HEADER SUGAR BINDING PROTEIN 14-DEC-22 8BZ3 TITLE STRUCTURE OD THE CARBOHYDRATE RECONITION DOMAIN OF GAL3 IN COMPLES TITLE 2 WITH SAF-2-010 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAL-3,35 KDA LECTIN,CARBOHYDRATE-BINDING PROTEIN 35,CBP 35, COMPND 5 GALACTOSE-SPECIFIC LECTIN 3,GALACTOSIDE-BINDING PROTEIN,GALBP,IGE- COMPND 6 BINDING PROTEIN,L-31,LAMININ-BINDING PROTEIN,LECTIN L-29,MAC-2 COMPND 7 ANTIGEN; COMPND 8 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 KEYWDS GAL3C, SAF-2-010, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.J.MEDRANO,A.ROMERO REVDAT 2 08-MAR-23 8BZ3 1 JRNL REVDAT 1 01-MAR-23 8BZ3 0 JRNL AUTH S.ABDULLAYEV,P.KADAV,P.BANDYOPADHYAY,F.J.MEDRANO, JRNL AUTH 2 G.A.RABINOVICH,T.K.DAM,A.ROMERO,R.ROY JRNL TITL SELECTIVELY MODIFIED LACTOSE AND N -ACETYLLACTOSAMINE JRNL TITL 2 ANALOGS AT THREE KEY POSITIONS TO AFFORD EFFECTIVE JRNL TITL 3 GALECTIN-3 LIGANDS. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 36835132 JRNL DOI 10.3390/IJMS24043718 REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.8 REMARK 3 NUMBER OF REFLECTIONS : 28015 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.7800 - 3.1500 0.99 2368 182 0.1464 0.1565 REMARK 3 2 3.1500 - 2.5000 0.99 2235 172 0.1583 0.1884 REMARK 3 3 2.5000 - 2.1900 0.98 2205 170 0.1474 0.2060 REMARK 3 4 2.1900 - 1.9900 0.98 2176 166 0.1312 0.1823 REMARK 3 5 1.9900 - 1.8400 0.97 2154 166 0.1369 0.1742 REMARK 3 6 1.8400 - 1.7400 0.97 2132 164 0.1497 0.2104 REMARK 3 7 1.7400 - 1.6500 0.96 2132 164 0.1542 0.2101 REMARK 3 8 1.6500 - 1.5800 0.96 2125 163 0.1497 0.1903 REMARK 3 9 1.5800 - 1.5200 0.96 2089 161 0.1550 0.2448 REMARK 3 10 1.5200 - 1.4600 0.95 2076 159 0.1907 0.2797 REMARK 3 11 1.4600 - 1.4200 0.93 2022 156 0.2309 0.2376 REMARK 3 12 1.4200 - 1.3800 0.64 1393 107 0.2812 0.3602 REMARK 3 13 1.3800 - 1.3400 0.33 716 54 0.3035 0.3977 REMARK 3 14 1.3400 - 1.3100 0.09 194 14 0.3049 0.3237 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.141 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.974 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.09 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1185 REMARK 3 ANGLE : 0.859 1613 REMARK 3 CHIRALITY : 0.087 182 REMARK 3 PLANARITY : 0.008 208 REMARK 3 DIHEDRAL : 13.626 439 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292127399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979260 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 57.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.16300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 44.3 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 2.94500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL AT PH 8.5, 28% PEG REMARK 280 6000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 18.38200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.69450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.99150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.69450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.38200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.99150 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 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 MET 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 O HOH A 401 O HOH A 455 2.09 REMARK 500 OE1 GLU A 193 O HOH A 401 2.11 REMARK 500 O HOH A 502 O HOH A 540 2.19 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 2.63 84.16 REMARK 500 ASN A 164 84.15 -154.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 569 DISTANCE = 6.66 ANGSTROMS DBREF 8BZ3 A 107 250 UNP P17931 LEG3_HUMAN 107 250 SEQADV 8BZ3 MET A 106 UNP P17931 INITIATING METHIONINE SEQRES 1 A 145 MET TYR GLY ALA PRO ALA GLY PRO LEU ILE VAL PRO TYR SEQRES 2 A 145 ASN LEU PRO LEU PRO GLY GLY VAL VAL PRO ARG MET LEU SEQRES 3 A 145 ILE THR ILE LEU GLY THR VAL LYS PRO ASN ALA ASN ARG SEQRES 4 A 145 ILE ALA LEU ASP PHE GLN ARG GLY ASN ASP VAL ALA PHE SEQRES 5 A 145 HIS PHE ASN PRO ARG PHE ASN GLU ASN ASN ARG ARG VAL SEQRES 6 A 145 ILE VAL CYS ASN THR LYS LEU ASP ASN ASN TRP GLY ARG SEQRES 7 A 145 GLU GLU ARG GLN SER VAL PHE PRO PHE GLU SER GLY LYS SEQRES 8 A 145 PRO PHE LYS ILE GLN VAL LEU VAL GLU PRO ASP HIS PHE SEQRES 9 A 145 LYS VAL ALA VAL ASN ASP ALA HIS LEU LEU GLN TYR ASN SEQRES 10 A 145 HIS ARG VAL LYS LYS LEU ASN GLU ILE SER LYS LEU GLY SEQRES 11 A 145 ILE SER GLY ASP ILE ASP LEU THR SER ALA SER TYR THR SEQRES 12 A 145 MET ILE HET SQR A 301 39 HETNAM SQR [(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{R}, HETNAM 2 SQR 5~{R},6~{S})-5-ACETAMIDO-2-(HYDROXYMETHYL)-6-(4- HETNAM 3 SQR NITROPHENOXY)-4-OXIDANYL-OXAN-3-YL]OXY-6- HETNAM 4 SQR (HYDROXYMETHYL)-3,5-BIS(OXIDANYL)OXAN-4-YL] HYDROGEN HETNAM 5 SQR SULFATE FORMUL 2 SQR C20 H28 N2 O16 S FORMUL 3 HOH *169(H2 O) HELIX 1 AA1 LYS A 227 ILE A 231 5 5 SHEET 1 AA1 6 TYR A 118 PRO A 121 0 SHEET 2 AA1 6 LYS A 233 GLY A 238 -1 O LEU A 234 N LEU A 120 SHEET 3 AA1 6 ILE A 145 ARG A 151 -1 N ASP A 148 O GLY A 235 SHEET 4 AA1 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 AA1 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 AA1 6 ASN A 180 TRP A 181 -1 O ASN A 180 N LEU A 177 SHEET 1 AA2 6 TYR A 118 PRO A 121 0 SHEET 2 AA2 6 LYS A 233 GLY A 238 -1 O LEU A 234 N LEU A 120 SHEET 3 AA2 6 ILE A 145 ARG A 151 -1 N ASP A 148 O GLY A 235 SHEET 4 AA2 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 AA2 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 AA2 6 GLU A 185 GLN A 187 -1 O GLU A 185 N CYS A 173 SHEET 1 AA3 5 ALA A 216 ASN A 222 0 SHEET 2 AA3 5 HIS A 208 VAL A 213 -1 N VAL A 211 O LEU A 219 SHEET 3 AA3 5 PRO A 197 VAL A 204 -1 N LEU A 203 O LYS A 210 SHEET 4 AA3 5 MET A 130 VAL A 138 -1 N GLY A 136 O PHE A 198 SHEET 5 AA3 5 ILE A 240 MET A 249 -1 O THR A 248 N LEU A 131 CISPEP 1 VAL A 116 PRO A 117 0 0.34 CRYST1 36.764 57.983 63.389 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 0.027201 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017246 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015776 0.00000