HEADER HYDROLASE 21-FEB-20 6M0E TITLE BEIJERINCKIA INDICA BETA-FRUCTOSYLTRANSFERASE COMPLEXED WITH FRUCTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEVANSUCRASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.4.1.10; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BEIJERINCKIA INDICA SUBSP. INDICA (STRAIN ATCC SOURCE 3 9039 / DSM 1715 / NCIB 8712); SOURCE 4 ORGANISM_TAXID: 395963; SOURCE 5 STRAIN: ATCC 9039 / DSM 1715 / NCIB 8712; SOURCE 6 GENE: BIND_2021; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GH68, FRUCTOOLIGOSACCHARIDE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.TONOZUKA REVDAT 6 06-NOV-24 6M0E 1 REMARK REVDAT 5 29-NOV-23 6M0E 1 REMARK REVDAT 4 18-NOV-20 6M0E 1 JRNL REVDAT 3 14-OCT-20 6M0E 1 JRNL REVDAT 2 19-AUG-20 6M0E 1 JRNL REVDAT 1 12-AUG-20 6M0E 0 JRNL AUTH T.TONOZUKA,J.KITAMURA,M.NAGAYA,R.KAWAI,A.NISHIKAWA,K.HIRANO, JRNL AUTH 2 K.TAMURA,T.FUJII,T.TOCHIO JRNL TITL CRYSTAL STRUCTURE OF A GLYCOSIDE HYDROLASE FAMILY 68 JRNL TITL 2 BETA-FRUCTOSYLTRANSFERASE FROM BEIJERINCKIA INDICA SUBSP. JRNL TITL 3 INDICA IN COMPLEX WITH FRUCTOSE. JRNL REF BIOSCI.BIOTECHNOL.BIOCHEM. V. 84 2508 2020 JRNL REFN ISSN 0916-8451 JRNL PMID 32752982 JRNL DOI 10.1080/09168451.2020.1804317 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 96024 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.856 REMARK 3 FREE R VALUE TEST SET COUNT : 4663 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 350 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3701 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 583 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.00100 REMARK 3 B33 (A**2) : 0.00100 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): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3884 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3338 ; 0.036 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5323 ; 1.470 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7780 ; 2.310 ; 1.575 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 477 ; 7.272 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;32.462 ;22.981 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 526 ;11.648 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;14.977 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 503 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4423 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 830 ; 0.010 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 673 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 48 ; 0.232 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1902 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 373 ; 0.111 ; 0.200 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): NULL ; NULL ; NULL 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): 1908 ; 1.082 ; 1.453 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1907 ; 1.067 ; 1.452 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2382 ; 1.735 ; 2.182 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2383 ; 1.738 ; 2.183 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1976 ; 1.499 ; 1.612 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1977 ; 1.498 ; 1.612 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2940 ; 2.345 ; 2.367 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2941 ; 2.345 ; 2.367 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6M0E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96105 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 45.