HEADER TRANSFERASE 11-OCT-07 2VDT TITLE CRYSTALLOGRAPHIC STRUCTURE OF LEVANSUCRASE FROM BACILLUS SUBTILIS TITLE 2 MUTANT S164A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEVANSUCRASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 34-472; COMPND 5 SYNONYM: BETA-D-FRUCTOFURANOSYL TRANSFERASE, SUCROSE 6-FRUCTOSYL COMPND 6 TRANSFERASE; COMPND 7 EC: 2.4.1.10; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET 22B KEYWDS BETA-PROPELLER, GLYCOSYLTRANSFERASE, GLYCOSIDE HYDROLASE, LEVAN, KEYWDS 2 SECRETED, TRANSFERASE, LEVANSUCRASE EXPDTA X-RAY DIFFRACTION AUTHOR M.E.ORTIZ-SOTO,M.RIVERA,E.RUDINO-PINERA,C.OLVERA,A.LOPEZ-MUNGUIA REVDAT 7 13-DEC-23 2VDT 1 LINK REVDAT 6 30-JAN-19 2VDT 1 REMARK REVDAT 5 20-JUN-18 2VDT 1 JRNL REVDAT 4 24-FEB-09 2VDT 1 VERSN REVDAT 3 23-SEP-08 2VDT 1 JRNL REMARK REVDAT 2 22-JUL-08 2VDT 1 REMARK REVDAT 1 15-JUL-08 2VDT 0 JRNL AUTH M.E.ORTIZ-SOTO,M.RIVERA,E.RUDINO-PINERA,C.OLVERA, JRNL AUTH 2 A.LOPEZ-MUNGUIA JRNL TITL SELECTED MUTATIONS IN BACILLUS SUBTILIS LEVANSUCRASE JRNL TITL 2 SEMI-CONSERVED REGIONS AFFECTING ITS BIOCHEMICAL PROPERTIES JRNL REF PROTEIN ENG.DES.SEL. V. 21 589 2008 JRNL REFN ISSN 1741-0126 JRNL PMID 18596022 JRNL DOI 10.1093/PROTEIN/GZN036 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : CNS LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 5605 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) : 0.265 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 287 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 892 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE : 0.4300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 56 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.058 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 70.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54100 REMARK 3 B22 (A**2) : -2.10800 REMARK 3 B33 (A**2) : 1.56700 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) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : 0.75 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) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.80 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 2.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.770 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) : 2.460 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.910 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.690 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.290 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 56.10 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2VDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1290034119. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200H REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU-MSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5627 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 39.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1OYG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED AFTER 12 DAYS REMARK 280 OF MICRODIALYSIS OF THE PURIFIED PROTEIN (8 G/L) AGAINST REMARK 280 DEIONIZED WATER., PH 7 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 25.