10 20 30 40 50 60 70 80 2GDV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 17-MAR-06 2GDV
TITLE SUCROSE PHOSPHORYLASE FROM BIFIDOBACTERIUM ADOLESCENTIS TITLE 2 REACTED WITH SUCROSE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCROSE PHOSPHORYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.4.1.7; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BIFIDOBACTERIUM ADOLESCENTIS; SOURCE 3 ORGANISM_TAXID: 1680; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: XL-1 BLUE MRF; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBLUESCRIPT
KEYWDS BETA-ALPHA-BARRELS, DIMER, GLYCOSIDE HYDROLASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR L.K.SKOV,O.MIRZA,M.GAJHEDE,J.S.KATSRUP
REVDAT 3 04-AUG-09 2GDV 1 FORMUL HET HETATM HETNAM REVDAT 3 2 1 SITE LINK REVDAT 2 24-FEB-09 2GDV 1 VERSN REVDAT 1 26-SEP-06 2GDV 0
JRNL AUTH O.MIRZA,L.K.SKOV,D.SPROGOE,L.A.M.VAN DEN BROEK, JRNL AUTH 2 A.G.J.VORAGEN,J.S.KATSRUP,M.GAJHEDE JRNL TITL STRUCTURAL REARRANGEMENTS OF SUCROSE PHOSPHORYLASE JRNL TITL 2 FROM BIFIDOBACTERIUM ADOLESCENTIS DURING SUCROSE JRNL TITL 3 CONVERSION JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2665797.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 79924 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) : 0.198 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4028 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 12314 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 619 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7930 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 1006 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.94000 REMARK 3 B22 (A**2) : 8.28000 REMARK 3 B33 (A**2) : -4.34000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.51 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) : 1.260 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.950 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 1.980 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.920 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 16.74 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.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : INT2.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN10.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : INT2.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2GDV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-06. REMARK 100 THE RCSB ID CODE IS RCSB036996.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80388 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1R7A REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, TRIS, REMARK 280 BICINE, SUCROSE, PH 8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K
