PDB Short entry for 1A3K HEADER GALECTIN 22-JAN-98 1A3K TITLE X-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE TITLE 2 RECOGNITION DOMAIN (CRD) AT 2.1 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE RECOGNITION DOMAIN (CRD); COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) COMPND 7 DIGESTION OF THE N-TERMINAL DOMAIN 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; SOURCE 7 OTHER_DETAILS: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) SOURCE 8 DIGESTION OF THE N-TERMINAL DOMAIN KEYWDS GALECTIN, GALAPTIN, LECTIN, IGE-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SEETHARAMAN,A.KANIGSBERG,R.SLAABY,H.LEFFLER,S.H.BARONDES,J.M.RINI REVDAT 5 29-JUL-20 1A3K 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 04-APR-18 1A3K 1 REMARK REVDAT 3 13-JUL-11 1A3K 1 VERSN REVDAT 2 24-FEB-09 1A3K 1 VERSN REVDAT 1 15-JUL-98 1A3K 0 JRNL AUTH J.SEETHARAMAN,A.KANIGSBERG,R.SLAABY,H.LEFFLER,S.H.BARONDES, JRNL AUTH 2 J.M.RINI JRNL TITL X-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE JRNL TITL 2 RECOGNITION DOMAIN AT 2.1-A RESOLUTION. JRNL REF J.BIOL.CHEM. V. 273 13047 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9582341 JRNL DOI 10.1074/JBC.273.21.13047 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.I.LIAO,G.KAPADIA,H.AHMED,G.R.VASTA,O.HERZBERG REMARK 1 TITL STRUCTURE OF S-LECTIN, A DEVELOPMENTALLY REGULATED REMARK 1 TITL 2 VERTEBRATE BETA-GALACTOSIDE-BINDING PROTEIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 91 1428 1994 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.D.LOBSANOV,M.A.GITT,H.LEFFLER,S.H.BARONDES,J.M.RINI REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF THE HUMAN DIMERIC S-LAC LECTIN, REMARK 1 TITL 2 L-14-II, IN COMPLEX WITH LACTOSE AT 2.9-A RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 268 27034 1993 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 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) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.170 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 204 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 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 : 1101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.60 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.700 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 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 : PARHCSDX_3.1.PRO REMARK 3 PARAMETER FILE 2 : PARAM3_MOD_3.1.CHO REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX_3.1.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH3_3.1.CHO REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE WAS SOLVED BY THE MULTIPLE ISOMORPHOUS REMARK 3 REPLACEMENT METHOD. REMARK 3 THE MODEL CONSISTS OF THE 137 AMINO ACID RESIDUE REMARK 3 CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH REMARK 3 N-ACETYLLACTOSAMINE AND 120 WATER MOLECULES. REMARK 3 THIS STRUCTURE REPRESENTS A CRD DETERMINED FROM A GALECTIN REMARK 3 WHICH DOES NOT SHOW THE CANONICAL 2-FOLD SYMMETRIC DIMER REMARK 3 ORGANIZATION SHOWN BY GALECTINS-1 AND -2. COMPARISON WITH REMARK 3 GALECTINS-1 AND -2 PROVIDES AN EXPLANATION FOR THE REMARK 3 DIFFERENCES IN CARBOHYDRATE-BINDING SPECIFICITY SHOWN BY REMARK 3 GALECTIN-3, AND FOR THE FACT THAT IT FAILS TO FORM DIMERS REMARK 3 BY ANALOGOUS CRD-CRD INTERACTIONS. REMARK 4 REMARK 4 1A3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-94 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 METHOD REMARK 200 SOFTWARE USED: PHASES, X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CRYSTALLIZED BY HANGING-DROP REMARK 280 VAPOUR DIFFUSION METHOD FROM DROPS CONTAINING EQUAL VOLUMES OF REMARK 280 PROTEIN(10-15MG/ML) IN CRYSTALLIZATION BUFFER CONTAINING 1MM REMARK 280 LACTOSE OR 30 MM N-ACETYLLACTOSAMINE AND THE WELL SOLUTION REMARK 280 COMPOSED OF 27-30% PEG 4000-6000, 100MM TRIS-HCL PH 8.5, 100 MM REMARK 280 MGCL2, AND 8 MM 2-MERCAPTOETHANOL., VAPOR DIFFUSION - HANGING REMARK 280 DROP, VAPOR DIFFUSION, HANGING DROP 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 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 -1.99 80.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A3K A 114 250 UNP P17931 LEG3_HUMAN 113 249 SEQRES 1 A 137 LEU ILE VAL PRO TYR ASN LEU PRO LEU PRO GLY GLY VAL SEQRES 2 A 137 VAL PRO ARG MET LEU ILE THR ILE LEU GLY THR VAL LYS SEQRES 3 A 137 PRO ASN ALA ASN ARG ILE ALA LEU ASP PHE GLN ARG GLY SEQRES 4 A 137 ASN ASP VAL ALA PHE HIS PHE ASN PRO ARG PHE ASN GLU SEQRES 5 A 137 ASN ASN ARG ARG VAL ILE VAL CYS ASN THR LYS LEU ASP SEQRES 6 A 137 ASN ASN TRP GLY ARG GLU GLU ARG GLN SER VAL PHE PRO SEQRES 7 A 137 PHE GLU SER GLY LYS PRO PHE LYS ILE GLN VAL LEU VAL SEQRES 8 A 137 GLU PRO ASP HIS PHE LYS VAL ALA VAL ASN ASP ALA HIS SEQRES 9 A 137 LEU LEU GLN TYR ASN HIS ARG VAL LYS LYS LEU ASN GLU SEQRES 10 A 137 ILE SER LYS LEU GLY ILE SER GLY ASP ILE ASP LEU THR SEQRES 11 A 137 SER ALA SER TYR THR MET ILE HET NAG B 1 15 HET GAL B 2 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE FORMUL 2 NAG C8 H15 N O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 HOH *120(H2 O) HELIX 1 1 LEU A 228 GLU A 230 5 3 SHEET 1 A 6 TYR A 118 PRO A 121 0 SHEET 2 A 6 LYS A 233 GLY A 238 -1 N ILE A 236 O TYR A 118 SHEET 3 A 6 ILE A 145 ARG A 151 -1 N GLN A 150 O LYS A 233 SHEET 4 A 6 ASP A 154 ARG A 162 -1 N PHE A 159 O LEU A 147 SHEET 5 A 6 VAL A 170 ASN A 174 -1 N ASN A 174 O HIS A 158 SHEET 6 A 6 GLU A 185 GLN A 187 -1 N GLN A 187 O ILE A 171 SHEET 1 B 5 ALA A 216 ASN A 222 0 SHEET 2 B 5 HIS A 208 VAL A 213 -1 N VAL A 213 O ALA A 216 SHEET 3 B 5 PRO A 197 VAL A 204 -1 N LEU A 203 O LYS A 210 SHEET 4 B 5 MET A 130 VAL A 138 -1 N GLY A 136 O PHE A 198 SHEET 5 B 5 ILE A 240 MET A 249 -1 N THR A 248 O 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 -0.02 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 0.026596 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015625 0.00000