HEADER SUGAR BINDING PROTEIN 23-JUL-19 6KJY TITLE GALECTIN-13 VARIANT C136S/C138S COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALACTOSIDE-BINDING SOLUBLE LECTIN 13; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GALECTIN-13,GAL-13,PLACENTAL TISSUE PROTEIN 13,PLACENTAL COMPND 5 PROTEIN 13; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: VARIANT C136S/C138S SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LGALS13, PLAC8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GALECTIN-13 VARIANT C136S/C138S, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SU REVDAT 3 27-MAR-24 6KJY 1 REMARK REVDAT 2 19-FEB-20 6KJY 1 JRNL REVDAT 1 16-OCT-19 6KJY 0 JRNL AUTH T.YANG,Y.YAO,X.WANG,Y.LI,Y.SI,X.LI,G.J.AYALA,Y.WANG, JRNL AUTH 2 K.H.MAYO,G.TAI,Y.ZHOU,J.SU JRNL TITL GALECTIN-13/PLACENTAL PROTEIN 13: REDOX-ACTIVE DISULFIDES AS JRNL TITL 2 SWITCHES FOR REGULATING STRUCTURE, FUNCTION AND CELLULAR JRNL TITL 3 DISTRIBUTION. JRNL REF GLYCOBIOLOGY V. 30 120 2020 JRNL REFN ESSN 1460-2423 JRNL PMID 31584064 JRNL DOI 10.1093/GLYCOB/CWZ081 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 27173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.360 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 19.4990 - 3.6082 1.00 1980 157 0.1737 0.1792 REMARK 3 2 3.6082 - 2.8669 1.00 1865 148 0.1728 0.1867 REMARK 3 3 2.8669 - 2.5053 1.00 1836 146 0.1874 0.2209 REMARK 3 4 2.5053 - 2.2767 1.00 1811 144 0.1807 0.1923 REMARK 3 5 2.2767 - 2.1137 1.00 1794 143 0.1795 0.2117 REMARK 3 6 2.1137 - 1.9892 1.00 1788 142 0.1884 0.2093 REMARK 3 7 1.9892 - 1.8897 1.00 1794 142 0.1867 0.2170 REMARK 3 8 1.8897 - 1.8075 1.00 1779 140 0.2012 0.2378 REMARK 3 9 1.8075 - 1.7379 1.00 1777 142 0.2077 0.2203 REMARK 3 10 1.7379 - 1.6780 1.00 1763 140 0.2061 0.2561 REMARK 3 11 1.6780 - 1.6256 1.00 1780 141 0.2160 0.2184 REMARK 3 12 1.6256 - 1.5791 1.00 1764 141 0.2158 0.2574 REMARK 3 13 1.5791 - 1.5376 0.99 1752 139 0.2422 0.2983 REMARK 3 14 1.5376 - 1.5001 0.96 1691 134 0.2675 0.3185 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.48 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 1164 REMARK 3 ANGLE : 1.006 1580 REMARK 3 CHIRALITY : 0.067 173 REMARK 3 PLANARITY : 0.007 203 REMARK 3 DIHEDRAL : 12.038 690 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 6KJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300013137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27251 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 56.88300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.75500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.32450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.75500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.75500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.44150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.75500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.75500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.32450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.75500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.75500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.44150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.88300 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 332 LIES ON A SPECIAL POSITION. 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 69 CZ NH1 NH2 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 ASN A 63 -73.06 -129.77 REMARK 500 MET A 76 -142.18 -102.02 REMARK 500 ARG A 131 -141.79 86.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KJY A 4 142 UNP Q9UHV8 PP13_HUMAN 1 139 SEQADV 6KJY GLY A 1 UNP Q9UHV8 EXPRESSION TAG SEQADV 6KJY SER A 2 UNP Q9UHV8 EXPRESSION TAG SEQADV 6KJY HIS A 3 UNP Q9UHV8 EXPRESSION TAG SEQADV 6KJY SER A 139 UNP Q9UHV8 CYS 136 VARIANT SEQADV 6KJY SER A 141 UNP Q9UHV8 CYS 138 VARIANT SEQRES 1 A 142 GLY SER HIS MET SER SER LEU PRO VAL PRO TYR LYS LEU SEQRES 2 A 142 PRO VAL SER LEU SER VAL GLY SER CYS VAL ILE ILE LYS SEQRES 3 A 142 GLY THR PRO ILE HIS SER PHE ILE ASN ASP PRO GLN LEU SEQRES 4 A 142 GLN VAL ASP PHE TYR THR ASP MET ASP GLU ASP SER ASP SEQRES 5 A 142 ILE ALA PHE ARG PHE ARG VAL HIS PHE GLY ASN HIS VAL SEQRES 6 A 142 VAL MET ASN ARG ARG GLU PHE GLY ILE TRP MET LEU GLU SEQRES 7 A 142 GLU THR THR ASP TYR VAL PRO PHE GLU ASP GLY LYS GLN SEQRES 8 A 142 PHE GLU LEU CYS ILE TYR VAL HIS TYR ASN GLU TYR GLU SEQRES 9 A 142 ILE LYS VAL ASN GLY ILE ARG ILE TYR GLY PHE VAL HIS SEQRES 10 A 142 ARG ILE PRO PRO SER PHE VAL LYS MET VAL GLN VAL SER SEQRES 11 A 142 ARG ASP ILE SER LEU THR SER VAL SER VAL SER ASN FORMUL 2 HOH *133(H2 O) HELIX 1 AA1 PRO A 120 VAL A 124 5 5 SHEET 1 AA1 6 TYR A 11 PRO A 14 0 SHEET 2 AA1 6 MET A 126 ARG A 131 -1 O VAL A 127 N LEU A 13 SHEET 3 AA1 6 GLN A 38 TYR A 44 -1 N GLN A 40 O SER A 130 SHEET 4 AA1 6 ILE A 53 HIS A 60 -1 O PHE A 57 N VAL A 41 SHEET 5 AA1 6 HIS A 64 GLU A 71 -1 O HIS A 64 N HIS A 60 SHEET 6 AA1 6 ILE A 74 TRP A 75 -1 O ILE A 74 N GLU A 71 SHEET 1 AA2 6 TYR A 11 PRO A 14 0 SHEET 2 AA2 6 MET A 126 ARG A 131 -1 O VAL A 127 N LEU A 13 SHEET 3 AA2 6 GLN A 38 TYR A 44 -1 N GLN A 40 O SER A 130 SHEET 4 AA2 6 ILE A 53 HIS A 60 -1 O PHE A 57 N VAL A 41 SHEET 5 AA2 6 HIS A 64 GLU A 71 -1 O HIS A 64 N HIS A 60 SHEET 6 AA2 6 GLU A 79 THR A 81 -1 O GLU A 79 N MET A 67 SHEET 1 AA3 5 ILE A 110 VAL A 116 0 SHEET 2 AA3 5 GLU A 102 VAL A 107 -1 N ILE A 105 O ILE A 112 SHEET 3 AA3 5 PHE A 92 VAL A 98 -1 N TYR A 97 O GLU A 104 SHEET 4 AA3 5 CYS A 22 PRO A 29 -1 N GLY A 27 O PHE A 92 SHEET 5 AA3 5 ILE A 133 SER A 141 -1 O SER A 139 N ILE A 24 CISPEP 1 VAL A 9 PRO A 10 0 8.85 CRYST1 53.510 53.510 113.766 90.00 90.00 90.00 P 43 21 2 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 0.018688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008790 0.00000