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 37.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.34500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.53500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.34500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.53500 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 ASP A 192 CG ASP A 192 OD2 0.183 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 12 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 12 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 16 CB - CG - OD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP A 16 CB - CG - OD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 ASP A 24 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 24 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 35 CB - CG - OD1 ANGL. DEV. = 9.5 DEGREES REMARK 500 ASP A 35 CB - CG - OD2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ASP A 47 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP A 50 CB - CG - OD1 ANGL. DEV. = 11.9 DEGREES REMARK 500 ASP A 50 CB - CG - OD2 ANGL. DEV. = -11.3 DEGREES REMARK 500 ASP A 54 CB - CG - OD1 ANGL. DEV. = 15.5 DEGREES REMARK 500 ASP A 54 CB - CG - OD2 ANGL. DEV. = -15.5 DEGREES REMARK 500 ASP A 57 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP A 70 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 GLU A 73 CG - CD - OE1 ANGL. DEV. = 13.2 DEGREES REMARK 500 GLU A 73 CG - CD - OE2 ANGL. DEV. = -12.8 DEGREES REMARK 500 GLU A 104 CG - CD - OE1 ANGL. DEV. = 12.5 DEGREES REMARK 500 GLU A 104 CG - CD - OE2 ANGL. DEV. = -12.3 DEGREES REMARK 500 GLU A 126 CG - CD - OE1 ANGL. DEV. = 19.6 DEGREES REMARK 500 GLU A 126 CG - CD - OE2 ANGL. DEV. = -18.1 DEGREES REMARK 500 ASP A 127 CB - CG - OD1 ANGL. DEV. = 12.9 DEGREES REMARK 500 ASP A 127 CB - CG - OD2 ANGL. DEV. = -12.7 DEGREES REMARK 500 ASP A 162 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 162 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ASP A 164 CB - CG - OD1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP A 164 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 166 CB - CG - OD1 ANGL. DEV. = 12.7 DEGREES REMARK 500 ASP A 166 CB - CG - OD2 ANGL. DEV. = -12.1 DEGREES REMARK 500 ASP A 168 CB - CG - OD1 ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP A 168 CB - CG - OD2 ANGL. DEV. = -11.3 DEGREES REMARK 500 ASP A 179 CB - CG - OD1 ANGL. DEV. = 9.6 DEGREES REMARK 500 ASP A 179 CB - CG - OD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 GLU A 220 CG - CD - OE1 ANGL. DEV. = 13.1 DEGREES REMARK 500 GLU A 220 CG - CD - OE2 ANGL. DEV. = -12.5 DEGREES REMARK 500 GLU A 221 CG - CD - OE1 ANGL. DEV. = 20.9 DEGREES REMARK 500 GLU A 221 CG - CD - OE2 ANGL. DEV. = -20.6 DEGREES REMARK 500 GLU A 242 CG - CD - OE1 ANGL. DEV. = 15.3 DEGREES REMARK 500 GLU A 242 CG - CD - OE2 ANGL. DEV. = -15.4 DEGREES REMARK 500 ASP A 276 CB - CG - OD1 ANGL. DEV. = -32.2 DEGREES REMARK 500 ASP A 276 CB - CG - OD2 ANGL. DEV. = 32.1 DEGREES REMARK 500 ASP A 287 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 287 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 300 CB - CG - OD1 ANGL. DEV. = 20.2 DEGREES REMARK 500 ASP A 300 CB - CG - OD2 ANGL. DEV. = -19.8 DEGREES REMARK 500 ASP A 303 CB - CG - OD1 ANGL. DEV. = 9.7 DEGREES REMARK 500 ASP A 303 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ASP A 312 CB - CG - OD1 ANGL. DEV. = 9.