10 20 30 40 50 60 70 80 1WDR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 17-MAY-04 1WDR
TITLE THE ROLE OF AN INNER LOOP IN THE CATALYTIC MECHANISM OF TITLE 2 SOYBEAN BETA-AMYLASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-AMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-ALPHA-D-GLUCAN MALTOHYDROLASE; COMPND 5 EC: 3.2.1.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKK233-2
KEYWDS (BETA/ALPHA)8 BARREL, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.N.KANG,M.ADACHI,S.UTSUMI,B.MIKAMI
REVDAT 2 24-FEB-09 1WDR 1 VERSN REVDAT 1 05-APR-05 1WDR 0
JRNL AUTH Y.N.KANG,A.TANABE,M.ADACHI,S.UTSUMI,B.MIKAMI JRNL TITL STRUCTURAL ANALYSIS OF THREONINE 342 MUTANTS OF JRNL TITL 2 SOYBEAN BETA-AMYLASE: ROLE OF A CONFORMATIONAL JRNL TITL 3 CHANGE OF THE INNER LOOP IN THE CATALYTIC JRNL TITL 4 MECHANISM. JRNL REF BIOCHEMISTRY V. 44 5106 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15794648 JRNL DOI 10.1021/BI0476580
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.131 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.115 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 6553 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 124411 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.115 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.100 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 5464 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 104100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 906 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 4914.26 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 3830.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 23 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 44765 REMARK 3 NUMBER OF RESTRAINTS : 53516 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.068 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.045 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.090 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WDR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB023468.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.71 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE- REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 509264 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM ACETATE, REMARK 280 2-MERCAPTOETHANOL, EDTA, PH 5.4, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.86600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.73200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.73200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.86600 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 962 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1209 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1254 LIES ON A SPECIAL POSITION.
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 ALA A 1 REMARK 465 THR A 2
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 TYR A 11 CA - CB - CG ANGL. DEV. = 17.6 DEGREES REMARK 500 ASP A 33 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 126 CD - NE - CZ ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 126 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 GLU A 199 C - N - CA ANGL. DEV. = 17.9 DEGREES REMARK 500 TYR A 209 CB - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 216 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 233 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASN A 239 CB - CG - OD1 ANGL. DEV. = 15.8 DEGREES REMARK 500 ASN A 282 CB - CG - ND2 ANGL. DEV. = 17.2 DEGREES REMARK 500 HIS A 300 CG - ND1 - CE1 ANGL. DEV. = 7.7 DEGREES REMARK 500 HIS A 300 ND1 - CE1 - NE2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 334 CD - NE - CZ ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 334 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 347 CD - NE - CZ ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 347 NH1 - CZ - NH2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG A 347 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 347 NE - CZ - NH2 ANGL. DEV. = 4.6 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 ASP A 4 -74.61 -40.38 REMARK 500 PHE A 145 78.94 -105.75 REMARK 500 PRO A 201 46.55 -101.99 REMARK 500 PHE A 341 -167.93 -101.06 REMARK 500 ASP A 494 30.68 87.88 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 A 609 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 660 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 670 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A 708 DISTANCE = 5.53 ANGSTROMS REMARK 525 HOH A 835 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 898 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 977 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A1034 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A1082 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A1086 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH A1087 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A1185 DISTANCE = 8.89 ANGSTROMS REMARK 525 HOH A1274 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH A1327 DISTANCE = 5.70 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAL A 496 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAL A 498 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 499 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2000 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2001 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2002 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2003 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2004 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2005
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q6C RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE COMPLEXED WITH MALTOSE REMARK 900 RELATED ID: 1BYB RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE COMPLEXED WITH 200MM MALTOSE AND REMARK 900 COMPLEXED WITH MALTOTETRAOSE REMARK 900 RELATED ID: 1BFN RELATED DB: PDB REMARK 900 RECOMBINANT SOYBEAN BETA-AMYLASE COMPLEXED WITH BETA- REMARK 900 CYCLODEXTRIN REMARK 900 RELATED ID: 1BYD RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE REACTED WITH 100MM MALTAL AND REMARK 900 COMPLEXED WITH D-DEOXYMALTOSE REMARK 900 RELATED ID: 1V3H RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE MUTANT (E186Q) COMPLEXED WITH REMARK 900 MALTOPENTAOSE REMARK 900 RELATED ID: 1V3I RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE MUTANT (E380Q) COMPLEXED WITH MALTOSE REMARK 900 RELATED ID: 1WDP RELATED DB: PDB REMARK 900 THE SAME PROTEIN, WILD TYPE REMARK 900 RELATED ID: 1WDQ RELATED DB: PDB REMARK 900 THE SAME PROTEIN, MUTANT (T342V) REMARK 900 RELATED ID: 1WDS RELATED DB: PDB REMARK 900 THE SAME PROTEIN, MUTANT (T342A)
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE REMARK 999 DATABASE REFERENCE. 76TH LEU WAS CAUSED NO EFFECTIVE CHANGE IN REMARK 999 ENZYNE PROPERTIES BASED ON A REASONABLE SPECIFIC ACTIVITY OF REMARK 999 CRUDE EXTRACT. AND, 202TH GLY AND 399TH ARG WERE VARIANT WHICH REMARK 999 IS REPORTED IN THE NUCLEOTIDE SEQUENCE, ACCESSION NO. D50866.
