PDB Short entry for 2XFR HEADER HYDROLASE 28-MAY-10 2XFR TITLE CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE AT ATOMIC RESOLUTION 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE; SOURCE 3 ORGANISM_COMMON: BARLEY; SOURCE 4 ORGANISM_TAXID: 4513; SOURCE 5 TISSUE: GRAIN ENDOSPERM; SOURCE 6 OTHER_DETAILS: PROTEIN PURCHASED FROM MEGAZYME KEYWDS HYDROLASE, CARBOHYDRATE METABOLISM, GLYCOSYL HYDROLASE FAMILY 14, KEYWDS 2 STARCH DEGRADATION, GERMINATION EXPDTA X-RAY DIFFRACTION AUTHOR M.REJZEK,C.E.M.STEVENSON,A.M.SOUTHARD,D.STANLEY,K.DENYER,A.M.SMITH, AUTHOR 2 M.J.NALDRETT,D.M.LAWSON,R.A.FIELD REVDAT 5 20-DEC-23 2XFR 1 REMARK REVDAT 4 22-MAY-19 2XFR 1 REMARK REVDAT 3 08-MAY-19 2XFR 1 REMARK REVDAT 2 11-JAN-12 2XFR 1 JRNL REMARK VERSN REVDAT 1 01-DEC-10 2XFR 0 JRNL AUTH M.REJZEK,C.E.M.STEVENSON,A.M.SOUTHARD,D.STANLEY,K.DENYER, JRNL AUTH 2 A.M.SMITH,M.J.NALDRETT,D.M.LAWSON,R.A.FIELD JRNL TITL CHEMICAL GENETICS AND CEREAL STARCH METABOLISM: STRUCTURAL JRNL TITL 2 BASIS OF THE NON-COVALENT AND COVALENT INHIBITION OF BARLEY JRNL TITL 3 BETA-AMYLASE. JRNL REF MOL.BIOSYST. V. 7 718 2011 JRNL REFN ISSN 1742-206X JRNL PMID 21085740 JRNL DOI 10.1039/C0MB00204F REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0091 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 253710 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) : 0.114 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 12779 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10016 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 53.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.4420 REMARK 3 BIN FREE R VALUE SET COUNT : 516 REMARK 3 BIN FREE R VALUE : 0.4590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3894 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 948 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32500 REMARK 3 B22 (A**2) : 0.07800 REMARK 3 B33 (A**2) : -0.40300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.019 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.019 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.010 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.421 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4429 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6082 ; 1.565 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 594 ; 5.999 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 233 ;36.115 ;23.863 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 756 ;11.689 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;14.432 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 620 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5129 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): 46 ; 0.240 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2634 ; 2.549 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1052 ; 1.362 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4300 ; 3.742 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1795 ; 5.159 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1736 ; 6.615 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7525 ; 2.647 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 948 ;19.168 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7356 ; 6.725 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2XFR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1290044084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9507 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 253864 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 49.