10 20 30 40 50 60 70 80 1WDQ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 17-MAY-04 1WDQ
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 1WDQ 1 VERSN REVDAT 1 05-APR-05 1WDQ 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. 1.28 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) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 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) : 0.117 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.135 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 7623 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 144557 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.099 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.115 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 6061 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 115244 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3959 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 810 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 4815.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 3827.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 9 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 43577 REMARK 3 NUMBER OF RESTRAINTS : 52029 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.075 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.087 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.079 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.096 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 1WDQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB023467.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-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 : BL38B1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 216884 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 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 (%) : 94.4 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) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.7 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 (%): 38.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 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 48.00767 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 96.01533 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 96.01533 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 48.00767 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER
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 847 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. = 15.7 DEGREES REMARK 500 TYR A 11 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 TYR A 11 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ASP A 26 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 162 NH1 - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG A 162 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 GLU A 199 C - N - CA ANGL. DEV. = 22.4 DEGREES REMARK 500 TYR A 209 CB - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 216 CB - CG - OD1 ANGL. DEV. = 9.9 DEGREES REMARK 500 ASP A 233 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 326 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 334 CD - NE - CZ ANGL. DEV. = 22.3 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 347 CD - NE - CZ ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG A 347 NH1 - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 347 NE - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 354 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 372 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 376 CD - NE - CZ ANGL. DEV. = 13.0 DEGREES REMARK 500 TYR A 386 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 LYS A 410 N - CA - CB ANGL. DEV. = 17.2 DEGREES REMARK 500 ASP A 494 CB - CG - OD1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP A 494 CB - CG - OD2 ANGL. DEV. = -5.7 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 PHE A 145 79.51 -106.11 REMARK 500 PRO A 201 47.71 -101.00 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 703 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH A 718 DISTANCE = 5.23 ANGSTROMS REMARK 525 HOH A 892 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A 915 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A1056 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH A1059 DISTANCE = 8.77 ANGSTROMS REMARK 525 HOH A1084 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A1085 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH A1167 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH A1291 DISTANCE = 7.01 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 SO4 A 2000 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2001 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2002 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2003 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2004
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: 1WDR RELATED DB: PDB REMARK 900 THE SAME PROTEIN, MUTANT (T342S) REMARK 900 RELATED ID: 1WDS RELATED DB: PDB REMARK 900 THE SAME PROTEIN, MUTANT (T342A)
DBREF 1WDQ A 1 495 UNP P10538 AMYB_SOYBN 1 495
SEQADV 1WDQ LEU A 76 UNP P10538 PHE 76 SEE REMARK 999 SEQADV 1WDQ GLY A 202 UNP P10538 ARG 202 SEE REMARK 999 SEQADV 1WDQ VAL A 342 UNP P10538 THR 342 ENGINEERED SEQADV 1WDQ 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 CYS 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 VAL 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
HET MAL A 496 23 HET MAL A 498 24 HET SO4 A2000 5 HET SO4 A2001 5 HET SO4 A2002 5 HET SO4 A2003 5 HET SO4 A2004 5
HETNAM MAL MALTOSE HETNAM SO4 SULFATE ION
FORMUL 2 MAL 2(C12 H22 O11) FORMUL 4 SO4 5(O4 S 2-) FORMUL 9 HOH *810(H2 O)
HELIX 1 1 SER A 3 LEU A 9 1 7 HELIX 2 2 ASP A 31 ALA A 45 1 15 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 SER A 422 GLN A 427 1 6 HELIX 22 22 GLN A 427 HIS A 442 1 16 HELIX 23 23 ASN A 450 ASN A 455 5 6 HELIX 24 24 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 VAL A 296 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
CISPEP 1 PHE A 200 PRO A 201 0 -2.75 CISPEP 2 LEU A 419 ARG A 420 0 -2.43
SITE 1 AC1 20 ASP A 53 TRP A 55 HIS A 93 VAL A 99 SITE 2 AC1 20 ASP A 101 ALA A 184 GLU A 186 LYS A 295 SITE 3 AC1 20 VAL A 342 GLU A 380 ASN A 381 ALA A 382 SITE 4 AC1 20 LEU A 419 ARG A 420 MAL A 498 HOH A 511 SITE 5 AC1 20 HOH A 512 HOH A 521 HOH A 555 HOH A 596 SITE 1 AC2 16 VAL A 99 GLU A 186 ARG A 188 TYR A 192 SITE 2 AC2 16 TRP A 198 PHE A 200 SER A 297 GLY A 298 SITE 3 AC2 16 HIS A 300 VAL A 342 CYS A 343 MET A 346 SITE 4 AC2 16 LEU A 383 MAL A 496 HOH A 552 HOH A 805 SITE 1 AC3 10 HIS A 146 ARG A 326 ARG A 330 ARG A 372 SITE 2 AC3 10 HOH A 867 HOH A 958 HOH A 977 HOH A1073 SITE 3 AC3 10 HOH A1138 HOH A1288 SITE 1 AC4 8 GLN A 77 ARG A 372 THR A 480 LEU A 481 SITE 2 AC4 8 HOH A 700 HOH A 774 HOH A 848 HOH A1069 SITE 1 AC5 5 HIS A 119 ARG A 130 HOH A 860 HOH A1025 SITE 2 AC5 5 HOH A1211 SITE 1 AC6 6 ARG A 347 SER A 349 LYS A 428 HOH A 746 SITE 2 AC6 6 HOH A 800 HOH A1150 SITE 1 AC7 5 LYS A 356 LYS A 453 HOH A 715 HOH A1035 SITE 2 AC7 5 HOH A1148
CRYST1 84.989 84.989 144.023 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 0.011766 0.006793 0.000000 0.00000
SCALE2 0.000000 0.013586 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006943 0.00000