DBREF 1WDR A 1 495 UNP P10538 AMYB_SOYBN 1 495
SEQADV 1WDR LEU A 76 UNP P10538 PHE 76 SEE REMARK 999 SEQADV 1WDR GLY A 202 UNP P10538 ARG 202 SEE REMARK 999 SEQADV 1WDR SER A 342 UNP P10538 THR 342 ENGINEERED SEQADV 1WDR ARG A 399 UNP P10538 LYS 399 SEE REMARK 999
SEQRES 1 A 495 ALA THR SER ASP SER ASN MET LEU LEU ASN TYR VAL PRO SEQRES 2 A 495 VAL TYR VAL MET LEU PRO LEU GLY VAL VAL ASN VAL ASP SEQRES 3 A 495 ASN VAL PHE GLU ASP PRO ASP GLY LEU LYS GLU GLN LEU SEQRES 4 A 495 LEU GLN LEU ARG ALA ALA GLY VAL ASP GLY VAL MET VAL SEQRES 5 A 495 ASP VAL TRP TRP GLY ILE ILE GLU LEU LYS GLY PRO LYS SEQRES 6 A 495 GLN TYR ASP TRP ARG ALA TYR ARG SER LEU LEU GLN LEU SEQRES 7 A 495 VAL GLN GLU CYS GLY LEU THR LEU GLN ALA ILE MET SER SEQRES 8 A 495 PHE HIS GLN CYS GLY GLY ASN VAL GLY ASP ILE VAL ASN SEQRES 9 A 495 ILE PRO ILE PRO GLN TRP VAL LEU ASP ILE GLY GLU SER SEQRES 10 A 495 ASN HIS ASP ILE PHE TYR THR ASN ARG SER GLY THR ARG SEQRES 11 A 495 ASN LYS GLU TYR LEU THR VAL GLY VAL ASP ASN GLU PRO SEQRES 12 A 495 ILE PHE HIS GLY ARG THR ALA ILE GLU ILE TYR SER ASP SEQRES 13 A 495 TYR MET LYS SER PHE ARG GLU ASN MET SER ASP PHE LEU SEQRES 14 A 495 GLU SER GLY LEU ILE ILE ASP ILE GLU VAL GLY LEU GLY SEQRES 15 A 495 PRO ALA GLY GLU LEU ARG TYR PRO SER TYR PRO GLN SER SEQRES 16 A 495 GLN GLY TRP GLU PHE PRO GLY ILE GLY GLU PHE GLN CYS SEQRES 17 A 495 TYR ASP LYS TYR LEU LYS ALA ASP PHE LYS ALA ALA VAL SEQRES 18 A 495 ALA ARG ALA GLY HIS PRO GLU TRP GLU LEU PRO ASP ASP SEQRES 19 A 495 ALA GLY LYS TYR ASN ASP VAL PRO GLU SER THR GLY PHE SEQRES 20 A 495 PHE LYS SER ASN GLY THR TYR VAL THR GLU LYS GLY LYS SEQRES 21 A 495 PHE PHE LEU THR TRP TYR SER ASN LYS LEU LEU ASN HIS SEQRES 22 A 495 GLY ASP GLN ILE LEU ASP GLU ALA ASN LYS ALA PHE LEU SEQRES 23 A 495 GLY CME LYS VAL LYS LEU ALA ILE LYS VAL SER GLY ILE SEQRES 24 A 495 HIS TRP TRP TYR LYS VAL GLU ASN HIS ALA ALA GLU LEU SEQRES 25 A 495 THR ALA GLY TYR TYR ASN LEU ASN ASP ARG ASP GLY TYR SEQRES 26 A 495 ARG PRO ILE ALA ARG MET LEU SER ARG HIS HIS ALA ILE SEQRES 27 A 495 LEU ASN PHE SER CYS LEU GLU MET ARG ASP SER GLU GLN SEQRES 28 A 495 PRO SER ASP ALA LYS SER GLY PRO GLN GLU LEU VAL GLN