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -9.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 5.280 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.09 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1B1Y REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN AT 291 K USING THE REMARK 280 HANGING DROP VAPOUR DIFFUSION METHOD WITH PROTEIN AT 10 MG PER REMARK 280 ML AND A PRECIPITANT COMPRISED OF 14 PERCENT PEG 3350 IN 100 MM REMARK 280 BIS-TRIS PROPANE BUFFER AT PH 5.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 34.41500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.32950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.66900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.32950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.66900 REMARK 290 SMTRY3 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 PRO A 490 REMARK 465 THR A 491 REMARK 465 GLY A 492 REMARK 465 GLY A 493 REMARK 465 MET A 494 REMARK 465 GLY A 495 REMARK 465 GLY A 496 REMARK 465 GLN A 497 REMARK 465 ALA A 498 REMARK 465 GLU A 499 REMARK 465 GLY A 500 REMARK 465 PRO A 501 REMARK 465 THR A 502 REMARK 465 CYS A 503 REMARK 465 GLY A 504 REMARK 465 MET A 505 REMARK 465 GLY A 506 REMARK 465 GLY A 507 REMARK 465 GLN A 508 REMARK 465 VAL A 509 REMARK 465 LYS A 510 REMARK 465 GLY A 511 REMARK 465 PRO A 512 REMARK 465 THR A 513 REMARK 465 GLY A 514 REMARK 465 GLY A 515 REMARK 465 MET A 516 REMARK 465 GLY A 517 REMARK 465 GLY A 518 REMARK 465 GLN A 519 REMARK 465 ALA A 520 REMARK 465 GLU A 521 REMARK 465 ASP A 522 REMARK 465 PRO A 523 REMARK 465 THR A 524 REMARK 465 SER A 525 REMARK 465 GLY A 526 REMARK 465 ILE A 527 REMARK 465 GLY A 528 REMARK 465 GLY A 529 REMARK 465 GLU A 530 REMARK 465 LEU A 531 REMARK 465 PRO A 532 REMARK 465 ALA A 533 REMARK 465 THR A 534 REMARK 465 MET A 535 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 26 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 O HOH A 2742 O HOH A 2744 1.90 REMARK 500 NE2 HIS A 125 O HOH A 2339 1.99 REMARK 500 O HOH A 2359 O HOH A 2756 2.14 REMARK 500 O HOH A 2770 O HOH A 2771 2.14 REMARK 500 O HOH A 2366 O HOH A 2803 2.16 REMARK 500 O HOH A 2348 O HOH A 2742 2.16 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 OD1 ASP A 31 OE1 GLN A 352 2555 1.97 REMARK 500 OD1 ASP A 31 CD GLN A 352 2555 2.05 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 ARG A 334 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 334 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = 4.4 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 ASN A 4 105.96 -161.32 REMARK 500 PHE A 90 39.55 -89.37 REMARK 500 SER A 193 -11.77 91.85 REMARK 500 HIS A 194 44.65 -143.81 REMARK 500 PRO A 199 51.86 -104.93 REMARK 500 ILE A 205 58.52 -114.36 REMARK 500 ASP A 232 41.28 -101.93 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 ARG A 242 0.10 SIDE CHAIN 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 A2019 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A2033 