HEADER SUGAR BINDING PROTEIN 07-MAY-13 4BM8 TITLE GALECTIN-3C IN COMPLEX WITH BISAMIDO-THIOGALACTOSIDE DERIVATE 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 114-250; COMPND 5 SYNONYM: GAL-3,35 KDA LECTIN, CARBOHYDRATE-BINDING PROTEIN 35, CBP COMPND 6 35, GALACTOSE-SPECIFIC LECTIN 3, GALACTOSIDE-BINDING PROTEIN, GALBP, COMPND 7 IGE-BINDING PROTEIN, L-31, LAMININ-BINDING PROTEIN, LECTIN L-29, MAC- COMPND 8 2 ANTIGEN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IGE-BINDING PROTEIN, LECTIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.L.NORESSON,C.T.OBERG,O.ENGSTROM,M.HAKANSSON,D.T.LOGAN,H.LEFFLER, AUTHOR 2 U.J.NILSSON REVDAT 3 20-DEC-23 4BM8 1 REMARK REVDAT 2 17-JAN-18 4BM8 1 REMARK REVDAT 1 21-MAY-14 4BM8 0 JRNL AUTH A.L.NORESSON,C.T.OBERG,O.ENGSTROM,M.HAKANSSON,D.T.LOGAN, JRNL AUTH 2 H.LEFFLER,U.J.NILSSON JRNL TITL CONTROLLING PROTEIN CONFORMATION THROUGH ELECTRONIC JRNL TITL 2 FINE-TUNING OF ARGININE-ARENE INTERACTIONS: SYNTHETIC, JRNL TITL 3 STRUCTURAL, AND BIOLOGICAL STUDIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.128 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.125 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3965 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 75348 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.117 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.114 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3140 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 60538 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1106 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 317 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1463.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1143.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 77 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 15022 REMARK 3 NUMBER OF RESTRAINTS : 20174 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.035 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.057 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.053 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.002 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.034 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.105 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4BM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1290056735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04077 REMARK 200 MONOCHROMATOR : BENT SILICON CRYSTAL REMARK 200 OPTICS : MULTILAYER MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79320 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.960 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3ZSL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19 MG/ML GALECTIN-3C, 100MM NACL, 29 % REMARK 280 W/V PEG 4000, 0.4 M NASCN, 18 MM BETA-MERCAPTOETHANOL,0.02 % REMARK 280 NAN3, 10 MM PHOSHATE, 100 MM MGCL2, 100 MM TRIS/HCL PH 7.5, 2.5 REMARK 280 MM LIGAND 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 17.92000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.37500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.12000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.37500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.92000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.12000 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 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 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 