SEQRES 29 A 495 GLN VAL LEU SER GLY GLY TRP ARG GLU ASP ILE ARG VAL SEQRES 30 A 495 ALA GLY GLU ASN ALA LEU PRO ARG TYR ASP ALA THR ALA SEQRES 31 A 495 TYR ASN GLN ILE ILE LEU ASN ALA ARG PRO GLN GLY VAL SEQRES 32 A 495 ASN ASN ASN GLY PRO PRO LYS LEU SER MET PHE GLY VAL SEQRES 33 A 495 THR TYR LEU ARG LEU SER ASP ASP LEU LEU GLN LYS SER SEQRES 34 A 495 ASN PHE ASN ILE PHE LYS LYS PHE VAL LEU LYS MET HIS SEQRES 35 A 495 ALA ASP GLN ASP TYR CYS ALA ASN PRO GLN LYS TYR ASN SEQRES 36 A 495 HIS ALA ILE THR PRO LEU LYS PRO SER ALA PRO LYS ILE SEQRES 37 A 495 PRO ILE GLU VAL LEU LEU GLU ALA THR LYS PRO THR LEU SEQRES 38 A 495 PRO PHE PRO TRP LEU PRO GLU THR ASP MET LYS VAL ASP SEQRES 39 A 495 GLY
MODRES 1WDR CME A 288 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE
HET CME A 288 10 HET MAL A 496 24 HET MAL A 498 23 HET GLC A 499 12 HET SO4 A2000 5 HET SO4 A2001 5 HET SO4 A2002 5 HET SO4 A2003 5 HET SO4 A2004 5 HET SO4 A2005 5
HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM MAL MALTOSE HETNAM GLC ALPHA-D-GLUCOSE HETNAM SO4 SULFATE ION
FORMUL 1 CME C5 H11 N O3 S2 FORMUL 2 MAL 2(C12 H22 O11) FORMUL 4 GLC C6 H12 O6 FORMUL 5 SO4 6(O4 S 2-) FORMUL 11 HOH *906(H2 O)
HELIX 1 1 SER A 3 LEU A 9 1 7 HELIX 2 2 ASP A 31 GLY A 46 1 16 HELIX 3 3 TRP A 56 GLU A 60 1 5 HELIX 4 4 TRP A 69 CYS A 82 1 14 HELIX 5 5 PRO A 108 ASN A 118 1 11 HELIX 6 6 VAL A 137 ASP A 140 5 4 HELIX 7 7 THR A 149 MET A 165 1 17 HELIX 8 8 MET A 165 SER A 171 1 7 HELIX 9 9 GLY A 182 GLU A 186 5 5 HELIX 10 10 PRO A 193 GLY A 197 5 5 HELIX 11 11 ASP A 210 ALA A 224 1 15 HELIX 12 12 VAL A 241 THR A 245 5 5 HELIX 13 13 GLY A 252 VAL A 255 5 4 HELIX 14 14 THR A 256 LEU A 286 1 31 HELIX 15 15 HIS A 308 GLY A 315 1 8 HELIX 16 16 TYR A 325 ARG A 334 1 10 HELIX 17 17 ARG A 347 GLN A 351 5 5 HELIX 18 18 PRO A 352 LYS A 356 5 5 HELIX 19 19 GLY A 358 GLU A 373 1 16 HELIX 20 20 ASP A 387 ARG A 399 1 13 HELIX 21 21 GLN A 427 HIS A 442 1 16 HELIX 22 22 ASN A 450 ASN A 455 5 6 HELIX 23 23 PRO A 469 ALA A 476 1 8