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A2041 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2070 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A2071 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A2087 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A2102 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A2141 DISTANCE = 6.73 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE REMARK 600 CRYOPROTECTANT REMARK 700 REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1490 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1491 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XG9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH 4-O-ALPHA-D- REMARK 900 GLUCOPYRANOSYLMORANOLINE REMARK 900 RELATED ID: 2XFY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH ALPHA- REMARK 900 CYCLODEXTRIN REMARK 900 RELATED ID: 2XGB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH 2,3- REMARK 900 EPOXYPROPYL-ALPHA-D- GLUCOPYRANOSIDE REMARK 900 RELATED ID: 2XGI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH 3,4- REMARK 900 EPOXYBUTYL ALPHA-D- GLUCOPYRANOSIDE REMARK 900 RELATED ID: 2XFF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH ACARBOSE REMARK 900 RELATED ID: 1B1Y RELATED DB: PDB REMARK 900 SEVENFOLD MUTANT OF BARLEY BETA-AMYLASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS REMARK 999 AT 3 POSITIONS TO UNIPROTKB DATABASE ENTRY P16098. THESE REMARK 999 CHANGES WERE IDENTIFIED FROM ELECTRON DENSITY MAPS. DBREF 2XFR A 1 535 UNP P16098 AMYB_HORVU 1 535 SEQADV 2XFR GLU A 165 UNP P16098 ASP 165 SEE REMARK 999 SEQADV 2XFR SER A 347 UNP P16098 LEU 347 SEE REMARK 999 SEQADV 2XFR ALA A 430 UNP P16098 VAL 430 SEE REMARK 999 SEQRES 1 A 535 MET GLU VAL ASN VAL LYS GLY ASN TYR VAL GLN VAL TYR SEQRES 2 A 535 VAL MET LEU PRO LEU ASP ALA VAL SER VAL ASN ASN ARG SEQRES 3 A 535 PHE GLU LYS GLY ASP GLU LEU ARG ALA GLN LEU ARG LYS SEQRES 4 A 535 LEU VAL GLU ALA GLY VAL ASP GLY VAL MET VAL ASP VAL SEQRES 5 A 535 TRP TRP GLY LEU VAL GLU GLY LYS GLY PRO LYS ALA TYR SEQRES 6 A 535 ASP TRP SER ALA TYR LYS GLN LEU PHE GLU LEU VAL GLN SEQRES 7 A 535 LYS ALA GLY LEU LYS LEU GLN ALA ILE MET SER PHE HIS SEQRES 8 A 535 GLN CYS GLY GLY ASN VAL GLY ASP ALA VAL ASN ILE PRO SEQRES 9 A 535 ILE PRO GLN TRP VAL ARG ASP VAL GLY THR ARG ASP PRO SEQRES 10 A 535 ASP ILE PHE TYR THR ASP GLY HIS GLY THR ARG ASN ILE SEQRES 11 A 535 GLU TYR LEU THR LEU GLY VAL ASP ASN GLN PRO LEU PHE SEQRES 12 A 535 HIS GLY ARG SER ALA VAL GLN MET TYR ALA ASP TYR MET SEQRES 13 A 535 THR SER PHE ARG GLU ASN MET LYS GLU PHE LEU ASP ALA SEQRES 14 A 535 GLY VAL ILE VAL ASP ILE GLU VAL GLY LEU GLY PRO ALA SEQRES 15 A 535 GLY GLU MET ARG TYR PRO SER TYR PRO GLN SER HIS GLY SEQRES 16 A 535 TRP SER PHE PRO GLY ILE GLY GLU PHE ILE CYS TYR ASP SEQRES 17 A 535 LYS TYR LEU GLN ALA ASP PHE LYS ALA ALA ALA ALA ALA SEQRES 18 A 535 VAL GLY HIS PRO GLU TRP GLU PHE PRO ASN ASP VAL GLY SEQRES 19 A 535 GLN TYR ASN ASP THR PRO GLU ARG THR GLN PHE PHE ARG SEQRES 20 A 535 ASP ASN GLY THR TYR LEU SER GLU LYS GLY ARG PHE PHE SEQRES 21 A 535 LEU ALA TRP TYR SER ASN ASN LEU ILE LYS HIS GLY ASP SEQRES 22 A 535 ARG ILE LEU ASP GLU ALA ASN LYS VAL PHE LEU GLY TYR SEQRES 23 A 535 LYS VAL GLN LEU ALA ILE LYS ILE SER GLY ILE HIS TRP SEQRES 24 A 535 