HEADER CELL ADHESION 29-MAY-20 6Z6Y TITLE GALECTIN-8 N-TERMINAL DOMAIN IN COMPLEX WITH A SULFATIDE MIMICKING A TITLE 2 SPHINGOLIPID COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAL-8,PO66 CARBOHYDRATE-BINDING PROTEIN,PO66-CBP,PROSTATE COMPND 5 CARCINOMA TUMOR ANTIGEN 1,PCTA-1; COMPND 6 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: LGALS8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GALECTIN-8, SPHINGOLIPID, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR A.ROMERO,F.J.MEDRANO REVDAT 4 24-JAN-24 6Z6Y 1 REMARK REVDAT 3 20-JUL-22 6Z6Y 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES HET HETNAM FORMUL REVDAT 3 3 1 HELIX SHEET SITE CRYST1 REVDAT 3 4 1 SCALE ATOM REVDAT 2 14-JUL-21 6Z6Y 1 JRNL REVDAT 1 30-DEC-20 6Z6Y 0 JRNL AUTH P.V.MURPHY,A.ROMERO,Q.XIAO,A.K.LUDWIG,S.JOGULA,N.V.SHILOVA, JRNL AUTH 2 T.SINGH,A.GABBA,B.JAVED,D.ZHANG,F.J.MEDRANO,H.KALTNER, JRNL AUTH 3 J.KOPITZ,N.V.BOVIN,A.M.WU,M.L.KLEIN,V.PERCEC,H.J.GABIUS JRNL TITL PROBING SULFATIDE-TISSUE LECTIN RECOGNITION WITH JRNL TITL 2 FUNCTIONALIZED GLYCODENDRIMERSOMES. JRNL REF ISCIENCE V. 24 01919 2021 JRNL REFN ESSN 2589-0042 JRNL PMID 33409472 JRNL DOI 10.1016/J.ISCI.2020.101919 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 39231 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 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 37.6100 - 3.2400 1.00 2767 148 0.1551 0.1784 REMARK 3 2 3.2400 - 2.5700 1.00 2670 144 0.1635 0.1991 REMARK 3 3 2.5700 - 2.2400 1.00 2690 144 0.1556 0.1774 REMARK 3 4 2.2400 - 2.0400 1.00 2658 143 0.1429 0.1859 REMARK 3 5 2.0400 - 1.8900 1.00 2678 142 0.1481 0.1842 REMARK 3 6 1.8900 - 1.7800 1.00 2655 142 0.1375 0.1711 REMARK 3 7 1.7800 - 1.6900 1.00 2660 144 0.1412 0.1824 REMARK 3 8 1.6900 - 1.6200 1.00 2675 144 0.1507 0.2160 REMARK 3 9 1.6200 - 1.5600 1.00 2652 142 0.1795 0.2385 REMARK 3 10 1.5600 - 1.5000 1.00 2631 141 0.1933 0.2169 REMARK 3 11 1.5000 - 1.4600 1.00 2680 145 0.2169 0.2916 REMARK 3 12 1.4600 - 1.4100 1.00 2647 140 0.2556 0.2811 REMARK 3 13 1.4100 - 1.3800 1.00 2633 142 0.3269 0.3292 REMARK 3 14 1.3800 - 1.3400 0.96 2537 137 0.4608 0.4336 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) : 0.171 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.861 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.86 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 : 0.009 1341 REMARK 3 ANGLE : 1.335 1813 REMARK 3 CHIRALITY : 0.084 201 REMARK 3 PLANARITY : 0.011 236 REMARK 3 DIHEDRAL : 8.141 179 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 6Z6Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292109052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 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) : 0.979257 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5GZE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-HEPES, PH 7.6, 10% PEG 4000 REMARK 280 AND 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.32000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.03300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.32000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.03300 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 419 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 98 CD CE NZ 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 HZ1 LYS A 101 O HOH A 418 1.49 REMARK 500 O THR A 95 O HOH A 310 2.10 REMARK 500 O HOH A 388 O HOH A 417 2.13 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 72 -127.16 56.