HEADER SUGAR BINDING PROTEIN 29-FEB-24 9AUQ TITLE CRYSTAL STRUCTURE OF 4-FLUORO-TRYPTOPHAN LABELED OSCILLATORIA AGARDHII TITLE 2 AGGLUTININ COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLANKTOTHRIX AGARDHII; SOURCE 3 ORGANISM_TAXID: 1160; SOURCE 4 GENE: OAA, NO365_04266; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LECTIN, BETA BARREL, CARBOHYDRATE BINDING, FLUORINATED, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.R.RUNGE,R.R.ZADOROZHNYI,C.M.QUINN,R.W.RUSSELL,M.LU,S.ANTOLINEZ, AUTHOR 2 J.STRUPPE,C.D.SCHWIETERS,I.L.BYEON,J.HADDEN-PERILLA,A.M.GRONENBORN, AUTHOR 3 T.POLENOVA REVDAT 2 20-NOV-24 9AUQ 1 JRNL REVDAT 1 06-NOV-24 9AUQ 0 JRNL AUTH B.R.RUNGE,R.ZADOROZHNYI,C.M.QUINN,R.W.RUSSELL,M.LU, JRNL AUTH 2 S.ANTOLINEZ,J.STRUPPE,C.D.SCHWIETERS,I.L.BYEON, JRNL AUTH 3 J.A.HADDEN-PERILLA,A.M.GRONENBORN,T.POLENOVA JRNL TITL INTEGRATING 19 F DISTANCE RESTRAINTS FOR ACCURATE PROTEIN JRNL TITL 2 STRUCTURE DETERMINATION BY MAGIC ANGLE SPINNING NMR JRNL TITL 3 SPECTROSCOPY. JRNL REF J.AM.CHEM.SOC. V. 146 30483 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 39440810 JRNL DOI 10.1021/JACS.4C11373 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 11299 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1134 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 29.9000 - 4.7400 0.96 1279 0 0.1370 0.2151 REMARK 3 2 4.7300 - 3.7600 0.96 1317 0 0.1304 0.1659 REMARK 3 3 3.7600 - 3.2900 0.97 1316 0 0.1489 0.2420 REMARK 3 4 3.2900 - 2.9900 0.96 1269 0 0.1978 0.2404 REMARK 3 5 2.9900 - 2.7700 0.96 1302 0 0.2056 0.2539 REMARK 3 6 2.7700 - 2.6100 0.95 1265 0 0.1994 0.3343 REMARK 3 7 2.6100 - 2.4800 0.95 1236 0 0.2016 0.3296 REMARK 3 8 2.4800 - 2.3700 0.89 1181 0 0.1625 0.2342 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.34 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 9AUQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1000280007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 93.15 REMARK 200 PH : 8 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 FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11304 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 42.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 1.930 REMARK 200 R MERGE (I) : 0.01400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.02500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M NAH2PO4/0.8 M K2HPO4, 0.2 M REMARK 280 LI2SO4, 0.1 M CAPS (PH 10.5), PH 8, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ASN A 5 CG REMARK 480 GLU A 19 CD REMARK 480 GLU A 24 CD REMARK 480 ASP A 30 CG REMARK 480 GLN A 45 CD REMARK 480 ASN A 68 C CG REMARK 480 GLU A 72 CD REMARK 480 GLU A 74 CD REMARK 480 ASP A 80 CG REMARK 480 GLU A 96 CD REMARK 480 ASN A 97 