS THR SER PHE ASN GLN SER VAL PHE ASP VAL SEQRES 23 A 483 PRO LEU HIS PHE ASN LEU GLN ALA ALA SER SER GLN GLY SEQRES 24 A 483 GLY GLY TYR ASP MET ARG LYS LEU LEU ASN GLY THR VAL SEQRES 25 A 483 VAL SER LYS HIS PRO LEU LYS SER VAL THR PHE VAL ASP SEQRES 26 A 483 ASN HIS ASP THR GLN PRO GLY GLN SER LEU GLU SER THR SEQRES 27 A 483 VAL GLN THR TRP PHE LYS PRO LEU ALA TYR ALA PHE ILE SEQRES 28 A 483 LEU THR ARG GLU SER GLY TYR PRO GLN VAL PHE TYR GLY SEQRES 29 A 483 ASP MET TYR GLY THR LYS GLY ASP SER GLN ARG GLU ILE SEQRES 30 A 483 PRO ALA LEU LYS HIS LYS ILE GLU PRO ILE LEU LYS ALA SEQRES 31 A 483 ARG LYS GLN TYR ALA TYR GLY ALA GLN HIS ASP TYR PHE SEQRES 32 A 483 ASP HIS HIS ASP ILE VAL GLY TRP THR ARG GLU GLY ASP SEQRES 33 A 483 SER SER VAL ALA ASN SER GLY LEU ALA ALA LEU ILE THR SEQRES 34 A 483 ASP GLY PRO GLY GLY ALA LYS ARG MET TYR VAL GLY ARG SEQRES 35 A 483 GLN ASN ALA GLY GLU THR TRP HIS ASP ILE THR GLY ASN SEQRES 36 A 483 ARG SER GLU PRO VAL VAL ILE ASN SER GLU GLY TRP GLY SEQRES 37 A 483 GLU PHE HIS VAL ASN GLY GLY SER VAL SER ILE TYR VAL SEQRES 38 A 483 GLN ARG HET CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HET NA A 505 1 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 2 CA 4(CA 2+) FORMUL 6 NA NA 1+ FORMUL 7 HOH *933(H2 O) HELIX 1 1 GLN A 18 GLY A 34 1 17 HELIX 2 2 THR A 77 ARG A 91 1 15 HELIX 3 3 HIS A 154 TYR A 156 5 3 HELIX 4 4 HIS A 205 SER A 224 1 20 HELIX 5 5 ALA A 232 ILE A 236 5 5 HELIX 6 6 LYS A 237 GLY A 253 1 17 HELIX 7 7 ASN A 266 THR A 277 1 12 HELIX 8 8 ASP A 285 GLN A 298 1 14 HELIX 9 9 ASP A 303 LEU A 307 5 5 HELIX 10 10 HIS A 316 LEU A 318 5 3 HELIX 11 11 PHE A 343 ARG A 354 1 12 HELIX 12 12 TYR A 363 GLY A 368 1 6 HELIX 13 13 LEU A 380 TYR A 394 1 15 HELIX 14 14 GLY A 441 ALA A 445 5 5 SHEET 1 A 7 VAL A 321 PHE A 323 0 SHEET 2 A 7 TYR A 358 PHE A 362 1 N TYR A 358 O THR A 322 SHEET 3 A 7 LEU A 5 GLN A 7 1 N LEU A 5 O VAL A 361 SHEET 4 A 7 ALA A 37 ILE A 40 1 N ALA A 37 O MET A 6 SHEET 5 A 7 GLN A 94 VAL A 99 1 N GLN A 94 O VAL A 38 SHEET 6 A 7 GLY A 227 ILE A 230 1 N GLY A 227 O GLY A 97 SHEET 7 A 7 PHE A 257 ALA A 260 1 N PHE A 257 O PHE A 228 SHEET 1 B 3 ILE A 172 PHE A 175 0 SHEET 2 B 3 ALA A 109 VAL A 118 -1 N VAL A 118 O ILE A 172 SHEET 3 B 3 TYR A 131 ASP A 138 -1 N ASP A 138 O ALA A 109 SHEET 1 C 5 GLN A 399 TYR A 402 0 SHEET 2 C 5 ILE A 408 ARG A 413 -1 N THR A 412 O HIS A 400 SHEET 3 C 5 LEU A 424 THR A 429 -1 N