PDB Short entry for 2GAL HEADER LECTIN 13-JUL-98 2GAL TITLE CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-7; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS GALAPTIN, LECTIN, GALECTIN, CARBOHYDRATE BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.D.LEONIDAS,K.R.ACHARYA REVDAT 6 03-APR-24 2GAL 1 REMARK REVDAT 5 14-FEB-24 2GAL 1 HETSYN REVDAT 4 29-JUL-20 2GAL 1 COMPND REMARK HETNAM SITE REVDAT 3 24-FEB-09 2GAL 1 VERSN REVDAT 2 01-APR-03 2GAL 1 JRNL REVDAT 1 04-NOV-98 2GAL 0 JRNL AUTH D.D.LEONIDAS,E.H.VATZAKI,H.VORUM,J.E.CELIS,P.MADSEN, JRNL AUTH 2 K.R.ACHARYA JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF CARBOHYDRATES BY JRNL TITL 2 HUMAN GALECTIN-7. JRNL REF BIOCHEMISTRY V. 37 13930 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9760227 JRNL DOI 10.1021/BI981056X REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 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) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 17475 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) : 0.187 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 847 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2686 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2081 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 30.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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) : 2.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.300 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.710 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.750 ; 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 : PROTEIN_REP REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : PARAM3.CHO REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PR REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : TOPH3.CHO REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2GAL 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_1000178118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 289 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.912 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18155 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: FREE GALECTIN-7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN USING THE HANGING REMARK 280 DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN REMARK 280 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM REMARK 280 IMIDAZOLE, 8.5% PEG 3350 AND 25 MM GALACTOSE. DROPS WERE REMARK 280 EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM REMARK 280 PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% REMARK 280 PEG 3350 AND 50 MM GALACTOSE., VAPOR DIFFUSION - HANGING DROP, REMARK 280 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 27.23500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.12000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.12000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.23500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.26000 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: DIMERIC 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 SER A 1 REMARK 465 ASN A 2 REMARK 465 SER B 1 REMARK 465 ASN B 2 REMARK 465 VAL B 3 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 ASP A 103 -5.12 83.03 REMARK 500 HIS B 5 120.86 -35.19 REMARK 500 GLU B 11 31.23 88.