CG REMARK 480 GLN A 112 CD REMARK 480 ASN B 5 CG REMARK 480 SER B 13 CA REMARK 480 SER B 14 CB REMARK 480 GLU B 19 CD REMARK 480 GLN B 22 CD REMARK 480 GLU B 24 OE1 OE2 REMARK 480 ASP B 30 CG REMARK 480 GLN B 45 CD REMARK 480 ASN B 48 CG REMARK 480 ASN B 68 C CG REMARK 480 GLU B 72 CD REMARK 480 ASP B 80 C CG REMARK 480 GLU B 96 CD REMARK 480 GLN B 112 CD DBREF 9AUQ A 2 133 UNP C0STD7 C0STD7_PLAAG 2 133 DBREF 9AUQ B 2 133 UNP C0STD7 C0STD7_PLAAG 2 133 SEQRES 1 A 132 ALA LEU TYR ASN VAL GLU ASN GLN 4FW GLY GLY SER SER SEQRES 2 A 132 ALA PRO 4FW ASN GLU GLY GLY GLN 4FW GLU ILE GLY SER SEQRES 3 A 132 ARG SER ASP GLN ASN VAL VAL ALA ILE ASN VAL GLU SER SEQRES 4 A 132 GLY ASP ASP GLY GLN THR LEU ASN GLY THR MET THR TYR SEQRES 5 A 132 ALA GLY GLU GLY PRO ILE GLY PHE ARG ALA THR LEU LEU SEQRES 6 A 132 GLY ASN ASN SER TYR GLU VAL GLU ASN GLN 4FW GLY GLY SEQRES 7 A 132 ASP SER ALA PRO 4FW HIS SER GLY GLY ASN 4FW ILE LEU SEQRES 8 A 132 GLY SER ARG GLU ASN GLN ASN VAL VAL ALA ILE ASN VAL SEQRES 9 A 132 GLU SER GLY ASP ASP GLY GLN THR LEU ASN GLY THR MET SEQRES 10 A 132 THR TYR ALA GLY GLU GLY PRO ILE GLY PHE LYS GLY THR SEQRES 11 A 132 LEU THR SEQRES 1 B 132 ALA LEU TYR ASN VAL GLU ASN GLN 4FW GLY GLY SER SER SEQRES 2 B 132 ALA PRO 4FW ASN GLU GLY GLY GLN 4FW GLU ILE GLY SER SEQRES 3 B 132 ARG SER ASP GLN ASN VAL VAL ALA ILE ASN VAL GLU SER SEQRES 4 B 132 GLY ASP ASP GLY GLN THR LEU ASN GLY THR MET THR TYR SEQRES 5 B 132 ALA GLY GLU GLY PRO ILE GLY PHE ARG ALA THR LEU LEU SEQRES 6 B 132 GLY ASN ASN SER TYR GLU VAL GLU ASN GLN 4FW GLY GLY SEQRES 7 B 132 ASP SER ALA PRO 4FW HIS SER GLY GLY ASN 4FW ILE LEU SEQRES 8 B 132 GLY SER ARG GLU ASN GLN ASN VAL VAL ALA ILE ASN VAL SEQRES 9 B 132 GLU SER GLY ASP ASP GLY GLN THR LEU ASN GLY THR MET SEQRES 10 B 132 THR TYR ALA GLY GLU GLY PRO ILE GLY PHE LYS GLY THR SEQRES 11 B 132 LEU THR MODRES 9AUQ 4FW A 10 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW A 17 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW A 23 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW A 77 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW A 84 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW A 90 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW B 10 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW B 17 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW B 23 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW B 77 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW B 84 TRP MODIFIED RESIDUE MODRES 9AUQ 4FW B 90 TRP MODIFIED RESIDUE HET 4FW A 10 15 HET 4FW A 17 15 HET 4FW A 23 15 HET 4FW A 77 15 HET 4FW A 84 15 HET 4FW A 90 15 HET 4FW B 10 15 HET 4FW B 17 15 HET 4FW B 23 15 HET 4FW B 77 15 HET 4FW B 84 15 HET 4FW