1V3H - Header Asymmetric Unit

HEADER HYDROLASE 02-NOV-03 1V3H

TITLE THE ROLES OF GLU186 AND GLU380 IN THE CATALYTIC REACTION 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 GENE: BMY1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 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 1V3H 1 VERSN REVDAT 1 22-JUN-04 1V3H 0

JRNL AUTH Y.N.KANG,M.ADACHI,S.UTSUMI,B.MIKAMI JRNL TITL THE ROLES OF GLU186 AND GLU380 IN THE CATALYTIC JRNL TITL 2 REACTION OF SOYBEAN BETA-AMYLASE. JRNL REF J.MOL.BIOL. V. 339 1129 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15178253 JRNL DOI 10.1016/J.JMB.2004.04.029

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2236708.550 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 80031 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 SET) : 0.163 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4054 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 12576 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE : 0.2260 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 673 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3935 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 787 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.90000 REMARK 3 B22 (A**2) : 2.43000 REMARK 3 B33 (A**2) : -5.33000 REMARK 3 B12 (A**2) : 1.28000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.84 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.940 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.450 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.730 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.550 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 59.70 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1V3H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-03. REMARK 100 THE RCSB ID CODE IS RCSB006158.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.986 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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80563 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 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) : 0.04300 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14100 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: PDB ENTRY 1BYB REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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 47.98633 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 95.97267 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 95.97267 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 47.98633 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 A1062 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1237 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1240 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 465 SER A 3 REMARK 465 ASP A 4

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 NH2 ARG A 162 O HOH A 1266 2.00 REMARK 500 O HOH A 738 O HOH A 1274 2.05 REMARK 500 O HOH A 1153 O HOH A 1287 2.07 REMARK 500 O HOH A 1084 O HOH A 1277 2.10 REMARK 500 O HOH A 830 O HOH A 1247 2.12 REMARK 500 O HOH A 1118 O HOH A 1271 2.15 REMARK 500 O HOH A 896 O HOH A 1189 2.17 REMARK 500 O HOH A 1225 O HOH A 1259 2.18 REMARK 500 O HOH A 943 O HOH A 1242 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 1271 O HOH A 1254 2665 0.45 REMARK 500 O HOH A 739 O HOH A 1276 6655 1.96 REMARK 500 O HOH A 1261 O HOH A 1002 3564 2.16 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 LYS A 65 17.77 59.95 REMARK 500 PHE A 92 31.31 -92.59 REMARK 500 PHE A 145 79.71 -107.69 REMARK 500 PRO A 201 47.43 -103.53 REMARK 500 PHE A 341 -156.26 -97.14 REMARK 500 ASP A 494 -138.13 -97.59 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 843 DISTANCE = 5.78 ANGSTROMS REMARK 525 HOH A 844 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 856 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A 883 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 898 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH A 902 DISTANCE = 5.36 ANGSTROMS REMARK 525 HOH A 934 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 966 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A1069 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH A1103 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH A1112 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH A1195 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH A1202 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A1284 DISTANCE = 6.71 ANGSTROMS

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 496 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 497 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 498 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 499 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 500 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2000 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2001 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2002 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2003 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2004 REMARK 800 SITE_IDENTIFIER: BC2 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: 1BYA RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE (APO FORM) REMARK 900 RELATED ID: 1BYB RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE REACTED WITH 200MM MALTOSE AND REMARK 900 COMPLEXED WITH MALTOTETRAOSE REMARK 900 RELATED ID: 1BYC RELATED DB: PDB REMARK 900 SOYBEAN BETA-AMYLASE REACTED WITH 8MM MALTOSE AND COMPLEXED REMARK 900 WITH MALTOTETRAOSE 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: 1BFN RELATED DB: PDB REMARK 900 RECOMBINANT SOYBEAN BETA-AMYLASE COMPLEXED WITH BETA- REMARK 900 CYCLODEXTRIN REMARK 900 RELATED ID: 1V3I RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH MALTOSE