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.90000 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: PQS 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 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 OG1 THR A 119 OE1 GLN A 161 1.89 REMARK 500 OD1 ASP A 153 OG SER A 216 1.90 REMARK 500 NE2 GLN A 159 OH TYR A 179 1.94 REMARK 500 OG SER A 381 O GLY A 386 1.95 REMARK 500 OG SER A 334 O THR A 338 1.96 REMARK 500 OG SER A 166 O PRO A 248 1.98 REMARK 500 O GLY A 273 OG SER A 276 2.01 REMARK 500 O ASN A 236 OG SER A 239 2.03 REMARK 500 OH TYR A 225 O MET A 328 2.06 REMARK 500 O VAL A 407 OG1 THR A 431 2.06 REMARK 500 CD2 LEU A 355 CD2 TYR A 388 2.07 REMARK 500 O LEU A 297 CB SER A 300 2.07 REMARK 500 OG1 THR A 338 O LYS A 363 2.08 REMARK 500 O ASP A 69 OG1 THR A 72 2.08 REMARK 500 O HIS A 49 NE2 GLN A 53 2.11 REMARK 500 O THR A 224 OD2 ASP A 269 2.12 REMARK 500 OD1 ASN A 310 OD1 ASP A 339 2.13 REMARK 500 O ASP A 253 N GLY A 255 2.14 REMARK 500 OG1 THR A 47 OD1 ASP A 50 2.15 REMARK 500 O SER A 202 N SER A 204 2.15 REMARK 500 CD2 LEU A 355 CE2 TYR A 388 2.17 REMARK 500 ND2 ASN A 392 O LEU A 396 2.18 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 OE2 GLU A 67 NZ LYS A 454 3545 1.97 REMARK 500 NZ LYS A 59 O GLY A 351 3545 2.03 REMARK 500 CG ASN A 99 ND2 ASN A 319 4455 2.04 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 61 CB GLU A 61 CG -0.165 REMARK 500 GLU A 61 CG GLU A 61 CD -0.176 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 PRO A 36 C - N - CA ANGL. DEV. = 10.6 DEGREES REMARK 500 LEU A 109 N - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 LYS A 114 CD - CE - NZ ANGL. DEV. = 38.0 DEGREES REMARK 500 VAL A 128 C - N - CA ANGL. DEV. = -15.9 DEGREES REMARK 500 TRP A 136 N - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 ASP A 203 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 241 CB - CG - OD1 ANGL. DEV. = -8.5 DEGREES REMARK 500 HIS A 256 N - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 TYR A 271 N - CA - CB ANGL. DEV. = -13.1 DEGREES REMARK 500 TYR A 271 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 LYS A 296 CA - C - N ANGL. DEV. = -22.5 DEGREES REMARK 500 LEU A 298 CB - CA - C ANGL. DEV. = 14.5 DEGREES REMARK 500 LEU A 298 CA - CB - CG ANGL. DEV. = 26.5 DEGREES REMARK 500 ASP A 301 N - CA - C ANGL. DEV. = -18.7 DEGREES REMARK 500 VAL A 327 N - CA - C ANGL. DEV. = -17.5 DEGREES REMARK 500 PHE A 356 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 MET A 376 N - CA - C ANGL. DEV. = -16.9 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 TYR A 41 18.10 53.83 REMARK 500 THR A 47 156.22 -38.90 REMARK 500 HIS A 49 -79.74 -45.77 REMARK 500 ASP A 50 -55.97 -26.89 REMARK 500 MET A 51 0.05 -61.86 REMARK 500 ILE A 54 -6.73 -47.92 REMARK 500 GLU A 56 -60.22 -91.85 REMARK 500 GLN A 58 2.70 -63.31 REMARK 500 VAL A 65 147.66 -38.26 REMARK 500 SER A 71 -8.71 -57.43 REMARK 500 THR A 72 -69.99 -92.19 REMARK 500 ILE A 73 125.52 -30.76 REMARK 500 SER A 77 -72.16 -47.65 REMARK 500 LYS A 80 58.55 81.94 REMARK 500 TRP A 85 -118.79 -105.37 REMARK 500 ASP A 86 109.59 -31.43 REMARK 500 THR A 96 148.38 -37.01 REMARK 500 HIS A 101 34.59 79.36 REMARK 500 ALA A 110 118.44 -170.63 REMARK 500 PRO A 113 -40.58 -24.46 REMARK 500 TYR A 125 147.90 -171.67 REMARK 500 THR A 131 -54.37 -124.83 REMARK 500 SER A 132 126.42 -39.51 REMARK 500 ASP A 134 2.46 -69.47 REMARK 500 LYS A 137 136.54 -27.61 REMARK 500 ASN A 152 35.33 82.33 REMARK 500 ALA A 167 94.28 -163.38 REMARK 500 ASP A 172 39.97 -96.47 REMARK 500 ALA A 195 150.72 169.73 REMARK 500 VAL A 197 71.91 -109.54 REMARK 500 ASP A 203 -2.54 -32.41 REMARK 500 SER A 204 -37.04 -145.53 REMARK 500 ILE A 208 66.01 -109.21 REMARK 500 ASN