HEADER SUGAR BINDING PROTEIN 28-NOV-19 6LF1 TITLE SEVIL, A GM1B/ASIALO-GM1 BINDING LECTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEVIL; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEPTIFER VIRGATUS; SOURCE 3 ORGANISM_TAXID: 182745; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TREFOIL, ANTI-CANCER, APOPTOSIS, MUSSEL, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.KAMATA,Y.OZEKI,S.-Y.PARK,J.R.H.TAME REVDAT 3 22-NOV-23 6LF1 1 REMARK REVDAT 2 30-DEC-20 6LF1 1 JRNL REVDAT 1 02-DEC-20 6LF1 0 JRNL AUTH K.KAMATA,K.MIZUTANI,K.TAKAHASHI,R.MARCHETTI,A.SILIPO,C.ADDY, JRNL AUTH 2 S.Y.PARK,Y.FUJII,H.FUJITA,T.KONUMA,T.IKEGAMI,Y.OZEKI, JRNL AUTH 3 J.R.H.TAME JRNL TITL THE STRUCTURE OF SEVIL, A GM1B/ASIALO-GM1 BINDING R-TYPE JRNL TITL 2 LECTIN FROM THE MUSSEL MYTILISEPTA VIRGATA. JRNL REF SCI REP V. 10 22102 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 33328520 JRNL DOI 10.1038/S41598-020-78926-7 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 31666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1523 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 43.1100 - 3.7800 0.99 2939 127 0.1641 0.1698 REMARK 3 2 3.7800 - 3.0000 0.99 2845 117 0.1779 0.2065 REMARK 3 3 3.0000 - 2.6200 0.99 2769 136 0.2164 0.2612 REMARK 3 4 2.6200 - 2.3800 0.98 2755 130 0.2142 0.2763 REMARK 3 5 2.3800 - 2.2100 0.98 2708 159 0.2116 0.2939 REMARK 3 6 2.2100 - 2.0800 0.98 2726 142 0.2095 0.2334 REMARK 3 7 2.0800 - 1.9800 0.98 2695 147 0.2012 0.2255 REMARK 3 8 1.9800 - 1.8900 0.97 2683 133 0.2104 0.2215 REMARK 3 9 1.8900 - 1.8200 0.97 2677 149 0.2187 0.2681 REMARK 3 10 1.8200 - 1.7500 0.97 2705 129 0.2395 0.3163 REMARK 3 11 1.7500 - 1.7000 0.97 2641 154 0.2386 0.2869 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.199 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.22 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 2133 REMARK 3 ANGLE : 0.736 2876 REMARK 3 CHIRALITY : 0.053 286 REMARK 3 PLANARITY : 0.004 373 REMARK 3 DIHEDRAL : 19.472 792 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 6LF1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 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 PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 371509 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 43.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 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: BALBES REMARK 200 STARTING MODEL: 4I40 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID, PH 3.5, 3 M NACL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-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 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 B 353 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 VAL B 4 REMARK 465 THR B 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 202 DBREF 6LF1 A -2 129 PDB 6LF1 6LF1 -2 129 DBREF 6LF1 B -2 129 PDB 6LF1 6LF1 -2 129 SEQRES 1 A 132 GLY SER HIS MET SER SER VAL THR ILE GLY LYS CYS TYR SEQRES 2 A 132 ILE GLN ASN ARG GLU ASN GLY GLY ARG ALA PHE TYR ASN SEQRES 3 A 132 LEU GLY ARG LYS ASP