ILE A 428 O VAL A 409 SHEET 4 C 5 VAL A 477 GLN A 482 -1 N TYR A 480 O ALA A 425 SHEET 5 C 5 TRP A 449 ASP A 451 -1 N HIS A 450 O VAL A 481 SHEET 1 D 2 GLY A 434 TYR A 439 0 SHEET 2 D 2 TRP A 467 VAL A 472 -1 N VAL A 472 O GLY A 434 LINK OD1 ASN A 102 CA CA A 501 1555 1555 2.30 LINK OD2 ASP A 159 CA CA A 502 1555 1555 2.53 LINK OD1 ASP A 159 CA CA A 502 1555 1555 2.47 LINK OD2 ASP A 159 NA NA A 505 1555 1555 2.33 LINK O ALA A 181 CA CA A 502 1555 1555 2.28 LINK OD1 ASP A 183 CA CA A 502 1555 1555 2.35 LINK OD2 ASP A 183 NA NA A 505 1555 1555 2.49 LINK O ASP A 194 CA CA A 501 1555 1555 2.33 LINK OD1 ASP A 194 CA CA A 501 1555 1555 2.26 LINK OD2 ASP A 194 NA NA A 505 1555 1555 2.32 LINK OD1 ASP A 200 CA CA A 501 1555 1555 2.28 LINK OD2 ASP A 200 CA CA A 501 1555 1555 3.31 LINK OD2 ASP A 200 NA NA A 505 1555 1555 2.36 LINK O VAL A 201 NA NA A 505 1555 1555 2.43 LINK OD1 ASP A 202 CA CA A 502 1555 1555 2.36 LINK OD2 ASP A 204 CA CA A 502 1555 1555 2.38 LINK O HIS A 235 CA CA A 501 1555 1555 2.38 LINK O GLY A 300 CA CA A 504 1555 1555 2.29 LINK O TYR A 302 CA CA A 504 1555 1555 2.37 LINK O HIS A 406 CA CA A 504 1555 1555 2.45 LINK OD1 ASP A 407 CA CA A 504 1555 1555 2.33 LINK OD1 ASP A 430 CA CA A 504 1555 1555 2.43 LINK OD2 ASP A 430 CA CA A 504 1555 1555 2.48 LINK OD1 ASN A 444 CA CA A 503 1555 1555 2.31 LINK OE1 GLU A 447 CA CA A 503 1555 1555 2.54 LINK OE2 GLU A 447 CA CA A 503 1555 1555 2.36 LINK CA CA A 501 O HOH A2341 1555 1555 2.43 LINK CA CA A 502 O HOH A2559 1555 1555 2.46 LINK CA CA A 503 O HOH A2853 1555 1555 2.47 LINK CA CA A 503 O HOH A2854 1555 1555 2.41 LINK CA CA A 503 O HOH A2875 1555 1555 2.56 LINK CA CA A 503 O HOH A2879 1555 1555 2.61 LINK CA CA A 503 O HOH A2929 1555 1555 2.44 LINK CA CA A 504 O HOH A2701 1555 1555 2.44 CISPEP 1 TRP A 184 GLU A 185 0 7.00 SITE 1 AC1 5 ASN A 102 ASP A 194 ASP A 200 HIS A 235 SITE 2 AC1 5 HOH A2341 SITE 1 AC2 6 ASP A 159 ALA A 181 ASP A 183 ASP A 202 SITE 2 AC2 6 ASP A 204 HOH A2559 SITE 1 AC3 7 ASN A 444 GLU A 447 HOH A2853 HOH A2854 SITE 2 AC3 7 HOH A2875 HOH A2879 HOH A2929 SITE 1 AC4 6 GLY A 300 TYR A 302 HIS A 406 ASP A 407 SITE 2 AC4 6 ASP A 430 HOH A2701 SITE 1 AC5 5 ASP A 159 ASP A 183 ASP A 194 ASP A 200 SITE 2 AC5 5 VAL A 201 CRYST1 52.200 76.100 236.500 90.00 90.00 90.00 C 2 2 21 8 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 0.019157 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004228 0.00000