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 167 ANGLE DEVIATIONS. 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 PRO A 41 113.13 -33.88 REMARK 500 ASP A 50 51.49 -140.42 REMARK 500 ALA A 51 55.66 39.64 REMARK 500 PHE A 156 -117.34 -111.34 REMARK 500 ALA A 384 52.93 38.78 REMARK 500 ASP A 446 89.80 7.46 REMARK 500 ASP A 447 -6.11 58.42 REMARK 500 ASP A 486 -153.65 -143.51 REMARK 500 ASP A 495 104.33 -160.22 REMARK 500 PRO B 41 114.59 -34.34 REMARK 500 ALA B 51 56.36 38.39 REMARK 500 PRO B 139 48.50 -81.68 REMARK 500 PHE B 156 -113.97 -109.77 REMARK 500 LEU B 286 -61.79 -122.85 REMARK 500 ASP B 290 -168.39 -103.16 REMARK 500 ALA B 337 -168.50 -121.47 REMARK 500 ASP B 445 -81.76 -96.56 REMARK 500 ASP B 446 -70.84 -140.93 REMARK 500 ASP B 447 -126.99 -127.79 REMARK 500 THR B 448 -70.22 44.36 REMARK 500 ASP B 486 -142.57 -136.29 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 A1365 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH B1480 DISTANCE = 5.34 ANGSTROMS REMARK 525 HOH A1604 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH B1611 DISTANCE = 5.32 ANGSTROMS REMARK 525 HOH A1662 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A1672 DISTANCE = 9.44 ANGSTROMS REMARK 525 HOH A1677 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH B1675 DISTANCE = 7.57 ANGSTROMS REMARK 525 HOH B1697 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH A1695 DISTANCE = 5.51 ANGSTROMS REMARK 525 HOH A1754 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A1755 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH A1767 DISTANCE = 6.25 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC A 700 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BGC B 701
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R7A RELATED DB: PDB REMARK 900 NATIVE STRUCTURE REMARK 900 RELATED ID: 2GDU RELATED DB: PDB REMARK 900 E232Q MUTANT IN COMPLEX WITH SUCROSE
DBREF 2GDV A 1 504 UNP Q84HQ2 Q84HQ2_BIFAD 1 504 DBREF 2GDV B 1 504 UNP Q84HQ2 Q84HQ2_BIFAD 1 504
SEQRES 1 A 504 MET LYS ASN LYS VAL GLN LEU ILE THR TYR ALA ASP ARG SEQRES 2 A 504 LEU GLY ASP GLY THR ILE LYS SER MET THR ASP ILE LEU SEQRES 3 A 504 ARG THR ARG PHE ASP GLY VAL TYR ASP GLY VAL HIS ILE SEQRES 4 A 504 LEU PRO PHE PHE THR PRO PHE ASP GLY ALA ASP ALA GLY SEQRES 5 A 504 PHE ASP PRO ILE ASP HIS THR LYS VAL ASP GLU ARG LEU SEQRES 6 A 504 GLY SER TRP ASP ASP VAL ALA GLU LEU SER LYS THR HIS SEQRES 7 A 504 ASN ILE MET VAL ASP ALA ILE VAL ASN HIS MET SER TRP SEQRES 8 A 504 GLU SER LYS GLN PHE GLN ASP VAL LEU ALA LYS GLY GLU SEQRES 9 A 504 GLU SER GLU TYR TYR PRO MET PHE LEU THR MET SER SER SEQRES 10 A 504 VAL PHE PRO ASN GLY ALA THR GLU GLU ASP LEU ALA GLY SEQRES 11 A 504 ILE TYR ARG PRO ARG PRO GLY LEU PRO PHE THR HIS TYR SEQRES 12 A 504 LYS PHE ALA GLY LYS THR ARG LEU VAL TRP VAL SER PHE SEQRES 13 A 504 THR PRO GLN GLN VAL ASP ILE ASP THR ASP SER ASP LYS SEQRES 14 A 504 GLY TRP GLU TYR LEU MET SER ILE PHE ASP GLN MET ALA SEQRES 