LEU GLY ILE PHE THR GLY LYS MET SEQRES 4 A 132 TYR ASP ASP GLN ILE TRP SER PHE GLN LYS SER ASP THR SEQRES 5 A 132 PRO GLY TYR TYR THR ILE GLY ARG GLU SER LYS PHE LEU SEQRES 6 A 132 GLN TYR ASN GLY GLU GLN VAL ILE MET SER ASP ILE GLU SEQRES 7 A 132 GLN ASP THR THR LEU TRP SER LEU GLU GLU VAL PRO GLU SEQRES 8 A 132 ASP LYS GLY PHE TYR ARG LEU LEU ASN LYS VAL HIS LYS SEQRES 9 A 132 ALA TYR LEU ASP TYR ASN GLY GLY ASP LEU VAL ALA ASN SEQRES 10 A 132 LYS HIS GLN THR GLU SER GLU LYS TRP ILE LEU PHE LYS SEQRES 11 A 132 ALA TYR SEQRES 1 B 132 GLY SER HIS MET SER SER VAL THR ILE GLY LYS CYS TYR SEQRES 2 B 132 ILE GLN ASN ARG GLU ASN GLY GLY ARG ALA PHE TYR ASN SEQRES 3 B 132 LEU GLY ARG LYS ASP LEU GLY ILE PHE THR GLY LYS MET SEQRES 4 B 132 TYR ASP ASP GLN ILE TRP SER PHE GLN LYS SER ASP THR SEQRES 5 B 132 PRO GLY TYR TYR THR ILE GLY ARG GLU SER LYS PHE LEU SEQRES 6 B 132 GLN TYR ASN GLY GLU GLN VAL ILE MET SER ASP ILE GLU SEQRES 7 B 132 GLN ASP THR THR LEU TRP SER LEU GLU GLU VAL PRO GLU SEQRES 8 B 132 ASP LYS GLY PHE TYR ARG LEU LEU ASN LYS VAL HIS LYS SEQRES 9 B 132 ALA TYR LEU ASP TYR ASN GLY GLY ASP LEU VAL ALA ASN SEQRES 10 B 132 LYS HIS GLN THR GLU SER GLU LYS TRP ILE LEU PHE LYS SEQRES 11 B 132 ALA TYR HET CL B 201 1 HET CL B 202 1 HETNAM CL CHLORIDE ION FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *113(H2 O) HELIX 1 AA1 TYR A 37 ILE A 41 5 5 HELIX 2 AA2 GLN A 76 THR A 79 5 4 HELIX 3 AA3 LEU B 24 LYS B 27 5 4 HELIX 4 AA4 TYR B 37 ILE B 41 5 5 HELIX 5 AA5 GLN B 76 THR B 79 5 4 HELIX 6 AA6 THR B 118 GLU B 121 5 4 SHEET 1 AA1 6 VAL A 69 SER A 72 0 SHEET 2 AA1 6 LYS A 60 TYR A 64 -1 N GLN A 63 O ILE A 70 SHEET 3 AA1 6 TYR A 53 ARG A 57 -1 N ILE A 55 O LEU A 62 SHEET 4 AA1 6 TRP A 42 LYS A 46 -1 N SER A 43 O GLY A 56 SHEET 5 AA1 6 GLY A 7 ASN A 13 -1 N CYS A 9 O TRP A 42 SHEET 6 AA1 6 TRP A 123 LYS A 127 -1 O ILE A 124 N GLN A 12 SHEET 1 AA2 2 ARG A 19 ASN A 23 0 SHEET 2 AA2 2 ASP A 28 PHE A 32 -1 O PHE A 32 N ARG A 19 SHEET 1 AA3 2 TRP A 81 GLU A 85 0 SHEET 2 AA3 2 TYR A 93 ASN A 97 -1 O ARG A 94 N GLU A 84 SHEET 1 AA4 2 TYR A 103 ASN A 107 0 SHEET 2 AA4 2 ASP A 110 ASN A 114 -1 O ASN A 114 N TYR A 103 SHEET 1 AA5 6 VAL B 69 SER B 72 0 SHEET 2 AA5 6 LYS B 60 TYR B 64 -1 N GLN B 63 O ILE B 70 SHEET 3 AA5 6 TYR B 53 ARG B 57 -1 N ILE B 55 O LEU B 62 SHEET 4 AA5 6 TRP B 42 LYS B 46 -1 N SER B 43 O GLY B 56 SHEET 5 AA5 6 GLY B 7 ASN B 13 -1 N CYS B 9 O TRP B 42 SHEET 6 AA5 6 TRP B 123 LYS B 127 -1 O PHE B 126 N TYR B 10 SHEET 1 AA6 2 ARG B 19 ASN B 23 0 SHEET 2 AA6 2 ASP B 28 PHE B 32 -1 O ASP B 28 N ASN B 23 SHEET 1 AA7 2 TRP B 81 GLU B 85 0 SHEET 2 AA7 2 TYR B 93 ASN B 97 -1 O LEU B 96 N SER B 82 SHEET 1 AA8 2 TYR B 103 ASN B 107 0 SHEET 2 AA8 2 ASP B 110 ASN B 114 -1 O VAL B 112 N ASP B 105 SITE 1 AC1 4 PHE B 21 ARG B 26 ASP B 39 GLN B 40 SITE 1 AC2 2 ARG B 26 ASP B 28 CRYST1 86.216 86.216 67.627 90.00 90.00 120.00 P 3 2 1 12 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 0.011599 0.006697 0.000000 0.00000 SCALE2 0.000000 0.013393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014787 0.00000