B 90 15 HET CXS A 201 14 HET CXS A 202 14 HET CXS B 201 14 HET CXS B 202 14 HETNAM 4FW 4-FLUOROTRYPTOPHANE HETNAM CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID FORMUL 1 4FW 12(C11 H11 F N2 O2) FORMUL 3 CXS 4(C9 H19 N O3 S) FORMUL 7 HOH *100(H2 O) SHEET 1 AA111 LEU A 3 GLN A 9 0 SHEET 2 AA111 ASN A 18 GLU A 24 -1 O GLY A 20 N VAL A 6 SHEET 3 AA111 HIS A 85 ILE A 91 -1 O ILE A 91 N GLU A 24 SHEET 4 AA111 SER A 70 GLN A 76 -1 N VAL A 73 O GLY A 87 SHEET 5 AA111 ILE A 59 GLY A 67 -1 N LEU A 66 O SER A 70 SHEET 6 AA111 THR A 46 TYR A 53 -1 N MET A 51 O ILE A 59 SHEET 7 AA111 VAL A 33 GLU A 39 -1 N VAL A 34 O THR A 52 SHEET 8 AA111 VAL A 100 GLU A 106 -1 O VAL A 105 N ILE A 36 SHEET 9 AA111 THR A 113 TYR A 120 -1 O THR A 117 N ASN A 104 SHEET 10 AA111 ILE A 126 LEU A 132 -1 O ILE A 126 N MET A 118 SHEET 11 AA111 LEU A 3 GLN A 9 -1 N GLN A 9 O GLY A 127 SHEET 1 AA211 LEU B 3 GLN B 9 0 SHEET 2 AA211 ASN B 18 GLU B 24 -1 O ASN B 18 N ASN B 8 SHEET 3 AA211 HIS B 85 ILE B 91 -1 O ILE B 91 N GLU B 24 SHEET 4 AA211 SER B 70 GLN B 76 -1 N VAL B 73 O GLY B 87 SHEET 5 AA211 ILE B 59 GLY B 67 -1 N LEU B 66 O SER B 70 SHEET 6 AA211 THR B 46 TYR B 53 -1 N MET B 51 O ILE B 59 SHEET 7 AA211 VAL B 33 GLU B 39 -1 N VAL B 34 O THR B 52 SHEET 8 AA211 VAL B 100 GLU B 106 -1 O ILE B 103 N VAL B 38 SHEET 9 AA211 THR B 113 TYR B 120 -1 O THR B 119 N VAL B 101 SHEET 10 AA211 ILE B 126 LEU B 132 -1 O GLY B 130 N LEU B 114 SHEET 11 AA211 LEU B 3 GLN B 9 -1 N GLN B 9 O GLY B 127 LINK C GLN A 9 N 4FW A 10 1555 1555 1.33 LINK C 4FW A 10 N GLY A 11 1555 1555 1.33 LINK C PRO A 16 N 4FW A 17 1555 1555 1.33 LINK C 4FW A 17 N ASN A 18 1555 1555 1.33 LINK C GLN A 22 N 4FW A 23 1555 1555 1.33 LINK C 4FW A 23 N GLU A 24 1555 1555 1.33 LINK C GLN A 76 N 4FW A 77 1555 1555 1.33 LINK C 4FW A 77 N GLY A 78 1555 1555 1.33 LINK C PRO A 83 N 4FW A 84 1555 1555 1.33 LINK C 4FW A 84 N HIS A 85 1555 1555 1.33 LINK C ASN A 89 N 4FW A 90 1555 1555 1.33 LINK C 4FW A 90 N ILE A 91 1555 1555 1.33 LINK C GLN B 9 N 4FW B 10 1555 1555 1.33 LINK C 4FW B 10 N GLY B 11 1555 1555 1.33 LINK C PRO B 16 N 4FW B 17 1555 1555 1.32 LINK C 4FW B 17 N ASN B 18 1555 1555 1.33 LINK C GLN B 22 N 4FW B 23 1555 1555 1.33 LINK C 4FW B 23 N GLU B 24 1555 1555 1.33 LINK C GLN B 76 N 4FW B 77 1555 1555 1.33 LINK C 4FW B 77 N GLY B 78 1555 1555 1.33 LINK C PRO B 83 N 4FW B 84 1555 1555 1.33 LINK C 4FW B 84 N HIS B 85 1555 1555 1.33 LINK C ASN B 89 N 4FW B 90 1555 1555 1.32 LINK C 4FW B 90 N ILE B 91 1555 1555 1.33 CRYST1 42.480 47.303 47.282 78.44 63.36 63.37 P 1 2 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 0.023541 -0.011802 -0.011816 0.00000 SCALE2 0.000000 0.023648 0.000018 0.00000 SCALE3 0.000000 0.000000 0.023661 0.00000