10 20 30 40 50 60 70 80 1BYA - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE(O-GLYCOSYL) 25-JAN-94 1BYA
TITLE CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH TITLE 2 BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR TITLE 3 APPARENT ROLE IN CATALYSIS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-AMYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.2; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847
KEYWDS HYDROLASE(O-GLYCOSYL)
EXPDTA X-RAY DIFFRACTION
AUTHOR B.MIKAMI,M.DEGANO,E.J.HEHRE,J.C.SACCHETTINI
REVDAT 3 24-FEB-09 1BYA 1 VERSN REVDAT 2 01-APR-03 1BYA 1 JRNL REVDAT 1 31-JUL-94 1BYA 0
JRNL AUTH B.MIKAMI,M.DEGANO,E.J.HEHRE,J.C.SACCHETTINI JRNL TITL CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED JRNL TITL 2 WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE JRNL TITL 3 COMPONENTS AND THEIR APPARENT ROLES IN CATALYSIS. JRNL REF BIOCHEMISTRY V. 33 7779 1994 JRNL REFN ISSN 0006-2960 JRNL PMID 8011643 JRNL DOI 10.1021/BI00191A005
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.MIKAMI,E.J.HEHRE,M.SATO,Y.KATSUBE,M.HIROSE, REMARK 1 AUTH 2 Y.MORITA,J.C.SACCHETTINI REMARK 1 TITL THE 2.0-ANGSTROMS RESOLUTION STRUCTURE OF SOYBEAN REMARK 1 TITL 2 BETA-AMYLASE COMPLEXED WITH ALPHA-CYCLODEXTRIN REMARK 1 REF BIOCHEMISTRY V. 32 6836 1993 REMARK 1 REFN ISSN 0006-2960
REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT, X-PLOR REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 45035 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3929 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1BYA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 48.06667 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 96.13333 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 96.13333 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 48.06667 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 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 O PHE A 200 N ARG A 202 1.82 REMARK 500 OE2 GLU A 178 OD1 ASN A 340 2.13 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 GLU A 30 CD GLU A 30 OE1 0.083 REMARK 500 GLU A 37 CD GLU A 37 OE2 0.106 REMARK 500 GLU A 60 CD GLU A 60 OE2 0.072 REMARK 500 GLU A 116 CD GLU A 116 OE1 0.084 REMARK 500 GLU A 152 CD GLU A 152 OE2 0.070 REMARK 500 GLU A 163 CD GLU A 163 OE2 0.105 REMARK 500 GLU A 170 CD GLU A 170 OE1 0.082 REMARK 500 GLU A 178 CD GLU A 178 OE1 0.117 REMARK 500 GLU A 205 CD GLU A 205 OE1 0.075 REMARK 500 GLU A 228 CD GLU A 228 OE1 0.067 REMARK 500 GLU A 230 CD GLU A 230 OE2 0.077 REMARK 500 GLU A 243 CD GLU A 243 OE1 0.079 REMARK 500 GLU A 280 CD GLU A 280 OE1 0.069 REMARK 500 GLU A 306 CD GLU A 306 OE1 0.089 REMARK 500 GLU A 311 CD GLU A 311 OE2 0.074 REMARK 500 GLU A 361 CD GLU A 361 OE1 0.070 REMARK 500 GLU A 471 CD GLU A 471 OE2 0.096 REMARK 500 GLU A 475 CD GLU A 475 OE1 0.081 REMARK 500 GLU A 488 CD GLU A 488 OE2 0.110 REMARK 500 GLY A 495 N GLY A 495 CA 1.220 REMARK 500 GLY A 495 CA GLY A 495 C 1.720 REMARK 500 GLY A 495 C GLY A 495 O 4.966 REMARK 500 GLY A 495 C GLY A 495 OXT 1.557 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 ASP A 31 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 33 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 70 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 LEU A 86 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 ASP A 120 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 140 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 156 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 156 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 167 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 167 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 202 CB - CA - C ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 234 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 234 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 240 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 240 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 279 CB - CG - OD1 ANGL. DEV. = -8.7 DEGREES REMARK 500 ASP A 279 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TYR A 316 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 321 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 321 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 323 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 323 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 330 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 330 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 MET A 346 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 347 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 374 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 385 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 387 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 420 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 446 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 446 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 GLY A 495 N - CA - C ANGL. DEV. = -40.8 DEGREES REMARK 500 GLY A 495 CA - C - O ANGL. DEV. = 47.3 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 ILE A 102 -85.82 -34.66 REMARK 500 TYR A 134 145.61 -173.14 REMARK 500 ASP A 140 -39.20 -38.85 REMARK 500 PHE A 145 75.51 -100.90 REMARK 500 ALA A 184 18.07 59.91 REMARK 500 TRP A 198 128.29 -39.23 REMARK 500 PHE A 200 -94.75 -48.82 REMARK 500 PRO A 201 26.06 -54.63 REMARK 500 HIS A 308 56.17 37.98 REMARK 500 ARG A 420 131.36 88.11 REMARK 500 LYS A 428 -71.70 -47.89 REMARK 500 ASP A 494 82.46 -52.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 11 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 133 10.99 REMARK 500 VAL A 241 12.68 REMARK 500 GLN A 276 11.21 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 545 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A 634 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH A 716 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH A 721 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 782 DISTANCE = 5.53 ANGSTROMS REMARK 525 HOH A 815 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 818 DISTANCE = 5.52 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 951
DBREF 1BYA A 1 495 UNP P10538 AMYB_SOYBN 1 495
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 PHE 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 ARG 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 LYS 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 SO4 A 951 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *320(H2 O)
HELIX 1 A1 PRO A 32 ALA A 45 1 14 HELIX 2 A2 ARG A 70 GLU A 81 1 12 HELIX 3 A3 GLN A 109 SER A 117 1 9 HELIX 4 A4 ALA A 150 GLU A 170 1 21 HELIX 5 A5 LYS A 211 ALA A 224 1 14 HELIX 6 A6 LYS A 258 ALA A 284 1 27 HELIX 7 A7 ALA A 309 THR A 313 1 5 HELIX 8 A8 TYR A 325 ARG A 334 1 10 HELIX 9 A9 PRO A 359 GLU A 373 1 15 HELIX 10 A10 ASP A 387 LYS A 399 1 13 HELIX 11 A11 GLN A 427 HIS A 442 1 16 HELIX 12 A12 PRO A 469 GLU A 475 1 7
SHEET 1 S1 8 PRO A 13 LEU A 20 0 SHEET 2 S1 8 GLY A 49 TRP A 55 1 O MET A 51 N LEU A 18 SHEET 3 S1 8 THR A 85 SER A 91 1 O GLN A 87 N VAL A 52 SHEET 4 S1 8 ASP A 176 LEU A 181 1 O ASP A 176 N ALA A 88 SHEET 5 S1 8 VAL A 290 VAL A 296 1 O LYS A 291 N ILE A 177 SHEET 6 S1 8 ALA A 337 CYS A 343 1 O ILE A 338 N ILE A 294 SHEET 7 S1 8 ILE A 375 ASN A 381 1 O ALA A 378 N PHE A 341 SHEET 8 S1 8 GLY A 415 LEU A 419 1 N THR A 417 O GLY A 379
SITE 1 AC1 3 HIS A 146 ARG A 326 ARG A 372
CRYST1 86.200 86.200 144.200 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 0.011601 0.006698 0.000000 0.00000
SCALE2 0.000000 0.013396 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006935 0.00000