15 A 504 ALA SER HIS VAL SER TYR ILE ARG LEU ASP ALA VAL GLY SEQRES 16 A 504 TYR GLY ALA LYS GLU ALA GLY THR SER CYS PHE MET THR SEQRES 17 A 504 PRO LYS THR PHE LYS LEU ILE SER ARG LEU ARG GLU GLU SEQRES 18 A 504 GLY VAL LYS ARG GLY LEU GLU ILE LEU ILE GLU VAL HIS SEQRES 19 A 504 SER TYR TYR LYS LYS GLN VAL GLU ILE ALA SER LYS VAL SEQRES 20 A 504 ASP ARG VAL TYR ASP PHE ALA LEU PRO PRO LEU LEU LEU SEQRES 21 A 504 HIS ALA LEU SER THR GLY HIS VAL GLU PRO VAL ALA HIS SEQRES 22 A 504 TRP THR ASP ILE ARG PRO ASN ASN ALA VAL THR VAL LEU SEQRES 23 A 504 ASP THR HIS ASP GLY ILE GLY VAL ILE ASP ILE GLY SER SEQRES 24 A 504 ASP GLN LEU ASP ARG SER LEU LYS GLY LEU VAL PRO ASP SEQRES 25 A 504 GLU ASP VAL ASP ASN LEU VAL ASN THR ILE HIS ALA ASN SEQRES 26 A 504 THR HIS GLY GLU SER GLN ALA ALA THR GLY ALA ALA ALA SEQRES 27 A 504 SER ASN LEU ASP LEU TYR GLN VAL ASN SER THR TYR TYR SEQRES 28 A 504 SER ALA LEU GLY CYS ASN ASP GLN HIS TYR ILE ALA ALA SEQRES 29 A 504 ARG ALA VAL GLN PHE PHE LEU PRO GLY VAL PRO GLN VAL SEQRES 30 A 504 TYR TYR VAL GLY ALA LEU ALA GLY LYS ASN ASP MET GLU SEQRES 31 A 504 LEU LEU ARG LYS THR ASN ASN GLY ARG ASP ILE ASN ARG SEQRES 32 A 504 HIS TYR TYR SER THR ALA GLU ILE ASP GLU ASN LEU LYS SEQRES 33 A 504 ARG PRO VAL VAL LYS ALA LEU ASN ALA LEU ALA LYS PHE SEQRES 34 A 504 ARG ASN GLU LEU ASP ALA PHE ASP GLY THR PHE SER TYR SEQRES 35 A 504 THR THR ASP ASP ASP THR SER ILE SER PHE THR TRP ARG SEQRES 36 A 504 GLY GLU THR SER GLN ALA THR LEU THR PHE GLU PRO LYS SEQRES 37 A 504 ARG GLY LEU GLY VAL ASP ASN THR THR PRO VAL ALA MET SEQRES 38 A 504 LEU GLU TRP GLU ASP SER ALA GLY ASP HIS ARG SER ASP SEQRES 39 A 504 ASP LEU ILE ALA ASN PRO PRO VAL VAL ALA SEQRES 1 B 504 MET LYS ASN LYS VAL GLN LEU ILE THR TYR ALA ASP ARG SEQRES 2 B 504 LEU GLY ASP GLY THR ILE LYS SER MET THR ASP ILE LEU SEQRES 3 B 504 ARG THR ARG PHE ASP GLY VAL TYR ASP GLY VAL HIS ILE SEQRES 4 B 504 LEU PRO PHE PHE THR PRO PHE ASP GLY ALA ASP ALA GLY SEQRES 5 B 504 PHE ASP PRO ILE ASP HIS THR LYS VAL ASP GLU ARG LEU SEQRES 6 B 504 GLY SER TRP ASP ASP VAL ALA GLU LEU SER LYS THR HIS SEQRES 7 B 504 ASN ILE MET VAL ASP ALA ILE VAL ASN HIS MET SER TRP SEQRES 8 B 504 GLU SER LYS GLN PHE GLN ASP VAL LEU ALA LYS GLY GLU SEQRES 9 B 504 GLU SER GLU TYR TYR PRO MET PHE LEU THR MET SER SER SEQRES 10 B 504 VAL PHE PRO ASN GLY ALA THR GLU GLU ASP LEU ALA GLY SEQRES 11 B 504 ILE TYR ARG PRO ARG PRO GLY LEU PRO PHE THR HIS TYR SEQRES 12 B 504 LYS PHE ALA GLY LYS THR ARG LEU VAL TRP VAL SER PHE SEQRES 13 B 504 THR PRO GLN GLN VAL ASP ILE ASP THR ASP SER ASP LYS SEQRES 14 B 504 GLY TRP GLU TYR LEU MET SER ILE PHE ASP GLN MET ALA SEQRES 15 B 504 ALA SER HIS VAL SER TYR ILE ARG LEU ASP ALA VAL GLY SEQRES 16 B 504 TYR GLY ALA LYS GLU ALA GLY THR SER CYS PHE MET THR SEQRES 17 B 504 PRO LYS THR PHE LYS LEU ILE SER ARG LEU ARG GLU GLU SEQRES 18 B 504 GLY VAL LYS ARG GLY LEU GLU ILE LEU ILE GLU VAL HIS SEQRES 19 B 504 SER TYR TYR LYS LYS GLN VAL GLU ILE ALA SER LYS VAL SEQRES 20 B 504 ASP ARG VAL TYR ASP PHE ALA LEU