DBREF 1V3H A 1 495 UNP P10538 AMYB_SOYBN 1 495

SEQADV 1V3H LEU A 76 UNP P10538 PHE 76 ENGINEERED SEQADV 1V3H GLN A 186 UNP P10538 GLU 186 ENGINEERED SEQADV 1V3H GLY A 202 UNP P10538 ARG 202 SEE REMARK 999 SEQADV 1V3H 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 GLN 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 THR 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 GLC A 496 11 HET GLC A 497 11 HET GLC A 498 11 HET GLC A 499 11 HET GLC A 500 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 GLC ALPHA-D-GLUCOSE HETNAM SO4 SULFATE ION

FORMUL 2 GLC 5(C6 H12 O6) FORMUL 3 SO4 6(O4 S 2-) FORMUL 9 HOH *787(H2 O)

HELIX 1 1 MET A 7 TYR A 11 5 5 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 GLN 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 LEU A 474 1 6 HELIX 24 24 GLU A 475 LYS A 478 5 4

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 LYS A 291 N ILE A 177 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 C1 GLC A 496 O4 GLC A 497 1555 1555 1.40 LINK C1 GLC A 497 O4 GLC A 498 1555 1555 1.40 LINK C1 GLC A 498 O4 GLC A 499 1555 1555 1.40 LINK C1 GLC A 499 O4 GLC A 500 1555 1555 1.40

CISPEP 1 PHE A 200 PRO A 201 0 0.38 CISPEP 2 LEU A 419 ARG A 420 0 0.81

SITE 1 AC1 10 ASP A 53 TRP A 55 HIS A 93 ASP A 101 SITE 2 AC1 10 ARG A 420 GLC A 497 HOH A 520 HOH A 544 SITE 3 AC1 10 HOH A 666 HOH A 820 SITE 1 AC2 13 MET A 17 VAL A 99 ALA A 184 GLN A 186 SITE 2 AC2 13 LYS A 295 GLU A 380 ALA A 382 LEU A 419 SITE 3 AC2 13 GLC A 496 GLC A 498 HOH A 544 HOH A 553 SITE 4 AC2 13 HOH A 712 SITE 1 AC3 9 GLN A 186 ARG A 188 TYR A 192 SER A 297 SITE 2 AC3 9 GLY A 298 THR A 342 CYS A 343 GLC A 497 SITE 3 AC3 9 GLC A 499 SITE 1 AC4 8 VAL A 99 GLN A 194 TRP A 198 HIS A 300 SITE 2 AC4 8 MET A 346 GLC A 498 GLC A 500 HOH A 576 SITE 1 AC5 4 VAL A 99 GLC A 499 HOH A1153 HOH A1155 SITE 1 AC6 7 HIS A 146 ARG A 326 ARG A 330 ARG A 372 SITE 2 AC6 7 LYS A 478 HOH A1120 HOH A1123 SITE 1 AC7 9 GLN A 77 ARG A 372 THR A 480 LEU A 481 SITE 2 AC7 9 HOH A 592 HOH A 640 HOH A 758 HOH A 927 SITE 3 AC7 9 HOH A1121 SITE 1 AC8 7 THR A 256 GLU A 257 HOH A 566 HOH A 842 SITE 2 AC8 7 HOH A1008 HOH A1262 HOH A1263 SITE 1 AC9 5 ARG A 347 SER A 349 HOH A 968 HOH A1009 SITE 2 AC9 5 HOH A1144 SITE 1 BC1 4 GLY A 225 LYS A 453 HOH A 816 HOH A1032 SITE 1 BC2 4 HIS A 119 ARG A 130 HOH A 904 HOH A 908

CRYST1 85.379 85.379 143.959 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 0.011713 0.006762 0.000000 0.00000

SCALE2 0.000000 0.013524 0.000000 0.00000

SCALE3 0.000000 0.000000 0.006946 0.00000