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6M0D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) POLYETHYLENE GLYCOL 10000, REMARK 280 0.2 M MGCL2, 0.1 M NA K TARTRATE, 0.1 M TRIS-HCL, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 27.18850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.54050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.76050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.54050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.18850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.76050 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 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 GLY A -6 REMARK 465 SER A -5 REMARK 465 GLY A -4 REMARK 465 MET A -3 REMARK 465 LYS A -2 REMARK 465 GLU A -1 REMARK 465 THR A 0 REMARK 465 ALA A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 PHE A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 REMARK 465 GLN A 8 REMARK 465 HIS A 9 REMARK 465 MET A 10 REMARK 465 ASP A 11 REMARK 465 SER A 12 REMARK 465 PRO A 13 REMARK 465 ASP A 14 REMARK 465 LEU A 15 REMARK 465 GLY A 16 REMARK 465 THR A 17 REMARK 465 ASP A 18 REMARK 465 ASP A 19 REMARK 465 ASP A 20 REMARK 465 ASP A 21 REMARK 465 LYS A 22 REMARK 465 ALA A 23 REMARK 465 MET A 24 REMARK 465 ALA A 25 REMARK 465 ASP A 26 REMARK 465 ILE A 27 REMARK 465 GLY A 28 REMARK 465 SER A 29 REMARK 465 SER A 30 REMARK 465 GLY A 31 REMARK 465 GLY A 197 REMARK 465 GLY A 198 REMARK 465 PRO A 204 REMARK 465 GLN A 205 REMARK 465 HIS A 206 REMARK 465 ALA A 207 REMARK 465 TYR A 208 REMARK 465 LEU A 209 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 TRP A 99 -116.22 -136.49 REMARK 500 ASN A 278 110.04 -160.98 REMARK 500 ASP A 285 60.71 77.00 REMARK 500 MET A 344 52.06 -142.00 REMARK 500 VAL A 372 -58.79 -122.29 REMARK 500 ARG A 378 57.79 36.29 REMARK 500 ASN A 425 77.74 65.31 REMARK 500 ALA A 447 77.60 -154.34 REMARK 500 ASP A 475 -71.26 -98.91 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 A1280 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1281 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A1282 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1283 DISTANCE = 6.29 ANGSTROMS 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 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 171 OD2 REMARK 620 2 HOH A 736 O 138.7 REMARK 620 3 HOH A 945 O 78.6 69.1 REMARK 620 4 HOH A1040 O 97.1 105.9 86.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 804 O REMARK 620 2 HOH A 867 O 87.8 REMARK 620 3 HOH A 940 O 87.5 84.6 REMARK 620 4 HOH A1124 O 169.9 86.1 99.9 REMARK 620 5 HOH A1219 O 87.6 169.7 86.0 99.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1010 O REMARK 620 2 HOH A1049 O 96.6 REMARK 620 3 HOH A1075 O 96.6 92.8 REMARK 620 4 HOH A1095 O 124.9 105.9 130.7 REMARK 620 5 HOH A1153 O 163.8 74.7 70.7 71.0 REMARK 620 6 HOH A1169 O 65.7 84.6 161.5 67.3 125.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FRU A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BDF A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BDF A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BDF A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BDF A 608 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE GENE WAS CLONED USING B. INDICA SUBSP. INDICA STRAIN NBRC 3744, REMARK 999 AND DNA PRIMERS FOR THE PCR AMPLIFICATION WAS DESIGNED USING THE REMARK 999 SEQUENCE OF BIND_2021 OF B. INDICA SUBSP. INDICA STRAIN ATCC 9039. REMARK 999 TWO AMINO ACID RESIDUES ARE DIFFERENT BETWEEN THE STRAIN NBRC 3744 