HEADER HYDROLASE 21-FEB-20 6M0D TITLE BEIJERINCKIA INDICA BETA-FRUCTOSYLTRANSFERASE 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 5 29-NOV-23 6M0D 1 REMARK REVDAT 4 18-NOV-20 6M0D 1 JRNL REVDAT 3 14-OCT-20 6M0D 1 JRNL REVDAT 2 19-AUG-20 6M0D 1 JRNL REVDAT 1 12-AUG-20 6M0D 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 20660 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) : 0.222 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.894 REMARK 3 FREE R VALUE TEST SET COUNT : 1011 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1419 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3693 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.00600 REMARK 3 B22 (A**2) : 0.01400 REMARK 3 B33 (A**2) : -0.00800 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): 0.450 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.261 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 : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3813 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3285 ; 0.036 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5217 ; 1.636 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7647 ; 2.410 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 475 ; 8.058 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;33.734 ;22.947 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 521 ;15.420 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.269 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 481 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4412 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 829 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 768 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 94 ; 0.271 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1810 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 136 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.149 ; 0.200 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): 1906 ; 2.233 ; 2.975 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1905 ; 2.231 ; 2.974 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2379 ; 3.269 ; 4.455 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2380 ; 3.269 ; 4.456 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1907 ; 2.601 ; 3.163 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1907 ; 2.601 ; 3.163 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2838 ; 3.815 ; 4.671 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2838 ; 3.814 ; 4.671 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 6M0D 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_1300015806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-19 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 : 20772 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 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: 1W18 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 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 26.44550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.33050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.33050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.44550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.45000 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: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17810 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 GLY A 202 REMARK 465 GLY A 203 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 465 LYS A 210 REMARK 465 ASN A 211 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 OG SER A 70 OD2 ASP A 171 3454 2.16 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 VAL A 69 75.91 -100.42 REMARK 500 TRP A 99 -107.15 -131.88 REMARK 500 PRO A 235 153.45 -49.74 REMARK 500 ASP A 249 -162.51 -128.37 REMARK 500 PHE A 283 99.36 -160.49 REMARK 500 LYS A 329 177.63 -58.78 REMARK 500 MET A 344 57.60 -144.75 REMARK 500 VAL A 372 -56.35 -126.13 REMARK 500 ARG A 378 63.54 27.34 REMARK 500 ASP A 420 82.39 -67.54 REMARK 500 ASN A 425 80.84 66.63 REMARK 500 PRO A 466 133.92 -39.34 REMARK 500 ASP A 475 -94.08 -93.96 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 SER A 419 ASP A 420 149.71 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 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 68 O REMARK 620 2 ASP A 171 OD2 100.1 REMARK 620 3 HOH A 716 O 99.4 4.6 REMARK 620 4 HOH A 730 O 99.1 3.1 1.6 REMARK 620 5 HOH A 745 O 97.2 3.4 3.6 2.3 REMARK 620 N 1 2 3 4 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 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 6M0D A 30 521 UNP B2IF78 B2IF78_BEII9 30 534 SEQADV 6M0D GLY A -6 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D SER A -5 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D GLY A -4 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D MET A -3 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D LYS A -2 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D GLU A -1 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D THR A 0 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ALA A 1 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ALA A 2 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ALA A 3 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D LYS A 4 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D PHE A 5 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D GLU A 6 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ARG A 7 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D GLN A 8 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D HIS A 9 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D MET A 10 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ASP A 11 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D SER A 12 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D PRO A 13 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ASP A 14 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D LEU A 15 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D GLY A 16 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D THR A 17 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ASP A 18 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ASP A 19 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ASP A 20 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ASP A 21 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D LYS A 22 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ALA A 23 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D MET A 24 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ALA A 25 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ASP A 26 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D ILE A 27 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D GLY A 28 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D SER A 29 UNP B2IF78 EXPRESSION TAG SEQADV 6M0D A UNP B2IF78 GLY 198 DELETION SEQADV 6M0D A UNP B2IF78 PRO 199 DELETION SEQADV 6M0D A UNP B2IF78 TYR 200 DELETION SEQADV 6M0D A UNP B2IF78 ALA 201 DELETION SEQADV 6M0D A UNP B2IF78 ASP 202 DELETION SEQADV 6M0D PRO A 479 UNP B2IF78 THR 479 CONFLICT SEQADV 6M0D GLY A 495 UNP B2IF78 ARG 495 CONFLICT SEQADV 6M0D A UNP B2IF78 LEU 522 DELETION SEQADV 6M0D A UNP B2IF78 GLY 523 DELETION SEQADV 6M0D A UNP B2IF78 GLN 524 DELETION SEQADV 6M0D A UNP B2IF78 GLY 525 DELETION SEQADV 6M0D A UNP B2IF78 ASN 526 DELETION SEQADV 6M0D A UNP B2IF78 GLY 527 DELETION SEQADV 6M0D A UNP B2IF78 HIS 528 DELETION SEQADV 6M0D A UNP B2IF78 GLY 529 DELETION SEQADV 6M0D A UNP B2IF78 VAL 530 DELETION SEQADV 6M0D A UNP B2IF78 THR 531 DELETION SEQADV 6M0D A UNP B2IF78 ASN 532 DELETION SEQADV 6M0D A UNP B2IF78 GLY 533 DELETION SEQADV 6M0D 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 HETNAM MG MAGNESIUM ION FORMUL 2 MG 2(MG 2+) FORMUL 4 HOH *66(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 VAL A 175 GLY A 179 5 5 HELIX 6 AA6 THR A 316 GLY A 321 1 6 HELIX 7 AA7 ASP A 331 SER A 338 1 8 HELIX 8 AA8 GLY A 339 GLN A 343 5 5 HELIX 9 AA9 HIS A 395 TYR A 399 5 5 HELIX 10 AB1 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 GLY A 304 O ASN A 346 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 TRP A 254 N GLN A 247 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 ILE A 393 N GLU A 377 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 ILE A 393 N GLU A 377 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 VAL A 464 0 SHEET 2 AA6 3 LEU A 469 ILE A 477 -1 O GLU A 471 N TYR A 463 SHEET 3 AA6 3 ARG A 480 LEU A 485 -1 O GLY A 482 N ASP A 475 SHEET 1 AA7 4 SER A 459 VAL A 464 0 SHEET 2 AA7 4 LEU A 469 ILE A 477 -1 O GLU A 471 N TYR A 463 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 SER A 497 N ASN A 494 SSBOND 1 CYS A 315 CYS A 371 1555 1555 2.05 LINK O PRO A 68 MG MG A 602 1555 3454 2.60 LINK OD2 ASP A 171 MG MG A 602 1555 1555 2.35 LINK MG MG A 601 O HOH A 738 1555 1555 2.03 LINK MG MG A 602 O HOH A 716 1555 3444 2.18 LINK MG MG A 602 O HOH A 730 1555 3444 1.84 LINK MG MG A 602 O HOH A 745 1555 1555 2.38 CISPEP 1 SER A 70 PRO A 71 0 28.26 SITE 1 AC1 1 HOH A 738 SITE 1 AC2 6 PRO A 68 SER A 70 ASP A 171 HOH A 716 SITE 2 AC2 6 HOH A 730 HOH A 745 CRYST1 52.891 80.900 92.661 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 0.018907 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012361 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010792 0.00000