HEADER SUGAR BINDING PROTEIN 04-DEC-01 1KJL TITLE HIGH RESOLUTION X-RAY STRUCTURE OF HUMAN GALECTIN-3 IN COMPLEX WITH TITLE 2 LACNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, CARBOHYDRATE RECOGNITION DOMAIN (CRD); COMPND 5 SYNONYM: GALACTOSE-SPECIFIC LECTIN 3, MAC-2 ANTIGEN, IGE-BINDING COMPND 6 PROTEIN, 35 KDA LECTIN, CARBOHYDRATE BINDING PROTEIN 35, CBP 35, COMPND 7 LAMININ-BINDING PROTEIN, LECTIN L-29, L-31, GALACTOSIDE-BINDING COMPND 8 PROTEIN, GALBP; 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 LACNAC COMPLEX, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.SORME,P.ARNOUX,B.KAHL-KNUTSSON,H.LEFFLER,J.M.RINI,U.J.NILSSON REVDAT 5 16-AUG-23 1KJL 1 HETSYN REVDAT 4 29-JUL-20 1KJL 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-JUL-11 1KJL 1 VERSN REVDAT 2 24-FEB-09 1KJL 1 VERSN REVDAT 1 12-APR-05 1KJL 0 JRNL AUTH P.SORME,P.ARNOUX,B.KAHL-KNUTSSON,H.LEFFLER,J.M.RINI, JRNL AUTH 2 U.J.NILSSON JRNL TITL STRUCTURAL AND THERMODYNAMIC STUDIES ON CATION-PI JRNL TITL 2 INTERACTIONS IN LECTIN-LIGAND COMPLEXES: HIGH-AFFINITY JRNL TITL 3 GALECTIN-3 INHIBITORS THROUGH FINE-TUNING OF AN JRNL TITL 4 ARGININE-ARENE INTERACTION. JRNL REF J.AM.CHEM.SOC. V. 127 1737 2005 JRNL REFN ISSN 0002-7863 JRNL PMID 15701008 JRNL DOI 10.1021/JA043475P REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 25018 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1212 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1107 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 1.080 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KJL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-00 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 : CHESS REMARK 200 BEAMLINE : F2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: PDB ENTRY 1A3K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS, MAGNESIUM CHLORIDE, 2 REMARK 280 -MERCAPTOETHANOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 18.80000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.80000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.20000 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 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 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 105 REMARK 465 PRO A 106 REMARK 465 TYR A 107 REMARK 465 GLY A 108 REMARK 465 ALA A 109 REMARK 465 PRO A 110 REMARK 465 ALA A 111 REMARK 465 GLY A 112 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O7 NAG B 1 O HOH A 749 2.14 REMARK 500 O HOH A 681 O HOH A 708 2.14 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 0.46 87.10 REMARK 500 ASN A 164 80.74 -150.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 LACNAC IS D-GALACTOSE COVALENTLY BOUND TO REMARK 600 N-ACETYL-D-GLUCOSAMINE. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A3K RELATED DB: PDB REMARK 900 2.1 A RESOLUTION REMARK 900 RELATED ID: 1KJR RELATED DB: PDB REMARK 900 GALECTIN-3 CRD IN COMPLEX WITH 2,3,5,6-TETRAFLUORO-4-METHOXY- REMARK 900 BENZAMIDE DBREF 1KJL A 105 250 UNP P17931 LEG3_HUMAN 104 249 SEQRES 1 A 146 GLY PRO TYR GLY ALA PRO ALA GLY PRO LEU ILE VAL PRO SEQRES 2 A 146 TYR ASN LEU PRO LEU PRO GLY GLY VAL VAL PRO ARG MET SEQRES 3 A 146 LEU ILE THR ILE LEU GLY THR VAL LYS PRO ASN ALA ASN SEQRES 4 A 146 ARG ILE ALA LEU ASP PHE GLN ARG GLY ASN ASP VAL ALA SEQRES 5 A 146 PHE HIS PHE ASN PRO ARG PHE ASN GLU ASN ASN ARG ARG SEQRES 6 A 146 VAL ILE VAL CYS ASN THR LYS LEU ASP ASN ASN TRP GLY SEQRES 7 A 146 ARG GLU GLU ARG GLN SER VAL PHE PRO PHE GLU SER GLY SEQRES 8 A 146 LYS PRO PHE LYS ILE GLN VAL LEU VAL GLU PRO ASP HIS SEQRES 9 A 146 PHE LYS VAL ALA VAL ASN ASP ALA HIS LEU LEU GLN TYR SEQRES 10 A 146 ASN HIS ARG VAL LYS LYS LEU ASN GLU ILE SER LYS LEU SEQRES 11 A 146 GLY ILE SER GLY ASP ILE ASP LEU THR SER ALA SER TYR SEQRES 12 A 146 THR MET ILE HET NAG B 1 15 HET GAL B 2 11 HET CL A 300 1 HET BR A 301 1 HET BR A 302 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM CL CHLORIDE ION HETNAM BR BROMIDE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 NAG C8 H15 N O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 CL CL 1- FORMUL 4 BR 2(BR 1-) FORMUL 6 HOH *160(H2 O) HELIX 1 1 LYS A 227 ILE A 231 5 5 SHEET 1 A 6 TYR A 118 PRO A 121 0 SHEET 2 A 6 LYS A 233 GLY A 238 -1 O ILE A 236 N TYR A 118 SHEET 3 A 6 ILE A 145 ARG A 151 -1 N ALA A 146 O SER A 237 SHEET 4 A 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 A 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 A 6 ASN A 180 TRP A 181 -1 O ASN A 180 N LEU A 177 SHEET 1 B 6 TYR A 118 PRO A 121 0 SHEET 2 B 6 LYS A 233 GLY A 238 -1 O ILE A 236 N TYR A 118 SHEET 3 B 6 ILE A 145 ARG A 151 -1 N ALA A 146 O SER A 237 SHEET 4 B 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 B 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 B 6 GLU A 185 GLN A 187 -1 O GLU A 185 N CYS A 173 SHEET 1 C 5 ALA A 216 ASN A 222 0 SHEET 2 C 5 HIS A 208 VAL A 213 -1 N VAL A 211 O LEU A 219 SHEET 3 C 5 PRO A 197 VAL A 204 -1 N LEU A 203 O LYS A 210 SHEET 4 C 5 MET A 130 VAL A 138 -1 N GLY A 136 O PHE A 198 SHEET 5 C 5 ILE A 240 MET A 249 -1 O THR A 248 N LEU A 131 LINK O4 NAG B 1 C1 GAL B 2 1555 1555 1.38 CISPEP 1 VAL A 116 PRO A 117 0 -0.10 CRYST1 37.600 58.400 64.000 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 0.026600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015620 0.00000