REMARK 999 (PRO479 AND GLY495) AND THE STRAIN ATCC 9039 (THR479 AND ARG495). REMARK 999 SEQUENCE DDBJ ACCESSION NUMBER LC522529. DBREF 6M0E A 32 521 UNP B2IF78 B2IF78_BEII9 31 534 SEQADV 6M0E GLY A -6 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E SER A -5 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E GLY A -4 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E MET A -3 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E LYS A -2 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E GLU A -1 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E THR A 0 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ALA A 1 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ALA A 2 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ALA A 3 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E LYS A 4 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E PHE A 5 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E GLU A 6 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ARG A 7 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E GLN A 8 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E HIS A 9 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E MET A 10 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ASP A 11 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E SER A 12 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E PRO A 13 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ASP A 14 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E LEU A 15 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E GLY A 16 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E THR A 17 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ASP A 18 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ASP A 19 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ASP A 20 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ASP A 21 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E LYS A 22 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ALA A 23 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E MET A 24 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ALA A 25 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ASP A 26 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E ILE A 27 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E GLY A 28 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E SER A 29 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E SER A 30 UNP B2IF78 EXPRESSION TAG SEQADV 6M0E A UNP B2IF78 PRO 199 DELETION SEQADV 6M0E A UNP B2IF78 TYR 200 DELETION SEQADV 6M0E A UNP B2IF78 ALA 201 DELETION SEQADV 6M0E A UNP B2IF78 ASP 202 DELETION SEQADV 6M0E A UNP B2IF78 GLY 203 DELETION SEQADV 6M0E PRO A 479 UNP B2IF78 THR 479 CONFLICT SEQADV 6M0E GLY A 495 UNP B2IF78 ARG 495 CONFLICT SEQADV 6M0E A UNP B2IF78 LEU 522 DELETION SEQADV 6M0E A UNP B2IF78 GLY 523 DELETION SEQADV 6M0E A UNP B2IF78 GLN 524 DELETION SEQADV 6M0E A UNP B2IF78 GLY 525 DELETION SEQADV 6M0E A UNP B2IF78 ASN 526 DELETION SEQADV 6M0E A UNP B2IF78 GLY 527 DELETION SEQADV 6M0E A UNP B2IF78 HIS 528 DELETION SEQADV 6M0E A UNP B2IF78 GLY 529 DELETION SEQADV 6M0E A UNP B2IF78 VAL 530 DELETION SEQADV 6M0E A UNP B2IF78 THR 531 DELETION SEQADV 6M0E A UNP B2IF78 ASN 532 DELETION SEQADV 6M0E A UNP B2IF78 GLY 533 DELETION SEQADV 6M0E A UNP B2IF78 GLN 534 DELETION SEQRES 1 A 523 GLY SER GLY MET LYS GLU THR ALA ALA ALA LYS PHE GLU SEQRES 2 A 523 ARG GLN HIS MET ASP SER PRO ASP LEU GLY THR ASP ASP SEQRES 3 A 523 ASP ASP LYS ALA MET