PRO PRO LEU LEU LEU SEQRES 21 B 504 HIS ALA LEU SER THR GLY HIS VAL GLU PRO VAL ALA HIS SEQRES 22 B 504 TRP THR ASP ILE ARG PRO ASN ASN ALA VAL THR VAL LEU SEQRES 23 B 504 ASP THR HIS ASP GLY ILE GLY VAL ILE ASP ILE GLY SER SEQRES 24 B 504 ASP GLN LEU ASP ARG SER LEU LYS GLY LEU VAL PRO ASP SEQRES 25 B 504 GLU ASP VAL ASP ASN LEU VAL ASN THR ILE HIS ALA ASN SEQRES 26 B 504 THR HIS GLY GLU SER GLN ALA ALA THR GLY ALA ALA ALA SEQRES 27 B 504 SER ASN LEU ASP LEU TYR GLN VAL ASN SER THR TYR TYR SEQRES 28 B 504 SER ALA LEU GLY CYS ASN ASP GLN HIS TYR ILE ALA ALA SEQRES 29 B 504 ARG ALA VAL GLN PHE PHE LEU PRO GLY VAL PRO GLN VAL SEQRES 30 B 504 TYR TYR VAL GLY ALA LEU ALA GLY LYS ASN ASP MET GLU SEQRES 31 B 504 LEU LEU ARG LYS THR ASN ASN GLY ARG ASP ILE ASN ARG SEQRES 32 B 504 HIS TYR TYR SER THR ALA GLU ILE ASP GLU ASN LEU LYS SEQRES 33 B 504 ARG PRO VAL VAL LYS ALA LEU ASN ALA LEU ALA LYS PHE SEQRES 34 B 504 ARG ASN GLU LEU ASP ALA PHE ASP GLY THR PHE SER TYR SEQRES 35 B 504 THR THR ASP ASP ASP THR SER ILE SER PHE THR TRP ARG SEQRES 36 B 504 GLY GLU THR SER GLN ALA THR LEU THR PHE GLU PRO LYS SEQRES 37 B 504 ARG GLY LEU GLY VAL ASP ASN THR THR PRO VAL ALA MET SEQRES 38 B 504 LEU GLU TRP GLU ASP SER ALA GLY ASP HIS ARG SER ASP SEQRES 39 B 504 ASP LEU ILE ALA ASN PRO PRO VAL VAL ALA
HET BGC A 700 11 HET BGC B 701 12
HETNAM BGC BETA-D-GLUCOSE
FORMUL 3 BGC 2(C6 H12 O6) FORMUL 5 HOH *1006(H2 O)
HELIX 1 1 THR A 18 PHE A 30 1 13 HELIX 2 2 SER A 67 SER A 75 1 9 HELIX 3 3 SER A 93 GLY A 103 1 11 HELIX 4 4 GLU A 104 SER A 106 5 3 HELIX 5 5 TYR A 108 PHE A 112 5 5 HELIX 6 6 THR A 114 PHE A 119 1 6 HELIX 7 7 THR A 124 GLY A 130 1 7 HELIX 8 8 SER A 167 SER A 184 1 18 HELIX 9 9 ALA A 193 GLY A 197 5 5 HELIX 10 10 THR A 208 LYS A 224 1 17 HELIX 11 11 TYR A 236 ALA A 244 1 9 HELIX 12 12 SER A 245 VAL A 247 5 3 HELIX 13 13 ALA A 254 GLY A 266 1 13 HELIX 14 14 VAL A 268 ARG A 278 1 11 HELIX 15 15 PRO A 311 THR A 326 1 16 HELIX 16 16 GLY A 328 THR A 334 1 7 HELIX 17 17 GLY A 335 ALA A 338 5 4 HELIX 18 18 THR A 349 LEU A 354 1 6 HELIX 19 19 ASN A 357 LEU A 371 1 15 HELIX 20 20 TYR A 379 LEU A 383 1 5 HELIX 21 21 ASP A 388 ASN A 396 1 9 HELIX 22 22 ASN A 397 ARG A 403 5 7 HELIX 23 23 SER A 407 LEU A 415 1 9 HELIX 24 24 ARG A 417 LEU A 433 1 17 HELIX 25 25 ASP A 434 GLY A 438 5 5 HELIX 26 26 PRO A 467 LEU A 471 5 5 HELIX 27 27 THR B 18 PHE B 30 1 13 HELIX 28 28 SER B 67 SER B 75 1 9 HELIX 29 29 SER B 93 GLY B 103 1 11 HELIX 30 30 GLU B 104 SER B 106 5 3 HELIX 31 31 TYR B 108 PHE B 112 5 5 HELIX 32 32 THR B 114 PHE B 119 1 6 HELIX 33 33 THR B 124 GLY B 130 1 7 HELIX 34 34 SER B 167 SER B 184 1 18 HELIX 35 35 ALA B 193 GLY B 197 5 5 HELIX 36 36 THR B 208 LYS B 224 1 17 HELIX 37 37 TYR B 236 SER B 245 1 10 HELIX 38 38 ALA B 254 GLY B 266 1 13 HELIX 39 39 VAL B 268 ARG B 278 1 11 HELIX 40 40 PRO B 311 THR B 326 1 16 HELIX 41 41 GLY B 328 THR B 334 1 7 HELIX 42 42 THR B 349 LEU B 354 1 6 HELIX 43 43 ASN B 357 LEU B 371 1 15 HELIX 44 44 TYR B 379 LEU B 383 1 5 HELIX 45 45 ASP B 388 ASN B 396 1 9 HELIX 46 46 ASN B 397 ARG B 403 5 7 HELIX 47 47 SER B 407 LEU B 415 1 9 HELIX 48 48 ARG B 417 LEU B 433 1 17 HELIX 49 49 ASP B 434 GLY B 438 5 5 HELIX 50 50 PRO B 467 GLY B 470 5 4
