HEADER SUGAR BINDING PROTEIN 23-JUL-19 6KJW TITLE GALECTIN-13 VARIANT C136S 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 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, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SU REVDAT 3 16-OCT-24 6KJW 1 REMARK REVDAT 2 19-FEB-20 6KJW 1 JRNL REVDAT 1 16-OCT-19 6KJW 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. 1.36 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 36213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.520 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 19.5010 - 3.2730 0.99 2654 155 0.1709 0.1567 REMARK 3 2 3.2730 - 2.5999 0.99 2495 146 0.1952 0.2097 REMARK 3 3 2.5999 - 2.2718 1.00 2488 145 0.1919 0.2005 REMARK 3 4 2.2718 - 2.0643 1.00 2437 143 0.1857 0.2147 REMARK 3 5 2.0643 - 1.9165 1.00 2459 143 0.1819 0.1824 REMARK 3 6 1.9165 - 1.8036 1.00 2420 143 0.2005 0.2244 REMARK 3 7 1.8036 - 1.7133 1.00 2437 141 0.2154 0.2594 REMARK 3 8 1.7133 - 1.6388 1.00 2414 141 0.2171 0.2289 REMARK 3 9 1.6388 - 1.5757 1.00 2386 140 0.2214 0.2761 REMARK 3 10 1.5757 - 1.5214 1.00 2424 142 0.2416 0.3010 REMARK 3 11 1.5214 - 1.4738 1.00 2418 142 0.2490 0.2461 REMARK 3 12 1.4738 - 1.4317 1.00 2402 139 0.2473 0.2520 REMARK 3 13 1.4317 - 1.3940 1.00 2386 141 0.2637 0.2835 REMARK 3 14 1.3940 - 1.3600 1.00 2393 139 0.2816 0.2876 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.44 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 1165 REMARK 3 ANGLE : 1.047 1582 REMARK 3 CHIRALITY : 0.087 173 REMARK 3 PLANARITY : 0.006 203 REMARK 3 DIHEDRAL : 18.894 429 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 6KJW 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_1300013135. 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 : 36278 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 19.501 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 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 (%): 50.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, VAPOR DIFFUSION, SITTING 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 56.91950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.71900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.71900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.37925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.71900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.71900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.45975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.71900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.71900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.37925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.71900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.71900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.45975 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 56.91950 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 338 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 118 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 -72.36 -133.50 REMARK 500 ARG A 131 -142.61 90.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KJW A 4 142 UNP Q9UHV8 PP13_HUMAN 1 139 SEQADV 6KJW GLY A 1 UNP Q9UHV8 EXPRESSION TAG SEQADV 6KJW SER A 2 UNP Q9UHV8 EXPRESSION TAG SEQADV 6KJW HIS A 3 UNP Q9UHV8 EXPRESSION TAG SEQADV 6KJW SER A 139 UNP Q9UHV8 CYS 136 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 CYS ASN FORMUL 2 HOH *142(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 TYR A 44 O MET A 126 SHEET 4 AA1 6 ILE A 53 HIS A 60 -1 O VAL A 59 N LEU A 39 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 TYR A 44 O MET A 126 SHEET 4 AA2 6 ILE A 53 HIS A 60 -1 O VAL A 59 N LEU A 39 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 CYS A 95 O LYS A 106 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 VAL A 140 -1 O SER A 139 N ILE A 24 SSBOND 1 CYS A 22 CYS A 141 1555 1555 2.02 CISPEP 1 VAL A 9 PRO A 10 0 8.35 CRYST1 53.438 53.438 113.839 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 0.018713 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008784 0.00000