HEADER LECTIN 20-MAR-98 1A78 TITLE COMPLEX OF TOAD OVARY GALECTIN WITH THIO-DIGALACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: S-LECTIN GALECTIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BUFO ARENARUM; SOURCE 3 ORGANISM_TAXID: 38577; SOURCE 4 ORGAN: OVARY KEYWDS S-LECTIN, CARBOHYDRATE BINDING, COMPLEX (LECTIN-SACCHARIDE), LECTIN EXPDTA X-RAY DIFFRACTION AUTHOR L.M.AMZEL,M.A.BIANCHET,H.AHMED,G.R.VASTA REVDAT 7 22-MAY-24 1A78 1 REMARK REVDAT 6 02-AUG-23 1A78 1 REMARK REVDAT 5 12-AUG-20 1A78 1 HETSYN LINK ATOM REVDAT 4 29-JUL-20 1A78 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 FORMUL LINK SITE ATOM REVDAT 3 24-FEB-09 1A78 1 VERSN REVDAT 2 01-APR-03 1A78 1 JRNL REVDAT 1 14-OCT-98 1A78 0 JRNL AUTH M.A.BIANCHET,H.AHMED,G.VASTA,L.M.AMZEL JRNL TITL SOLUBLE BETA-GALACTOSYL-BINDING LECTIN (GALECTIN) FROM TOAD JRNL TITL 2 OVARY: CRYSTALLOGRAPHIC STUDIES OF TWO PROTEIN-SUGAR JRNL TITL 3 COMPLEXES JRNL REF PROTEINS V. 40 378 2000 JRNL REFN ISSN 0887-3585 JRNL PMID 10861929 JRNL DOI 10.1002/1097-0134(20000815)40:3<378::AID-PROT40>3.0.CO;2-7 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.5 REMARK 3 NUMBER OF REFLECTIONS : 15569 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) : 0.194 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1550 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 36.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 769 REMARK 3 BIN R VALUE (WORKING SET) : 0.2869 REMARK 3 BIN FREE R VALUE : 0.2578 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.46 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 82 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 : 2074 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.739 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.12 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.400 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.820 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.130 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.720 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.940 ; 2.500 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.PRO REMARK 3 PARAMETER FILE 2 : PARAM3.CHO REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH3.CHO REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A78 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_1000170479. 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) : 300 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS V. 3.4 REMARK 200 DATA SCALING SOFTWARE : R-AXIS V 3.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14540 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.945 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 68.6 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.08600 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1GAN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS OF EQUAL AMOUNT OF 10-12 MG/ML REMARK 280 PROTEIN AND RESERVOIR SOLUTION WERE EQUILIBRATED AGAINST 1 ML OF REMARK 280 (NH4)2SO4 AT 56% SATURATION IN 100MM TRIS-ACETATE BUFFER, PH 6.6 REMARK 280 AND 1% MPD AND 1% DTT REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.50000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 LEU A 121 CA - CB - CG ANGL. DEV. = 15.3 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 SER A 2 102.28 114.41 REMARK 500 ALA A 3 -95.14 -123.05 REMARK 500 PRO A 79 43.17 -87.74 REMARK 500 SER B 2 173.24 177.62 REMARK 500 PRO B 26 36.46 -77.38 REMARK 500 ASP B 27 19.58 -171.61 REMARK 500 ALA B 39 21.07 -71.21 REMARK 500 PRO B 79 17.64 -67.