SHEET 1 A 9 GLN A 6 THR A 9 0 SHEET 2 A 9 GLY A 36 ILE A 39 1 O HIS A 38 N LEU A 7 SHEET 3 A 9 ASN A 79 ILE A 85 1 O MET A 81 N VAL A 37 SHEET 4 A 9 TYR A 188 ASP A 192 1 O TYR A 188 N ILE A 80 SHEET 5 A 9 GLU A 228 ILE A 231 1 O GLU A 228 N ILE A 189 SHEET 6 A 9 ARG A 249 ASP A 252 1 O ARG A 249 N ILE A 231 SHEET 7 A 9 ALA A 282 THR A 284 1 O VAL A 283 N ASP A 252 SHEET 8 A 9 VAL A 374 TYR A 378 1 O GLN A 376 N THR A 284 SHEET 9 A 9 GLN A 6 THR A 9 1 N GLN A 6 O VAL A 377 SHEET 1 B 2 PHE A 43 THR A 44 0 SHEET 2 B 2 ASP A 57 VAL A 61 -1 N ASP A 57 O THR A 44 SHEET 1 C 2 HIS A 88 SER A 90 0 SHEET 2 C 2 GLN A 160 ASP A 162 -1 O VAL A 161 N MET A 89 SHEET 1 D 2 PHE A 140 PHE A 145 0 SHEET 2 D 2 LYS A 148 TRP A 153 -1 O ARG A 150 N TYR A 143 SHEET 1 E 5 THR A 439 ASP A 445 0 SHEET 2 E 5 SER A 449 ARG A 455 -1 O THR A 453 N SER A 441 SHEET 3 E 5 GLN A 460 PHE A 465 -1 O PHE A 465 N ILE A 450 SHEET 4 E 5 ALA A 480 ASP A 486 -1 O GLU A 483 N THR A 462 SHEET 5 E 5 GLY A 489 SER A 493 -1 O SER A 493 N LEU A 482 SHEET 1 F 9 GLN B 6 THR B 9 0 SHEET 2 F 9 GLY B 36 ILE B 39 1 O HIS B 38 N LEU B 7 SHEET 3 F 9 ASN B 79 ILE B 85 1 O MET B 81 N VAL B 37 SHEET 4 F 9 TYR B 188 ASP B 192 1 O TYR B 188 N ILE B 80 SHEET 5 F 9 GLU B 228 ILE B 231 1 O GLU B 228 N ILE B 189 SHEET 6 F 9 ARG B 249 ASP B 252 1 O ARG B 249 N ILE B 231 SHEET 7 F 9 ALA B 282 THR B 284 1 O VAL B 283 N ASP B 252 SHEET 8 F 9 VAL B 374 TYR B 378 1 O GLN B 376 N THR B 284 SHEET 9 F 9 GLN B 6 THR B 9 1 N GLN B 6 O VAL B 377 SHEET 1 G 2 PHE B 43 THR B 44 0 SHEET 2 G 2 ASP B 57 VAL B 61 -1 N ASP B 57 O THR B 44 SHEET 1 H 2 HIS B 88 SER B 90 0 SHEET 2 H 2 GLN B 160 ASP B 162 -1 O VAL B 161 N MET B 89 SHEET 1 I 2 PHE B 140 PHE B 145 0 SHEET 2 I 2 LYS B 148 TRP B 153 -1 O ARG B 150 N TYR B 143 SHEET 1 J 2 ILE B 292 GLY B 293 0 SHEET 2 J 2 GLN B 345 VAL B 346 -1 O VAL B 346 N ILE B 292 SHEET 1 K 5 THR B 439 THR B 444 0 SHEET 2 K 5 ILE B 450 ARG B 455 -1 O THR B 453 N SER B 441 SHEET 3 K 5 GLN B 460 PHE B 465 -1 O LEU B 463 N PHE B 452 SHEET 4 K 5 ALA B 480 ASP B 486 -1 O GLU B 483 N THR B 462 SHEET 5 K 5 GLY B 489 SER B 493 -1 O SER B 493 N LEU B 482
LINK C1 BGC A 700 OD2 ASP A 192 1555 1555 1.49
CISPEP 1 THR A 44 PRO A 45 0 -0.52 CISPEP 2 THR B 44 PRO B 45 0 -0.51
SITE 1 AC1 10 ASP A 50 PHE A 53 HIS A 88 ARG A 190 SITE 2 AC1 10 ASP A 192 GLU A 232 HIS A 289 ASP A 290 SITE 3 AC1 10 ARG A 399 HOH A 971 SITE 1 AC2 14 ASP B 50 PHE B 53 HIS B 88 ARG B 135 SITE 2 AC2 14 PHE B 156 ARG B 190 ASP B 192 GLU B 232 SITE 3 AC2 14 HIS B 289 ASP B 290 ARG B 399 HOH B 835 SITE 4 AC2 14 HOH B 908 HOH B1515
CRYST1 75.740 103.070 150.690 90.00 90.00 90.00 P 21 21 21 8
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 0.013203 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009702 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006636 0.00000