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Z6Y A 5 160 UNP O00214 LEG8_HUMAN 5 160 SEQRES 1 A 156 LEU ASN ASN LEU GLN ASN ILE ILE TYR ASN PRO VAL ILE SEQRES 2 A 156 PRO PHE VAL GLY THR ILE PRO ASP GLN LEU ASP PRO GLY SEQRES 3 A 156 THR LEU ILE VAL ILE ARG GLY HIS VAL PRO SER ASP ALA SEQRES 4 A 156 ASP ARG PHE GLN VAL ASP LEU GLN ASN GLY SER SER MET SEQRES 5 A 156 LYS PRO ARG ALA ASP VAL ALA PHE HIS PHE ASN PRO ARG SEQRES 6 A 156 PHE LYS ARG ALA GLY CYS ILE VAL CYS ASN THR LEU ILE SEQRES 7 A 156 ASN GLU LYS TRP GLY ARG GLU GLU ILE THR TYR ASP THR SEQRES 8 A 156 PRO PHE LYS ARG GLU LYS SER PHE GLU ILE VAL ILE MET SEQRES 9 A 156 VAL LEU LYS ASP LYS PHE GLN VAL ALA VAL ASN GLY LYS SEQRES 10 A 156 HIS THR LEU LEU TYR GLY HIS ARG ILE GLY PRO GLU LYS SEQRES 11 A 156 ILE ASP THR LEU GLY ILE TYR GLY LYS VAL ASN ILE HIS SEQRES 12 A 156 SER ILE GLY PHE SER PHE SER SER ASP LEU GLN SER THR HET L4L A 201 46 HET ACT A 202 7 HET ACT A 203 7 HET ACT A 204 7 HET ACT A 205 7 HET ACT A 206 7 HET ACT A 207 7 HET PGE A 208 24 HETNAM L4L [(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S})-2- HETNAM 2 L4L ACETAMIDO-3-OXIDANYLIDENE-PENT-4-ENOXY]-6- HETNAM 3 L4L (HYDROXYMETHYL)-3,5-BIS(OXIDANYL)OXAN-4-YL] HYDROGEN HETNAM 4 L4L SULFATE HETNAM ACT ACETATE ION HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 L4L C13 H21 N O11 S FORMUL 3 ACT 6(C2 H3 O2 1-) FORMUL 9 PGE C6 H14 O4 FORMUL 10 HOH *122(H2 O) HELIX 1 AA1 GLY A 131 ILE A 135 5 5 HELIX 2 AA2 ASP A 156 THR A 160 5 5 SHEET 1 AA1 6 GLN A 9 TYR A 13 0 SHEET 2 AA1 6 ASN A 145 PHE A 153 -1 O ILE A 149 N ILE A 11 SHEET 3 AA1 6 THR A 31 HIS A 38 -1 N VAL A 34 O GLY A 150 SHEET 4 AA1 6 SER A 102 VAL A 109 -1 O ILE A 105 N ILE A 35 SHEET 5 AA1 6 LYS A 113 VAL A 118 -1 O GLN A 115 N MET A 108 SHEET 6 AA1 6 LYS A 121 GLY A 127 -1 O THR A 123 N VAL A 116 SHEET 1 AA2 6 PHE A 19 THR A 22 0 SHEET 2 AA2 6 THR A 137 GLY A 142 -1 O LEU A 138 N GLY A 21 SHEET 3 AA2 6 PHE A 46 ASN A 52 -1 N GLN A 51 O THR A 137 SHEET 4 AA2 6 ASP A 61 ARG A 69 -1 O PHE A 64 N LEU A 50 SHEET 5 AA2 6 CYS A 75 ILE A 82 -1 O CYS A 75 N ARG A 69 SHEET 6 AA2 6 LYS A 85 TRP A 86 -1 O LYS A 85 N ILE A 82 SHEET 1 AA3 6 PHE A 19 THR A 22 0 SHEET 2 AA3 6 THR A 137 GLY A 142 -1 O LEU A 138 N GLY A 21 SHEET 3 AA3 6 PHE A 46 ASN A 52 -1 N GLN A 51 O THR A 137 SHEET 4 AA3 6 ASP A 61 ARG A 69 -1 O PHE A 64 N LEU A 50 SHEET 5 AA3 6 CYS A 75 ILE A 82 -1 O CYS A 75 N ARG A 69 SHEET 6 AA3 6 GLU A 90 THR A 92 -1 O THR A 92 N ILE A 76 CISPEP 1 ILE A 17 PRO A 18 0 6.92 CISPEP 2 LYS A 57 PRO A 58 0 -7.19 CRYST1 110.640 40.066 40.701 90.00 99.80 90.00 C 1 2 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 0.009038 0.000000 0.001562 0.00000 SCALE2 0.000000 0.024959 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024933 0.00000