HEADER SUGAR BINDING PROTEIN 03-MAY-13 4BLJ TITLE GALECTIN-3C IN COMPLEX WITH BISAMIDO-THIOGALACTOSIDE DERIVATE 2 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 SUGAR BINDING PROTEIN, LECTIN 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 4BLJ 1 REMARK REVDAT 2 17-JAN-18 4BLJ 1 REMARK REVDAT 1 14-MAY-14 4BLJ 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 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) : 0.126 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.123 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2019 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 38785 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.105 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.102 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1571 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 29885 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1109 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1266.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1159.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 49 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14159 REMARK 3 NUMBER OF RESTRAINTS : 18742 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.034 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.085 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.074 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.032 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.101 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 4BLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1290056517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-08 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) : 1.0379 REMARK 200 MONOCHROMATOR : BENT SILICON CRYSTAL REMARK 200 OPTICS : MULTILAYER MIRROR 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 : 40084 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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 1A3K REMARK 200 REMARK 200 REMARK: THE MODEL COULD BE USED DIRECTLY IN REFINEMENT SINCE IT IS REMARK 200 THE SAME SPACE GROUP REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19 MG/ML GALECTIN-3C, 100MM NACL,100 REMARK 280 MM LACTOSE, 29 % W/V PEG 4000, 0.4 M NASCN, 18 MM BETA- REMARK 280 MERCAPTOETHANOL,0.02 % NAN3, 10 MM PHOSHATE, 100 MM MGCL2, 100 REMARK 280 MM TRIS/HCL PH 7.5, 5 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 18.12000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.28000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.28000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.12000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.94000 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 183 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 ARG A 129 -6.65 93.06 REMARK 500 ARG A 129 3.41 85.21 REMARK 500 ASN A 141 55.84 -118.89 REMARK 500 ASN A 164 79.48 -156.23 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 A2076 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2085 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2138 DISTANCE = 6.36 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 70B 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: 4BM8 RELATED DB: PDB REMARK 900 GALECTIN-3C IN COMPLEX WITH BISAMIDO-THIOGALACTOSIDE DERIVATE 3 DBREF 4BLJ A 114 250 UNP P17931 LEG3_HUMAN 114 250 SEQADV 4BLJ MET A 113 UNP P17931 EXPRESSION TAG SEQRES 1 A 138 MET 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 70B A1251 43 HETNAM 70B BIS-(3-DEOXY-3-(3-METHOXY-BENZAMIDO)-B-D- HETNAM 2 70B GALACTOPYRANOSYL)-SULFIDE FORMUL 2 70B C28 H36 N2 O12 S FORMUL 3 HOH *263(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 -0.02 SITE 1 AC1 15 MET A 113 ILE A 115 ARG A 144 HIS A 158 SITE 2 AC1 15 ASN A 160 ARG A 162 ASN A 174 GLU A 184 SITE 3 AC1 15 ARG A 186 HOH A2005 HOH A2051 HOH A2255 SITE 4 AC1 15 HOH A2258 HOH A2261 HOH A2262 CRYST1 36.240 57.880 62.560 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 0.027594 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017277 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015985 0.00000