ARG A 129 0.60 88.02 REMARK 500 ASN A 164 76.06 -155.29 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 A2074 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2093 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A2094 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A2097 DISTANCE = 7.03 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A6J A 1251 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BLI RELATED DB: PDB REMARK 900 GALECTIN-3C IN COMPLEX WITH BISAMIDO-THIOGALACTOSIDE DERIVATE 1 REMARK 900 RELATED ID: 4BLJ RELATED DB: PDB REMARK 900 GALECTIN-3C IN COMPLEX WITH BISAMIDO-THIOGALACTOSIDE DERIVATE 2 DBREF 4BM8 A 114 250 UNP P17931 LEG3_HUMAN 114 250 SEQADV 4BM8 ALA A 113 UNP P17931 EXPRESSION TAG SEQRES 1 A 138 ALA LEU ILE VAL PRO TYR ASN LEU PRO LEU PRO GLY GLY SEQRES 2 A 138 VAL VAL PRO ARG MET LEU ILE THR ILE LEU GLY THR VAL SEQRES 3 A 138 LYS PRO ASN ALA ASN ARG ILE ALA LEU ASP PHE GLN ARG SEQRES 4 A 138 GLY ASN ASP VAL ALA PHE HIS PHE ASN PRO ARG PHE ASN SEQRES 5 A 138 GLU ASN ASN ARG ARG VAL ILE VAL CYS ASN THR LYS LEU SEQRES 6 A 138 ASP ASN ASN TRP GLY ARG GLU GLU ARG GLN SER VAL PHE SEQRES 7 A 138 PRO PHE GLU SER GLY LYS PRO PHE LYS ILE GLN VAL LEU SEQRES 8 A 138 VAL GLU PRO ASP HIS PHE LYS VAL ALA VAL ASN ASP ALA SEQRES 9 A 138 HIS LEU LEU GLN TYR ASN HIS ARG VAL LYS LYS LEU ASN SEQRES 10 A 138 GLU ILE SER LYS LEU GLY ILE SER GLY ASP ILE ASP LEU SEQRES 11 A 138 THR SER ALA SER TYR THR MET ILE HET A6J A1251 55 HETNAM A6J (3-DEOXY-3-(2,3,5,6-TETRA-FLUORO-4-METHOXY-BENZAMIDO)- HETNAM 2 A6J B-D-GALACTOPYRANOSYL)-(3-DEOXY-3-(2,3,5,6-TETRA- HETNAM 3 A6J FLUORO-4-METHOXY-BENZAMIDO)-2-O-SULFO-B-D- HETNAM 4 A6J GALACTOPYRANOSYL)-SULFIDE FORMUL 2 A6J C28 H28 F8 N2 O15 S2 FORMUL 3 HOH *317(H2 O) HELIX 1 1 LYS A 227 ILE A 231 5 5 SHEET 1 AA 6 TYR A 118 PRO A 121 0 SHEET 2 AA 6 LYS A 233 GLY A 238 -1 O LEU A 234 N LEU A 120 SHEET 3 AA 6 ILE A 145 ARG A 151 -1 O ALA A 146 N SER A 237 SHEET 4 AA 6 ASP A 154 GLU A 165 -1 O ASP A 154 N ARG A 151 SHEET 5 AA 6 ARG A 168 LEU A 177 -1 O ARG A 168 N GLU A 165 SHEET 6 AA 6 ASN A 180 TRP A 181 -1 O ASN A 180 N LEU A 177 SHEET 1 AB 6 TYR A 118 PRO A 121 0 SHEET 2 AB 6 LYS A 233 GLY A 238 -1 O LEU A 234 N LEU A 120 SHEET 3 AB 6 ILE A 145 ARG A 151 -1 O ALA A 146 N SER A 237 SHEET 4 AB 6 ASP A 154 GLU A 165 -1 O ASP A 154 N ARG A 151 SHEET 5 AB 6 ARG A 168 LEU A 177 -1 O ARG A 168 N GLU A 165 SHEET 6 AB 6 GLU A 185 GLN A 187 -1 O GLU A 185 N CYS A 173 SHEET 1 AC 2 ASN A 180 TRP A 181 0 SHEET 2 AC 2 ARG A 168 LEU A 177 -1 O LEU A 177 N ASN A 180 SHEET 1 AD 5 ALA A 216 ASN A 222 0 SHEET 2 AD 5 HIS A 208 VAL A 213 -1 O PHE A 209 N TYR A 221 SHEET 3 AD 5 PRO A 197 VAL A 204 -1 O GLN A 201 N ALA A 212 SHEET 4 AD 5 MET A 130 VAL A 138 -1 O MET A 130 N VAL A 204 SHEET 5 AD 5 ILE A 240 MET A 249 -1 O ASP A 241 N THR A 137 CISPEP 1 VAL A 116 PRO A 117 0 2.43 CISPEP 2 VAL A 116 PRO A 117 0 3.08 SITE 1 AC1 27 ILE A 115 ARG A 144 ALA A 146 HIS A 158 SITE 2 AC1 27 ASN A 160 ARG A 162 GLU A 165 ASN A 166 SITE 3 AC1 27 ASN A 174 TRP A 181 GLU A 184 ARG A 186 SITE 4 AC1 27 GLY A 238 HOH A2004 HOH A2008 HOH A2055 SITE 5 AC1 27 HOH A2056 HOH A2057 HOH A2109 HOH A2121 SITE 6 AC1 27 HOH A2122 HOH A2124 HOH A2196 HOH A2310 SITE 7 AC1 27 HOH A2312 HOH A2316 HOH A2317 CRYST1 35.840 58.240 62.750 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 0.027902 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015936 0.00000