ALA ASP ILE GLY SER SER GLY TYR SEQRES 4 A 523 PRO ILE PRO THR PRO HIS SER GLY GLN ALA TYR ASP PRO SEQRES 5 A 523 PHE ALA ASP PHE THR ALA LYS TRP THR ARG ALA ASN ALA SEQRES 6 A 523 ARG GLN ILE LYS ALA GLN SER HIS VAL PRO VAL SER PRO SEQRES 7 A 523 ASP GLN ASN SER LEU PRO LEU ASN LEU THR MET PRO ASP SEQRES 8 A 523 ILE PRO ALA ASP PHE PRO GLN THR ASN PRO ASP VAL TRP SEQRES 9 A 523 VAL TRP ASP THR TRP PRO LEU ALA ASP VAL HIS GLY ASN SEQRES 10 A 523 GLN LEU SER PHE GLN GLY TRP GLU VAL ILE PHE SER LEU SEQRES 11 A 523 THR ALA ASP PRO HIS ALA GLY TYR VAL PHE ASP ASP ARG SEQRES 12 A 523 HIS VAL HIS ALA ARG ILE GLY PHE PHE TYR ARG LYS ALA SEQRES 13 A 523 GLY ILE PRO ALA ASN GLN ARG PRO ILE ASP GLY GLY TRP SEQRES 14 A 523 ILE TYR GLY GLY HIS LEU PHE PRO ASP GLY SER SER VAL SEQRES 15 A 523 LYS VAL PHE GLY ASN VAL PRO MET THR GLN ASN ALA GLU SEQRES 16 A 523 TRP SER GLY GLY ALA ARG PHE VAL GLY GLY PRO GLN HIS SEQRES 17 A 523 ALA TYR LEU LYS ASN ASN ASN VAL SER LEU TYR TYR THR SEQRES 18 A 523 ALA THR SER PHE ASN ARG ASN ALA GLN GLY GLY ASN ILE SEQRES 19 A 523 THR PRO PRO ILE ALA ILE ILE SER ARG ALA ASP GLY GLN SEQRES 20 A 523 ILE GLN ALA ASP ASP LYS HIS VAL TRP PHE THR GLY PHE SEQRES 21 A 523 ASP GLN HIS LEU PRO LEU LEU ALA PRO ASP GLY LYS TYR SEQRES 22 A 523 TYR GLN THR GLY GLN GLN ASN GLU PHE PHE SER PHE ARG SEQRES 23 A 523 ASP PRO TYR VAL PHE LEU ASP PRO ALA HIS PRO GLY LYS SEQRES 24 A 523 THR PHE MET VAL PHE GLU GLY ASN THR ALA VAL GLN ARG SEQRES 25 A 523 GLY SER ARG SER CYS THR GLU ALA ASP LEU GLY TYR SER SEQRES 26 A 523 PRO ASN ASP PRO ASN LYS GLU ASP LEU ASN ALA VAL MET SEQRES 27 A 523 ASP SER GLY ALA ILE TYR GLN MET ALA ASN VAL GLY LEU SEQRES 28 A 523 ALA VAL ALA THR ASN ASP GLU LEU THR GLN TRP LYS PHE SEQRES 29 A 523 LEU PRO PRO ILE LEU SER GLY ASN CYS VAL ASN ASP GLN SEQRES 30 A 523 THR GLU ARG PRO GLN ILE TYR LEU LYS ASP GLY LYS TYR SEQRES 31 A 523 TYR LEU PHE THR ILE SER HIS ARG THR THR TYR ALA ALA SEQRES 32 A 523 GLY VAL ASP GLY PRO ASP GLY VAL TYR GLY PHE VAL GLY SEQRES 33 A 523 ASP GLY ILE ARG SER ASP PHE ILE PRO LEU ASN GLY LEU SEQRES 34 A 523 SER GLY LEU THR LEU GLY ASN PRO THR ASP LEU TYR GLN SEQRES 35 A 523 PRO ALA GLY ALA PRO TYR ALA LEU ASN PRO ASN GLN ASN SEQRES 36 A 523 PRO ARG THR PHE GLN SER TYR SER HIS TYR VAL MET PRO SEQRES 37 A 523 GLY GLY LEU VAL GLU SER PHE ILE ASP ALA ILE GLY PRO SEQRES 38 A 523 ARG ARG GLY GLY ALA LEU ALA PRO THR VAL LYS ILE ASN SEQRES 39 A 523 ILE ASN GLY THR SER THR ILE LEU ASP ARG THR TYR GLY SEQRES 40 A 523 ASN ALA GLY LEU GLY GLY TYR GLY ASP ILE PRO ALA ASN SEQRES 41 A 523 LEU PRO ALA HET MG A 601 1 HET MG A 602 1 HET MG A 603 1 HET FRU A 604 12 HET BDF A 605 12 HET BDF A 606 12 HET BDF A 607 12 HET BDF A 608 12 HETNAM MG MAGNESIUM ION HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM BDF BETA-D-FRUCTOPYRANOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN BDF BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE FORMUL 2 MG 3(MG 2+) FORMUL 5 FRU C6 H12 O6 FORMUL 6 BDF 4(C6 H12 O6) FORMUL 10 HOH *583(H2 O) HELIX 1 AA1 THR A 54 ARG A 59 1 6 HELIX 2 AA2 ARG A 59 SER A 65 1 7 HELIX 3 AA3 PRO A 77 THR A 81 5 5 HELIX 4 AA4 VAL A 132 ALA A 140 5 9 HELIX 5 AA5 PRO A 152 ARG A 156 5 5 HELIX 6 AA6 SER A 173 GLY A 179 5 7 HELIX 7 AA7 THR A 316 GLY A 321 1 6 HELIX 8 AA8 ASP A 331 SER A 338 1 8 HELIX 9 AA9 GLY A 339 GLN A 343 5 5 HELIX 10 AB1 HIS A 395 TYR A 399 5 5 HELIX 11 AB2 LEU A 424 SER A 428 1 5 SHEET 1 AA1 5 ALA A 51 LYS A 52 0 SHEET 2 AA1 5 TRP A 360 SER A 368 1 O SER A 368 N ALA A 51 SHEET 3 AA1 5 ALA A 345 