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A78 A 1 134 UNP P56217 LEG1_BUFAR 1 134 DBREF 1A78 B 1 134 UNP P56217 LEG1_BUFAR 1 134 SEQRES 1 A 134 ALA SER ALA GLY VAL ALA VAL THR ASN LEU ASN LEU LYS SEQRES 2 A 134 PRO GLY HIS CYS VAL GLU ILE LYS GLY SER ILE PRO PRO SEQRES 3 A 134 ASP CYS LYS GLY PHE ALA VAL ASN LEU GLY GLU ASP ALA SEQRES 4 A 134 SER ASN PHE LEU LEU HIS PHE ASN ALA ARG PHE ASP LEU SEQRES 5 A 134 HIS GLY ASP VAL ASN LYS ILE VAL CYS ASN SER LYS GLU SEQRES 6 A 134 ALA ASP ALA TRP GLY SER GLU GLN ARG GLU GLU VAL PHE SEQRES 7 A 134 PRO PHE GLN GLN GLY ALA GLU VAL MET VAL CYS PHE GLU SEQRES 8 A 134 TYR GLN THR GLN LYS ILE ILE ILE LYS PHE SER SER GLY SEQRES 9 A 134 ASP GLN PHE SER PHE PRO VAL ARG LYS VAL LEU PRO SER SEQRES 10 A 134 ILE PRO PHE LEU SER LEU GLU GLY LEU ALA PHE LYS SER SEQRES 11 A 134 ILE THR THR GLU SEQRES 1 B 134 ALA SER ALA GLY VAL ALA VAL THR ASN LEU ASN LEU LYS SEQRES 2 B 134 PRO GLY HIS CYS VAL GLU ILE LYS GLY SER ILE PRO PRO SEQRES 3 B 134 ASP CYS LYS GLY PHE ALA VAL ASN LEU GLY GLU ASP ALA SEQRES 4 B 134 SER ASN PHE LEU LEU HIS PHE ASN ALA ARG PHE ASP LEU SEQRES 5 B 134 HIS GLY ASP VAL ASN LYS ILE VAL CYS ASN SER LYS GLU SEQRES 6 B 134 ALA ASP ALA TRP GLY SER GLU GLN ARG GLU GLU VAL PHE SEQRES 7 B 134 PRO PHE GLN GLN GLY ALA GLU VAL MET VAL CYS PHE GLU SEQRES 8 B 134 TYR GLN THR GLN LYS ILE ILE ILE LYS PHE SER SER GLY SEQRES 9 B 134 ASP GLN PHE SER PHE PRO VAL ARG LYS VAL LEU PRO SER SEQRES 10 B 134 ILE PRO PHE LEU SER LEU GLU GLY LEU ALA PHE LYS SER SEQRES 11 B 134 ILE THR THR GLU HET YIO E 1 12 HET GAL E 2 11 HET YIO F 1 12 HET GAL F 2 11 HET DTT A 136 8 HETNAM YIO 1-THIO-BETA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN YIO (2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3, HETSYN 2 YIO 4,5-TRIOL; 1-THIO-BETA-D-GALACTOSE; 1-THIO-D- HETSYN 3 YIO GALACTOSE; 1-THIO-GALACTOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 3 YIO 2(C6 H12 O5 S) FORMUL 3 GAL 2(C6 H12 O6) FORMUL 5 DTT C4 H10 O2 S2 FORMUL 6 HOH *46(H2 O) SHEET 1 A 6 ALA A 6 THR A 8 0 SHEET 2 A 6 PHE A 120 GLU A 124 -1 N LEU A 121 O VAL A 7 SHEET 3 A 6 GLY A 30 GLY A 36 -1 N GLY A 36 O PHE A 120 SHEET 4 A 6 PHE A 42 ARG A 49 -1 N ALA A 48 O PHE A 31 SHEET 5 A 6 LYS A 58 ASN A 62 -1 N ASN A 62 O HIS A 45 SHEET 6 A 6 GLN A 73 GLU A 75 -1 N GLU A 75 O ILE A 59 SHEET 1 B 5 GLN A 106 PRO A 110 0 SHEET 2 B 5 LYS A 96 PHE A 101 -1 N ILE A 99 O PHE A 107 SHEET 3 B 5 GLU A 85 TYR A 92 -1 N GLU A 91 O ILE A 98 SHEET 4 B 5 HIS A 16 SER A 23 -1 N GLY A 22 O VAL A 86 SHEET 5 B 5 ALA A 127 THR A 133 -1 N THR A 132 O GLU A 19 SHEET 1 C 6 ALA B 6 THR B 8 0 SHEET 2 C 6 PHE B 120 GLU B 124 -1 N LEU B 121 O VAL B 7 SHEET 3 C 6 GLY B 30 GLY B 36 -1 N GLY B 36 O PHE B 120 SHEET 4 C 6 PHE B 42 ARG B 49 -1 N ALA B 48 O PHE B 31 SHEET 5 C 6 LYS B 58 ASN B 62 -1 N ASN B 62 O HIS B 45 SHEET 6 C 6 GLN B 73 GLU B 75 -1 N GLU B 75 O ILE B 59 SHEET 1 D 5 GLN B 106 PRO B 110 0 SHEET 2 D 5 LYS B 96 PHE B 101 -1 N ILE B 99 O PHE B 107 SHEET 3 D 5 GLU B 85 TYR B 92 -1 N GLU B 91 O ILE B 98 SHEET 4 D 5 HIS B 16 ILE B 24 -1 N GLY B 22 O VAL B 86 SHEET 5 D 5 LEU B 126 GLU B 134 -1 N GLU B 134 O CYS B 17 LINK S1 YIO E 1 C1 GAL E 2 1555 1555 1.83 LINK S1 YIO F 1 C1 GAL F 2 1555 1555 1.80 CRYST1 51.800 51.000 56.300 90.00 97.20 90.00 P 1 21 1 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 0.019305 0.000000 0.002439 0.00000 SCALE2 0.000000 0.019608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017903 0.00000 MTRIX1 1 0.606149 0.675442 -0.419954 6.67420 1 MTRIX2 1 0.684481 -0.711912 -0.157060 -7.67920 1 MTRIX3 1 -0.405055 -0.192248 -0.893852 14.58580 1