HEADER SUGAR BINDING PROTEIN 11-AUG-23 8Q6C TITLE THE RSL-D32N - SULFONATO-CALIX[8]ARENE COMPLEX, P63 FORM, ACETATE PH TITLE 2 4.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUCOSE-BINDING LECTIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE FUCOSE-BINDING LECTIN PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA SOLANACEARUM; SOURCE 3 ORGANISM_TAXID: 305; SOURCE 4 GENE: E7Z57_08365, HF909_06975, HXP36_18875, RSP795_21825, SOURCE 5 RSP822_19650, RUN39_V1_50103; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BIOMATERIALS, BETA-PROPELLER, CRYSTAL ENGINEERING, MOLECULAR GLUE, KEYWDS 2 SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.J.FLOOD,P.B.CROWLEY REVDAT 2 20-MAR-24 8Q6C 1 JRNL REVDAT 1 06-MAR-24 8Q6C 0 JRNL AUTH R.J.FLOOD,N.M.MOCKLER,A.THUREAU,M.MALINSKA,P.B.CROWLEY JRNL TITL SUPRAMOLECULAR SYNTHONS IN PROTEIN-LIGAND FRAMEWORKS. JRNL REF CRYST.GROWTH DES. V. 24 2149 2024 JRNL REFN ISSN 1528-7483 JRNL PMID 38463617 JRNL DOI 10.1021/ACS.CGD.3C01480 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.O.RAMBERG,S.ENGILBERGE,T.SKOREK,P.B.CROWLEY REMARK 1 TITL FACILE FABRICATION OF PROTEIN-MACROCYCLE FRAMEWORKS. REMARK 1 REF J AM CHEM SOC V. 143 1896 2021 REMARK 1 REFN ESSN 1520-5126 REMARK 1 PMID 33470808 REMARK 1 DOI 10.1107/S2052252519003622 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26953 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1320 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 51.8100 - 2.8700 1.00 2915 145 0.1754 0.1689 REMARK 3 2 2.8700 - 2.2800 1.00 2856 152 0.2158 0.2155 REMARK 3 3 2.2800 - 1.9900 1.00 2833 149 0.2057 0.2077 REMARK 3 4 1.9900 - 1.8100 1.00 2850 149 0.1892 0.2302 REMARK 3 5 1.8100 - 1.6800 1.00 2841 145 0.2071 0.2070 REMARK 3 6 1.6800 - 1.5800 1.00 2846 125 0.1832 0.1686 REMARK 3 7 1.5800 - 1.5000 1.00 2840 143 0.1907 0.2040 REMARK 3 8 1.5000 - 1.4400 1.00 2843 150 0.2216 0.2317 REMARK 3 9 1.4400 - 1.3800 1.00 2809 162 0.2531 0.2663 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.164 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 830 REMARK 3 ANGLE : 0.756 1166 REMARK 3 CHIRALITY : 0.075 110 REMARK 3 PLANARITY : 0.005 201 REMARK 3 DIHEDRAL : 7.754 130 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8Q6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132670. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 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 : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26994 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 59.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM ACETATE PH 4.0, 50 MM REMARK 280 NACL, BATCH MODE, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.33900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.33900 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.33900 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -59.82400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -29.91200 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -51.80910 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 254 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 256 LIES ON A SPECIAL POSITION. REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 SER A 1 REMARK 475 SER A 2 REMARK 475 THR A 89 REMARK 475 ASN A 90 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 25 CE NZ REMARK 480 ALA A 88 C O CB 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 LYS A 34 80.39 -156.84 REMARK 500 ASN A 79 55.17 -144.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Z5Q RELATED DB: PDB DBREF1 8Q6C A 1 90 UNP A0A0S4TLR1_RALSL DBREF2 8Q6C A A0A0S4TLR1 2 91 SEQADV 8Q6C ASN A 32 UNP A0A0S4TLR ASP 33 ENGINEERED MUTATION SEQRES 1 A 90 SER SER VAL GLN THR ALA ALA THR SER TRP GLY THR VAL SEQRES 2 A 90 PRO SER ILE ARG VAL TYR THR ALA ASN ASN GLY LYS ILE SEQRES 3 A 90 THR GLU ARG CYS TRP ASN GLY LYS GLY TRP TYR THR GLY SEQRES 4 A 90 ALA PHE ASN GLU PRO GLY ASP ASN VAL SER VAL THR SER SEQRES 5 A 90 TRP LEU VAL GLY SER ALA ILE HIS ILE ARG VAL TYR ALA SEQRES 6 A 90 SER THR GLY THR THR THR THR GLU TRP CYS TRP ASP GLY SEQRES 7 A 90 ASN GLY TRP THR LYS GLY ALA TYR THR ALA THR ASN HET GOL A 101 6 HET BDF A 102 12 HET EVB A 103 96 HETNAM GOL GLYCEROL HETNAM BDF BETA-D-FRUCTOPYRANOSE HETNAM EVB SULFONATO-CALIX[8]ARENE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN BDF BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE FORMUL 2 GOL C3 H8 O3 FORMUL 3 BDF C6 H12 O6 FORMUL 4 EVB C56 H48 O32 S8 FORMUL 5 HOH *58(H2 O) SHEET 1 AA1 4 GLN A 4 TRP A 10 0 SHEET 2 AA1 4 SER A 15 ASN A 22 -1 O TYR A 19 N ALA A 6 SHEET 3 AA1 4 LYS A 25 TRP A 31 -1 O LYS A 25 N ASN A 22 SHEET 4 AA1 4 TRP A 36 PRO A 44 -1 O TYR A 37 N CYS A 30 SHEET 1 AA2 4 ASN A 47 VAL A 55 0 SHEET 2 AA2 4 ALA A 58 THR A 67 -1 O TYR A 64 N SER A 49 SHEET 3 AA2 4 THR A 70 TRP A 76 -1 O THR A 72 N ALA A 65 SHEET 4 AA2 4 TRP A 81 LYS A 83 -1 O THR A 82 N CYS A 75 CISPEP 1 VAL A 13 PRO A 14 0 -3.61 CRYST1 59.824 59.824 64.678 90.00 90.00 120.00 P 63 6 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 0.016716 0.009651 0.000000 0.00000 SCALE2 0.000000 0.019302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015461 0.00000