ALA A 352 -1 N LEU A 349 O LEU A 363 SHEET 4 AA1 5 PHE A 299 ASN A 305 -1 N PHE A 302 O GLY A 348 SHEET 5 AA1 5 ARG A 284 PHE A 289 -1 N ARG A 284 O GLU A 303 SHEET 1 AA2 8 ILE A 163 HIS A 167 0 SHEET 2 AA2 8 ARG A 141 LYS A 148 -1 N TYR A 146 O ILE A 163 SHEET 3 AA2 8 TRP A 117 ALA A 125 -1 N GLU A 118 O ARG A 147 SHEET 4 AA2 8 TRP A 97 ALA A 105 -1 N TRP A 97 O ALA A 125 SHEET 5 AA2 8 GLN A 185 PHE A 195 1 O PHE A 195 N ALA A 105 SHEET 6 AA2 8 VAL A 214 ARG A 225 -1 O THR A 219 N TRP A 189 SHEET 7 AA2 8 ASN A 231 ALA A 248 -1 O ILE A 232 N ASN A 224 SHEET 8 AA2 8 VAL A 253 LEU A 265 -1 O LEU A 262 N ARG A 241 SHEET 1 AA3 2 LEU A 112 SER A 113 0 SHEET 2 AA3 2 LEU A 519 PRO A 520 1 O LEU A 519 N SER A 113 SHEET 1 AA4 4 GLU A 377 LYS A 384 0 SHEET 2 AA4 4 LYS A 387 SER A 394 -1 O TYR A 389 N TYR A 382 SHEET 3 AA4 4 GLY A 408 GLY A 414 -1 O TYR A 410 N THR A 392 SHEET 4 AA4 4 ILE A 422 PRO A 423 -1 O ILE A 422 N VAL A 413 SHEET 1 AA5 4 GLU A 377 LYS A 384 0 SHEET 2 AA5 4 LYS A 387 SER A 394 -1 O TYR A 389 N TYR A 382 SHEET 3 AA5 4 GLY A 408 GLY A 414 -1 O TYR A 410 N THR A 392 SHEET 4 AA5 4 LEU A 430 GLY A 433 -1 O LEU A 432 N VAL A 409 SHEET 1 AA6 3 SER A 459 MET A 465 0 SHEET 2 AA6 3 LEU A 469 ILE A 477 -1 O LEU A 469 N MET A 465 SHEET 3 AA6 3 ARG A 480 LEU A 485 -1 O ALA A 484 N ILE A 474 SHEET 1 AA7 4 SER A 459 MET A 465 0 SHEET 2 AA7 4 LEU A 469 ILE A 477 -1 O LEU A 469 N MET A 465 SHEET 3 AA7 4 VAL A 489 ASN A 494 -1 O VAL A 489 N VAL A 470 SHEET 4 AA7 4 SER A 497 LEU A 500 -1 O ILE A 499 N ASN A 492 SSBOND 1 CYS A 315 CYS A 371 1555 1555 2.04 LINK OD2 ASP A 171 MG MG A 603 1555 1555 2.30 LINK MG MG A 601 O HOH A 804 1555 1555 2.12 LINK MG MG A 601 O HOH A 867 1555 1555 2.13 LINK MG MG A 601 O HOH A 940 1555 1555 2.26 LINK MG MG A 601 O HOH A1124 1555 3655 2.09 LINK MG MG A 601 O HOH A1219 1555 1555 2.16 LINK MG MG A 602 O HOH A1010 1555 3655 2.11 LINK MG MG A 602 O HOH A1049 1555 3655 2.86 LINK MG MG A 602 O HOH A1075 1555 1555 2.48 LINK MG MG A 602 O HOH A1095 1555 1555 2.41 LINK MG MG A 602 O HOH A1153 1555 1555 2.42 LINK MG MG A 602 O HOH A1169 1555 3655 2.89 LINK MG MG A 603 O HOH A 736 1555 3645 2.37 LINK MG MG A 603 O HOH A 945 1555 1555 2.76 LINK MG MG A 603 O HOH A1040 1555 3645 2.80 CISPEP 1 SER A 70 PRO A 71 0 4.58 SITE 1 AC1 5 HOH A 804 HOH A 867 HOH A 940 HOH A1124 SITE 2 AC1 5 HOH A1219 SITE 1 AC2 7 ASN A 451 HOH A1010 HOH A1049 HOH A1075 SITE 2 AC2 7 HOH A1095 HOH A1153 HOH A1169 SITE 1 AC3 5 PRO A 68 ASP A 171 HOH A 736 HOH A 945 SITE 2 AC3 5 HOH A1040 SITE 1 AC4 11 TRP A 99 ASP A 100 HIS A 137 TRP A 189 SITE 2 AC4 11 ARG A 284 ASP A 285 GLU A 303 GLU A 377 SITE 3 AC4 11 BDF A 605 HOH A 759 HOH A 846 SITE 1 AC5 9 ARG A 136 HIS A 137 HIS A 395 FRU A 604 SITE 2 AC5 9 HOH A 729 HOH A 731 HOH A 768 HOH A 846 SITE 3 AC5 9 HOH A1076 SITE 1 AC6 11 THR A 50 LYS A 52 SER A 314 ASP A 319 SITE 2 AC6 11 SER A 368 ASN A 370 HOH A 816 HOH A 824 SITE 3 AC6 11 HOH A 844 HOH A 960 HOH A1012 SITE 1 AC7 15 GLN A 41 ALA A 42 TYR A 43 GLN A 277 SITE 2 AC7 15 ALA A 307 VAL A 308 GLN A 309 SER A 312 SITE 3 AC7 15 HOH A 701 HOH A 803 HOH A 854 HOH A 864 SITE 4 AC7 15 HOH A 881 HOH A 928 HOH A1021 SITE 1 AC8 11 ALA A 87 ASN A 354 ASP A 355 GLU A 356 SITE 2 AC8 11 ARG A 455 HOH A 705 HOH A 717 HOH A 767 SITE 3 AC8 11 HOH A 840 HOH A 885 HOH A 942 CRYST1 54.377 81.521 99.081 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 0.018390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012267 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010093 0.00000