A 209 -57.94 -29.76 REMARK 500 ASP A 213 47.40 36.49 REMARK 500 VAL A 228 -6.76 -52.12 REMARK 500 ASN A 236 -135.47 100.50 REMARK 500 LEU A 245 87.17 -153.95 REMARK 500 ASP A 247 43.53 71.27 REMARK 500 ASP A 253 -145.41 -127.04 REMARK 500 LYS A 254 74.67 -34.80 REMARK 500 THR A 267 44.10 -87.10 REMARK 500 GLU A 268 -25.95 -164.81 REMARK 500 GLU A 275 -65.32 -29.76 REMARK 500 SER A 276 -58.35 -6.95 REMARK 500 LEU A 277 0.22 -69.53 REMARK 500 LYS A 285 -66.03 54.14 REMARK 500 THR A 287 -101.63 -47.61 REMARK 500 SER A 288 -27.32 -17.19 REMARK 500 PHE A 289 -83.00 -60.88 REMARK 500 REMARK 500 THIS ENTRY HAS 90 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 386 PRO A 387 -85.58 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 271 0.07 SIDE CHAIN REMARK 500 TYR A 379 0.12 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 ANGLE, 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 LYS A 296 14.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1473 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 241 OD1 REMARK 620 2 ASN A 242 O 84.9 REMARK 620 3 ASN A 264 ND2 149.3 66.0 REMARK 620 4 GLN A 272 OE1 93.2 159.9 117.5 REMARK 620 5 ASN A 310 OD1 132.0 134.9 71.6 58.5 REMARK 620 6 ASP A 339 OD2 91.2 53.4 64.3 146.7 95.0 REMARK 620 7 ASP A 339 OD1 109.2 101.4 69.8 98.1 48.3 49.6 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1473 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PT2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LEVANSUCRASE (E342A) COMPLEXED WITHSUCROSE REMARK 900 RELATED ID: 1OYG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LEVANSUCRASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTATION AT RESIDUE 164 FROM SER TO ALA DBREF 2VDT A 34 472 UNP P05655 SACB_BACSU 34 472 SEQADV 2VDT ALA A 164 UNP P05655 SER 164 ENGINEERED MUTATION SEQRES 1 A 439 GLN LYS PRO TYR LYS GLU THR TYR GLY ILE SER HIS ILE SEQRES 2 A 439 THR ARG HIS ASP MET LEU GLN ILE PRO GLU GLN GLN LYS SEQRES 3 A 439 ASN GLU LYS TYR GLN VAL PRO GLU PHE ASP SER SER THR SEQRES 4 A 439 ILE LYS ASN ILE SER SER ALA LYS GLY LEU ASP VAL TRP SEQRES 5 A 439 ASP SER TRP PRO LEU GLN ASN ALA ASP GLY THR VAL ALA SEQRES 6 A 439 ASN TYR HIS GLY TYR HIS ILE VAL PHE ALA LEU ALA GLY SEQRES 7 A 439 ASP PRO LYS ASN ALA ASP ASP THR SER ILE TYR MET PHE SEQRES 8 A 439 TYR GLN LYS VAL GLY GLU THR SER ILE ASP SER TRP LYS SEQRES 9 A 439 ASN ALA GLY ARG VAL PHE LYS ASP SER ASP LYS PHE ASP SEQRES 10 A 439 ALA ASN ASP SER ILE LEU LYS ASP GLN THR GLN GLU TRP SEQRES 11 A 439 ALA GLY SER ALA THR PHE THR SER ASP GLY LYS ILE ARG SEQRES 12 A 439 LEU PHE TYR THR ASP PHE SER GLY LYS HIS TYR GLY LYS SEQRES 13 A 439 GLN THR LEU THR THR ALA GLN VAL ASN VAL SER ALA SER SEQRES 14 A 439 ASP SER SER LEU ASN ILE ASN GLY VAL GLU ASP TYR LYS SEQRES 15 A 439 SER ILE PHE ASP GLY ASP GLY LYS THR TYR GLN ASN VAL SEQRES 16 A 439 GLN GLN PHE ILE ASP GLU GLY ASN TYR SER SER GLY ASP SEQRES 17 A 439 ASN HIS THR LEU ARG ASP PRO HIS TYR VAL GLU ASP LYS SEQRES 18 A 439 GLY HIS LYS TYR LEU VAL PHE GLU ALA ASN THR GLY THR SEQRES 19 A 439 GLU ASP GLY TYR GLN GLY GLU GLU SER LEU PHE ASN LYS SEQRES 20 A 439 ALA TYR TYR GLY LYS SER THR SER PHE PHE ARG GLN GLU SEQRES 21 A 439 SER GLN LYS LEU LEU GLN SER ASP LYS LYS ARG THR ALA SEQRES 22 A 439 GLU LEU ALA ASN GLY ALA LEU GLY MET ILE GLU LEU ASN SEQRES 23 A 439 ASP ASP TYR THR LEU LYS LYS VAL MET LYS PRO LEU ILE SEQRES 24 A 439 ALA SER ASN THR VAL THR ASP GLU ILE