TRP TYR LYS VAL PRO SER HIS ALA ALA GLU LEU THR ALA SEQRES 25 A 535 GLY TYR TYR ASN LEU HIS ASP ARG ASP GLY TYR ARG THR SEQRES 26 A 535 ILE ALA ARG MET LEU LYS ARG HIS ARG ALA SER ILE ASN SEQRES 27 A 535 PHE THR CYS ALA GLU MET ARG ASP SER GLU GLN SER SER SEQRES 28 A 535 GLN ALA MET SER ALA PRO GLU GLU LEU VAL GLN GLN VAL SEQRES 29 A 535 LEU SER ALA GLY TRP ARG GLU GLY LEU ASN VAL ALA CYS SEQRES 30 A 535 GLU ASN ALA LEU PRO ARG TYR ASP PRO THR ALA TYR ASN SEQRES 31 A 535 THR ILE LEU ARG ASN ALA ARG PRO HIS GLY ILE ASN GLN SEQRES 32 A 535 SER GLY PRO PRO GLU HIS LYS LEU PHE GLY PHE THR TYR SEQRES 33 A 535 LEU ARG LEU SER ASN GLN LEU VAL GLU GLY GLN ASN TYR SEQRES 34 A 535 ALA ASN PHE LYS THR PHE VAL ASP ARG MET HIS ALA ASN SEQRES 35 A 535 LEU PRO ARG ASP PRO TYR VAL ASP PRO MET ALA PRO LEU SEQRES 36 A 535 PRO ARG SER GLY PRO GLU ILE SER ILE GLU MET ILE LEU SEQRES 37 A 535 GLN ALA ALA GLN PRO LYS LEU GLN PRO PHE PRO PHE GLN SEQRES 38 A 535 GLU HIS THR ASP LEU PRO VAL GLY PRO THR GLY GLY MET SEQRES 39 A 535 GLY GLY GLN ALA GLU GLY PRO THR CYS GLY MET GLY GLY SEQRES 40 A 535 GLN VAL LYS GLY PRO THR GLY GLY MET GLY GLY GLN ALA SEQRES 41 A 535 GLU ASP PRO THR SER GLY ILE GLY GLY GLU LEU PRO ALA SEQRES 42 A 535 THR MET HET EDO A1490 4 HET EDO A1491 8 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 HOH *948(H2 O) HELIX 1 1 VAL A 5 TYR A 9 5 5 HELIX 2 2 LYS A 29 ALA A 43 1 15 HELIX 3 3 TRP A 54 GLU A 58 1 5 HELIX 4 4 TRP A 67 ALA A 80 1 14 HELIX 5 5 PRO A 106 ASP A 116 1 11 HELIX 6 6 LEU A 135 ASP A 138 5 4 HELIX 7 7 SER A 147 ALA A 169 1 23 HELIX 8 8 GLY A 180 GLU A 184 5 5 HELIX 9 9 ASP A 208 VAL A 222 1 15 HELIX 10 10 THR A 239 THR A 243 5 5 HELIX 11 11 GLY A 250 LEU A 253 5 4 HELIX 12 12 SER A 254 LEU A 284 1 31 HELIX 13 13 HIS A 306 GLY A 313 1 8 HELIX 14 14 TYR A 323 ARG A 332 1 10 HELIX 15 15 ARG A 345 GLN A 349 5 5 HELIX 16 16 SER A 350 MET A 354 5 5 HELIX 17 17 ALA A 356 GLU A 371 1 16 HELIX 18 18 ASP A 385 ARG A 397 1 13 HELIX 19 19 GLU A 425 HIS A 440 1 16 HELIX 20 20 SER A 463 GLN A 469 1 7 HELIX 21 21 ALA A 470 GLN A 472 5 3 SHEET 1 AA 9 GLN A 11 MET A 15 0 SHEET 2 AA 9 GLY A 413 TYR A 416 1 O PHE A 414 N TYR A 13 SHEET 3 AA 9 VAL A 375 GLU A 378 1 O CYS A 377 N THR A 415 SHEET 4 AA 9 SER A 336 PHE A 339 1 O ILE A 337 N ALA A 376 SHEET 5 AA 9 GLN A 289 LYS A 293 1 O LEU A 290 N SER A 336 SHEET 6 AA 9 ILE A 172 VAL A 177 1 O VAL A 173 N GLN A 289 SHEET 7 AA 9 LYS A 83 SER A 89 1 O LEU A 84 N VAL A 173 SHEET 8 AA 9 GLY A 47 TRP A 53 1 O VAL A 48 N GLN A 85 SHEET 9 AA 9 GLN A 11 MET A 15 1 O VAL A 14 N MET A 49 SHEET 1 AB 2 PHE A 120 THR A 122 0 SHEET 2 AB 2 ARG A 128 LEU A 133 -1 N ASN A 129 O TYR A 121 CISPEP 1 PHE A 198 PRO A 199 0 1.05 CISPEP 2 LEU A 417 ARG A 418 0 -1.05 CISPEP 3 LEU A 417 ARG A 418 0 -2.92 CISPEP 4 LEU A 417 ARG A 418 0 -10.33 CISPEP 5 GLN A 472 PRO A 473 0 -10.65 CISPEP 6 GLN A 472 PRO A 473 0 -7.21 SITE 1 AC1 7 THR A 127 ASN A 129 PRO A 188 PRO A 191 SITE 2 AC1 7 TYR A 236 HOH A2492 HOH A2943 SITE 1 AC2 7 GLN A 212 PHE A 215 GLU A 228 PHE A 229 SITE 2 AC2 7 HOH A2945 HOH A2947 HOH A2948 CRYST1 68.830 71.338 92.659 90.00 90.00 90.00 P 21 21 21 4 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 0.014529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010792 0.00000