HEADER SUGAR BINDING PROTEIN 04-MAY-11 3AYD TITLE CRYSTAL STRUCTURE OF GALECTIN-3 CRD DOMIAN COMPLEXED WITH TFN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 117-250; 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 GENE: LGALS3, MAC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS ROSSMANN FOLD, A BETA-GALACTOSE-BINDING PROTEIN, BETA-GALACTOSIDES, KEYWDS 2 CELL-SURFACE, NUCLEAR, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.F.BIAN,D.F.LI,D.C.WANG REVDAT 3 01-NOV-23 3AYD 1 HETSYN REVDAT 2 29-JUL-20 3AYD 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 12-OCT-11 3AYD 0 JRNL AUTH C.F.BIAN,Y.ZHANG,H.SUN,D.F.LI,D.C.WANG JRNL TITL STRUCTURAL BASIS FOR DISTINCT BINDING PROPERTIES OF THE JRNL TITL 2 HUMAN GALECTINS TO THOMSEN-FRIEDENREICH ANTIGEN JRNL REF PLOS ONE V. 6 25007 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21949831 JRNL DOI 10.1371/JOURNAL.PONE.0025007 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 11093 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1270 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 206 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1086 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.04000 REMARK 3 B22 (A**2) : 2.04000 REMARK 3 B33 (A**2) : -4.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 1.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.528 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.289 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.103 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.128 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 63.84 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : TFN-.PARAM REMARK 3 PARAMETER FILE 5 : BME.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES REMARK 3 PROCEDURE. REMARK 4 REMARK 4 3AYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000029849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 85 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.07600 REMARK 200 R SYM FOR SHELL (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 15.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2NN8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 A.S., 0.1MBIS-TRIS, 5MM BETA REMARK 280 -MERCAPTOETHANOL, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 71.18667 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 35.59333 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 35.59333 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 71.18667 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, B, C 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 -7.04 89.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 TF P-NITROPHENYLS ARE COMPOSED OF RESIDUES 251-253 AND 254-256 (NPO- REMARK 600 A2G-GAL) RESPECTIVELY. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AYA RELATED DB: PDB REMARK 900 RELATED ID: 3AYC RELATED DB: PDB REMARK 900 RELATED ID: 3AYE RELATED DB: PDB DBREF 3AYD A 117 250 UNP P17931 LEG3_HUMAN 117 250 SEQADV 3AYD MET A 116 UNP P17931 EXPRESSION TAG SEQRES 1 A 135 MET PRO TYR ASN LEU PRO LEU PRO GLY GLY VAL VAL PRO SEQRES 2 A 135 ARG MET LEU ILE THR ILE LEU GLY THR VAL LYS PRO ASN SEQRES 3 A 135 ALA ASN ARG ILE ALA LEU ASP PHE GLN ARG GLY ASN ASP SEQRES 4 A 135 VAL ALA PHE HIS PHE ASN PRO ARG PHE ASN GLU ASN ASN SEQRES 5 A 135 ARG ARG VAL ILE VAL CYS ASN THR LYS LEU ASP ASN ASN SEQRES 6 A 135 TRP GLY ARG GLU GLU ARG GLN SER VAL PHE PRO PHE GLU SEQRES 7 A 135 SER GLY LYS PRO PHE LYS ILE GLN VAL LEU VAL GLU PRO SEQRES 8 A 135 ASP HIS PHE LYS VAL ALA VAL ASN ASP ALA HIS LEU LEU SEQRES 9 A 135 GLN TYR ASN HIS ARG VAL LYS LYS LEU ASN GLU ILE SER SEQRES 10 A 135 LYS LEU GLY ILE SER GLY ASP ILE ASP LEU THR SER ALA SEQRES 11 A 135 SER TYR THR MET ILE HET A2G B 1 14 HET GAL B 2 11 HET A2G C 1 14 HET GAL C 2 11 HET NPO A 251 10 HET NPO A 254 10 HET SO4 A 1 5 HET SO4 A 2 5 HET SO4 A 3 5 HET SO4 A 4 5 HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM NPO P-NITROPHENOL HETNAM SO4 SULFATE ION HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 A2G 2(C8 H15 N O6) FORMUL 2 GAL 2(C6 H12 O6) FORMUL 4 NPO 2(C6 H5 N O3) FORMUL 6 SO4 4(O4 S 2-) FORMUL 10 HOH *245(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 ASP A 148 O GLY A 235 SHEET 4 A 6 ASP A 154 ARG A 162 -1 O PHE A 157 N PHE A 149 SHEET 5 A 6 VAL A 170 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 ASP A 148 O GLY A 235 SHEET 4 B 6 ASP A 154 ARG A 162 -1 O PHE A 157 N PHE A 149 SHEET 5 B 6 VAL A 170 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 GLN A 201 O ALA A 212 SHEET 4 C 5 MET A 130 VAL A 138 -1 N ILE A 134 O ILE A 200 SHEET 5 C 5 ILE A 240 MET A 249 -1 O THR A 243 N LEU A 135 LINK OH NPO A 251 C1 A2G B 1 1555 1555 1.44 LINK OH NPO A 254 C1 A2G C 1 1555 1555 1.43 LINK O3 A2G B 1 C1 GAL B 2 1555 1555 1.43 LINK O3 A2G C 1 C1 GAL C 2 1555 1555 1.43 CRYST1 50.730 50.730 106.780 90.00 90.00 120.00 P 32 2 1 6 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 0.019712 0.011381 0.000000 0.00000 SCALE2 0.000000 0.022762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009365 0.00000