SHEET 1 A 9 VAL A 14 MET A 17 0 SHEET 2 A 9 GLY A 49 TRP A 55 1 O MET A 51 N VAL A 16 SHEET 3 A 9 THR A 85 SER A 91 1 O ILE A 89 N VAL A 52 SHEET 4 A 9 ILE A 174 VAL A 179 1 O GLU A 178 N MET A 90 SHEET 5 A 9 LYS A 291 LYS A 295 1 O ALA A 293 N VAL A 179 SHEET 6 A 9 ILE A 338 PHE A 341 1 O ASN A 340 N ILE A 294 SHEET 7 A 9 VAL A 377 GLU A 380 1 O ALA A 378 N PHE A 341 SHEET 8 A 9 GLY A 415 TYR A 418 1 O THR A 417 N GLY A 379 SHEET 9 A 9 VAL A 14 MET A 17 1 N TYR A 15 O TYR A 418 SHEET 1 B 2 PHE A 122 THR A 124 0 SHEET 2 B 2 ARG A 130 LEU A 135 -1 O ASN A 131 N TYR A 123
LINK C GLY A 287 N CME A 288 1555 1555 1.33 LINK C CME A 288 N LYS A 289 1555 1555 1.34 LINK C1' MAL A 496 O4 AMAL A 498 1555 1555 1.78
CISPEP 1 PHE A 200 PRO A 201 0 -2.73 CISPEP 2 LEU A 419 ARG A 420 0 0.23
SITE 1 AC1 20 ASP A 53 TRP A 55 HIS A 93 ASP A 101 SITE 2 AC1 20 ALA A 184 GLU A 186 LYS A 295 SER A 342 SITE 3 AC1 20 GLU A 380 ALA A 382 LEU A 419 ARG A 420 SITE 4 AC1 20 MAL A 498 GLC A 499 HOH A 595 HOH A 628 SITE 5 AC1 20 HOH A 712 HOH A 755 HOH A 776 HOH A1030 SITE 1 AC2 19 VAL A 99 GLU A 186 ARG A 188 TYR A 192 SITE 2 AC2 19 TRP A 198 PHE A 200 SER A 297 GLY A 298 SITE 3 AC2 19 HIS A 300 TRP A 301 SER A 342 MET A 346 SITE 4 AC2 19 LEU A 383 MAL A 496 HOH A 630 HOH A 875 SITE 5 AC2 19 HOH A1099 HOH A1303 HOH A1304 SITE 1 AC3 11 VAL A 99 TYR A 192 TRP A 198 HIS A 300 SITE 2 AC3 11 MET A 346 MAL A 496 HOH A 630 HOH A 875 SITE 3 AC3 11 HOH A1099 HOH A1303 HOH A1304 SITE 1 AC4 8 HIS A 146 ARG A 326 ARG A 330 ARG A 372 SITE 2 AC4 8 HOH A 945 HOH A 954 HOH A1171 HOH A1295 SITE 1 AC5 5 HIS A 119 ARG A 130 HOH A1053 HOH A1088 SITE 2 AC5 5 HOH A1297 SITE 1 AC6 5 GLY A 225 LYS A 304 LYS A 453 HOH A1010 SITE 2 AC6 5 HOH A1104 SITE 1 AC7 7 ARG A 347 SER A 349 HOH A 610 HOH A 762 SITE 2 AC7 7 HOH A1059 HOH A1189 HOH A1318 SITE 1 AC8 10 GLN A 77 ARG A 372 THR A 480 LEU A 481 SITE 2 AC8 10 HOH A 626 HOH A 627 HOH A 729 HOH A 861 SITE 3 AC8 10 HOH A1081 HOH A1198 SITE 1 AC9 9 THR A 256 GLU A 257 HOH A 609 HOH A 933 SITE 2 AC9 9 HOH A1002 HOH A1147 HOH A1165 HOH A1232 SITE 3 AC9 9 HOH A1349
CRYST1 85.128 85.128 143.598 90.00 90.00 120.00 P 31 2 1 6
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 0.011747 0.006782 0.000000 0.00000
SCALE2 0.000000 0.013564 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006964 0.00000