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 2GAL A 1 135 UNP P47929 LEG7_HUMAN 1 135 DBREF 2GAL B 1 135 UNP P47929 LEG7_HUMAN 1 135 SEQRES 1 A 135 SER ASN VAL PRO HIS LYS SER SER LEU PRO GLU GLY ILE SEQRES 2 A 135 ARG PRO GLY THR VAL LEU ARG ILE ARG GLY LEU VAL PRO SEQRES 3 A 135 PRO ASN ALA SER ARG PHE HIS VAL ASN LEU LEU CYS GLY SEQRES 4 A 135 GLU GLU GLN GLY SER ASP ALA ALA LEU HIS PHE ASN PRO SEQRES 5 A 135 ARG LEU ASP THR SER GLU VAL VAL PHE ASN SER LYS GLU SEQRES 6 A 135 GLN GLY SER TRP GLY ARG GLU GLU ARG GLY PRO GLY VAL SEQRES 7 A 135 PRO PHE GLN ARG GLY GLN PRO PHE GLU VAL LEU ILE ILE SEQRES 8 A 135 ALA SER ASP ASP GLY PHE LYS ALA VAL VAL GLY ASP ALA SEQRES 9 A 135 GLN TYR HIS HIS PHE ARG HIS ARG LEU PRO LEU ALA ARG SEQRES 10 A 135 VAL ARG LEU VAL GLU VAL GLY GLY ASP VAL GLN LEU ASP SEQRES 11 A 135 SER VAL ARG ILE PHE SEQRES 1 B 135 SER ASN VAL PRO HIS LYS SER SER LEU PRO GLU GLY ILE SEQRES 2 B 135 ARG PRO GLY THR VAL LEU ARG ILE ARG GLY LEU VAL PRO SEQRES 3 B 135 PRO ASN ALA SER ARG PHE HIS VAL ASN LEU LEU CYS GLY SEQRES 4 B 135 GLU GLU GLN GLY SER ASP ALA ALA LEU HIS PHE ASN PRO SEQRES 5 B 135 ARG LEU ASP THR SER GLU VAL VAL PHE ASN SER LYS GLU SEQRES 6 B 135 GLN GLY SER TRP GLY ARG GLU GLU ARG GLY PRO GLY VAL SEQRES 7 B 135 PRO PHE GLN ARG GLY GLN PRO PHE GLU VAL LEU ILE ILE SEQRES 8 B 135 ALA SER ASP ASP GLY PHE LYS ALA VAL VAL GLY ASP ALA SEQRES 9 B 135 GLN TYR HIS HIS PHE ARG HIS ARG LEU PRO LEU ALA ARG SEQRES 10 B 135 VAL ARG LEU VAL GLU VAL GLY GLY ASP VAL GLN LEU ASP SEQRES 11 B 135 SER VAL ARG ILE PHE HET GAL A 998 12 HET GAL B 999 12 HETNAM GAL BETA-D-GALACTOPYRANOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 3 GAL 2(C6 H12 O6) FORMUL 5 HOH *76(H2 O) HELIX 1 1 LEU A 115 ARG A 117 5 3 HELIX 2 2 LEU B 115 ARG B 117 5 3 SHEET 1 A 5 HIS A 5 SER A 8 0 SHEET 2 A 5 LEU A 120 GLY A 125 -1 N VAL A 123 O HIS A 5 SHEET 3 A 5 PHE A 32 LEU A 37 -1 N LEU A 37 O LEU A 120 SHEET 4 A 5 ALA A 46 ARG A 53 -1 N PHE A 50 O VAL A 34 SHEET 5 A 5 GLU A 58 ASN A 62 -1 N ASN A 62 O HIS A 49 SHEET 1 B 5 ALA A 104 ARG A 110 0 SHEET 2 B 5 GLY A 96 VAL A 101 -1 N VAL A 101 O ALA A 104 SHEET 3 B 5 PRO A 85 ALA A 92 -1 N ILE A 91 O LYS A 98 SHEET 4 B 5 VAL A 18 LEU A 24 -1 N GLY A 23 O PHE A 86 SHEET 5 B 5 GLN A 128 PHE A 135 -1 N PHE A 135 O VAL A 18 SHEET 1 C 5 LYS B 6 SER B 8 0 SHEET 2 C 5 LEU B 120 GLY B 125 -1 N VAL B 121 O SER B 7 SHEET 3 C 5 PHE B 32 LEU B 37 -1 N LEU B 37 O LEU B 120 SHEET 4 C 5 ALA B 46 ARG B 53 -1 N PHE B 50 O VAL B 34 SHEET 5 C 5 GLU B 58 ASN B 62 -1 N ASN B 62 O HIS B 49 SHEET 1 D 5 ALA B 104 ARG B 110 0 SHEET 2 D 5 GLY B 96 VAL B 101 -1 N VAL B 101 O ALA B 104 SHEET 3 D 5 PRO B 85 ALA B 92 -1 N ILE B 91 O LYS B 98 SHEET 4 D 5 VAL B 18 LEU B 24 -1 N GLY B 23 O PHE B 86 SHEET 5 D 5 GLN B 128 PHE B 135 -1 N PHE B 135 O VAL B 18 CRYST1 54.470 64.520 72.240 90.00 90.00 90.00 P 21 21 21 8 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 0.018359 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013843 0.00000 MTRIX1 1 -0.364826 -0.736594 0.569501 47.25281 1 MTRIX2 1 -0.776798 -0.096414 -0.622325 59.21492 1 MTRIX3 1 0.513309 -0.669428 -0.537010 28.66626 1