GLU ARG ALA ASN SEQRES 25 A 439 VAL PHE LYS MET ASN GLY LYS TRP TYR LEU PHE THR ASP SEQRES 26 A 439 SER ARG GLY SER LYS MET THR ILE ASP GLY ILE THR SER SEQRES 27 A 439 ASN ASP ILE TYR MET LEU GLY TYR VAL SER ASN SER LEU SEQRES 28 A 439 THR GLY PRO TYR LYS PRO LEU ASN LYS THR GLY LEU VAL SEQRES 29 A 439 LEU LYS MET ASP LEU ASP PRO ASN ASP VAL THR PHE THR SEQRES 30 A 439 TYR SER HIS PHE ALA VAL PRO GLN ALA LYS GLY ASN ASN SEQRES 31 A 439 VAL VAL ILE THR SER TYR MET THR ASN ARG GLY PHE TYR SEQRES 32 A 439 ALA ASP LYS GLN SER THR PHE ALA PRO SER PHE LEU LEU SEQRES 33 A 439 ASN ILE LYS GLY LYS LYS THR SER VAL VAL LYS ASP SER SEQRES 34 A 439 ILE LEU GLU GLN GLY GLN LEU THR VAL ASN HET CA A1473 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 HIS A 49 GLN A 53 5 5 HELIX 2 2 GLU A 56 ASN A 60 5 5 HELIX 3 3 ASN A 60 TYR A 63 5 4 HELIX 4 4 SER A 132 TRP A 136 5 5 HELIX 5 5 SER A 146 ALA A 151 1 6 HELIX 6 6 ASP A 153 ASP A 158 5 6 HELIX 7 7 ASN A 227 ASP A 233 1 7 HELIX 8 8 GLU A 274 PHE A 278 5 5 HELIX 9 9 LYS A 280 TYR A 283 5 4 HELIX 10 10 SER A 286 GLN A 299 1 14 HELIX 11 11 LYS A 303 LEU A 308 1 6 HELIX 12 12 ARG A 360 MET A 364 5 5 SHEET 1 AA 3 SER A 87 PRO A 89 0 SHEET 2 AA 3 TYR A 103 ALA A 108 -1 O PHE A 107 N TRP A 88 SHEET 3 AA 3 TYR A 125 LYS A 127 -1 O GLN A 126 N HIS A 104 SHEET 1 AB 4 GLN A 161 PHE A 169 0 SHEET 2 AB 4 ILE A 175 SER A 183 -1 O ARG A 176 N THR A 168 SHEET 3 AB 4 LYS A 189 GLN A 196 -1 O LYS A 189 N SER A 183 SHEET 4 AB 4 SER A 216 PHE A 218 -1 N ILE A 217 O LEU A 192 SHEET 1 AC 2 SER A 200 ALA A 201 0 SHEET 2 AC 2 LEU A 206 ASN A 207 -1 O ASN A 207 N SER A 200 SHEET 1 AD 4 ARG A 246 ASP A 253 0 SHEET 2 AD 4 HIS A 256 ALA A 263 -1 O HIS A 256 N ASP A 253 SHEET 3 AD 4 ALA A 312 LEU A 318 -1 O ALA A 312 N ALA A 263 SHEET 4 AD 4 ILE A 332 ALA A 333 -1 O ILE A 332 N LEU A 313 SHEET 1 AE 4 ARG A 246 ASP A 253 0 SHEET 2 AE 4 HIS A 256 ALA A 263 -1 O HIS A 256 N ASP A 253 SHEET 3 AE 4 ALA A 312 LEU A 318 -1 O ALA A 312 N ALA A 263 SHEET 4 AE 4 LEU A 324 VAL A 327 -1 N LYS A 325 O GLU A 317 SHEET 1 AF 4 VAL A 346 MET A 349 0 SHEET 2 AF 4 LYS A 352 SER A 359 -1 O LYS A 352 N MET A 349 SHEET 3 AF 4 TYR A 375 SER A 381 -1 O TYR A 375 N SER A 359 SHEET 4 AF 4 LEU A 396 LYS A 399 -1 N VAL A 397 O MET A 376 SHEET 1 AG 4 VAL A 346 MET A 349 0 SHEET 2 AG 4 LYS A 352 SER A 359 -1 O LYS A 352 N MET A 349 SHEET 3 AG 4 TYR A 375 SER A 381 -1 O TYR A 375 N SER A 359 SHEET 4 AG 4 LYS A 389 PRO A 390 -1 O LYS A 389 N VAL A 380 SHEET 1 AH 4 THR A 410 VAL A 416 0 SHEET 2 AH 4 ASN A 423 MET A 430 -1 O VAL A 425 N VAL A 416 SHEET 3 AH 4 LEU A 448 LYS A 452 -1 O LEU A 449 N VAL A 424 SHEET 4 AH 4 LYS A 455 VAL A 458 -1 O LYS A 455 N LYS A 452 SHEET 1 AI 3 THR A 410 VAL A 416 0 SHEET 2 AI 3 ASN A 423 MET A 430 -1 O VAL A 425 N VAL A 416 SHEET 3 AI 3 THR A 442 PHE A 443 -1 O THR A 442 N MET A 430 LINK OD1 ASP A 241 CA CA A1473 1555 1555 2.20 LINK O ASN A 242 CA CA A1473 1555 1555 2.68 LINK ND2 ASN A 264 CA CA A1473 1555 1555 3.02 LINK OE1 GLN A 272 CA CA A1473 1555 1555 2.62 LINK OD1 ASN A 310 CA CA A1473 1555 1555 2.57 LINK OD2 ASP A 339 CA CA A1473 1555 1555 2.64 LINK OD1 ASP A 339 CA CA A1473 1555 1555 2.64 SITE 1 AC1 7 ASP A 241 ASN A 242 ASN A 264 GLN A 272 SITE 2 AC1 7 LEU A 308 ASN A 310 ASP A 339 CRYST1 50.880 55.800 124.600 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 0.019654 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008026 0.00000