PDB Short entry for 2YV8 HEADER SUGAR BINDING PROTEIN 10-APR-07 2YV8 TITLE CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN GALECTIN-8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-8 VARIANT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-165; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PK050620-06; SOURCE 7 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS TWO BETA SHEETS, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KISHISHITA,A.NISHINO,K.MURAYAMA,T.TERADA,M.SHIROUZU, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI) REVDAT 2 24-FEB-09 2YV8 1 VERSN REVDAT 1 15-APR-08 2YV8 0 JRNL AUTH S.KISHISHITA,A.NISHINO,M.KAZUTAKA,T.TERADA, JRNL AUTH 2 M.SHIROUZU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN JRNL TITL 2 GALECTIN-8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 207194.760 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 24089 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) : 0.186 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1152 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3648 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 203 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1188 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.83000 REMARK 3 B22 (A**2) : -4.02000 REMARK 3 B33 (A**2) : -1.80000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.05 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.79 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 48.31 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.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YV8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUL-07. REMARK 100 THE RCSB ID CODE IS RCSB027176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792, 0.9797, 0.964 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26234 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 60.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07600 REMARK 200 R SYM FOR SHELL (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 29.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MAGNESIUM FORMATE, 15% PEG REMARK 280 3350, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 23.83400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.68150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.00600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.68150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.83400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.00600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 MET A 8 REMARK 465 MET A 9 REMARK 465 LEU A 10 REMARK 465 SER A 11 REMARK 465 LEU A 12 REMARK 465 ASN A 13 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 79 -128.32 62.96 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 349 DISTANCE = 6.45 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002002300.1 RELATED DB: TARGETDB DBREF 2YV8 A 8 158 UNP Q59E97 Q59E97_HUMAN 22 172 SEQADV 2YV8 GLY A 1 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 SER A 2 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 SER A 3 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 GLY A 4 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 SER A 5 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 SER A 6 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 GLY A 7 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 SER A 159 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 GLY A 160 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 PRO A 161 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 SER A 162 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 SER A 163 UNP Q59E97 EXPRESSION TAG SEQADV 2YV8 GLY A 164 UNP Q59E97 EXPRESSION TAG SEQRES 1 A 164 GLY SER SER GLY SER SER GLY MET MET LEU SER LEU ASN SEQRES 2 A 164 ASN LEU GLN ASN ILE ILE TYR ASN PRO VAL ILE PRO TYR SEQRES 3 A 164 VAL GLY THR ILE PRO ASP GLN LEU ASP PRO GLY THR LEU SEQRES 4 A 164 ILE VAL ILE CYS GLY HIS VAL PRO SER ASP ALA ASP ARG SEQRES 5 A 164 PHE GLN VAL ASP LEU GLN ASN GLY SER SER VAL LYS PRO SEQRES 6 A 164 ARG ALA ASP VAL ALA PHE HIS PHE ASN PRO ARG PHE LYS SEQRES 7 A 164 ARG ALA GLY CYS ILE VAL CYS ASN THR LEU ILE ASN GLU SEQRES 8 A 164 LYS TRP GLY ARG GLU GLU ILE THR TYR ASP THR PRO PHE SEQRES 9 A 164 LYS ARG GLU LYS SER PHE GLU ILE VAL ILE MSE VAL LEU SEQRES 10 A 164 LYS ASP LYS PHE GLN VAL ALA VAL ASN GLY LYS HIS THR SEQRES 11 A 164 LEU LEU TYR GLY HIS ARG ILE GLY PRO GLU LYS ILE ASP SEQRES 12 A 164 THR LEU GLY ILE TYR GLY LYS VAL ASN ILE HIS SER ILE SEQRES 13 A 164 GLY PHE SER GLY PRO SER SER GLY MODRES 2YV8 MSE A 115 MET SELENOMETHIONINE HET MSE A 115 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *197(H2 O) HELIX 1 1 GLY A 138 ILE A 142 5 5 SHEET 1 A 6 GLN A 16 TYR A 20 0 SHEET 2 A 6 ASN A 152 SER A 159 -1 O PHE A 158 N GLN A 16 SHEET 3 A 6 THR A 38 HIS A 45 -1 N VAL A 41 O GLY A 157 SHEET 4 A 6 SER A 109 VAL A 116 -1 O ILE A 112 N ILE A 42 SHEET 5 A 6 LYS A 120 VAL A 125 -1 O GLN A 122 N MSE A 115 SHEET 6 A 6 LYS A 128 GLY A 134 -1 O THR A 130 N VAL A 123 SHEET 1 B 6 TYR A 26 THR A 29 0 SHEET 2 B 6 THR A 144 GLY A 149 -1 O LEU A 145 N GLY A 28 SHEET 3 B 6 PHE A 53 ASN A 59 -1 N ASP A 56 O GLY A 146 SHEET 4 B 6 ASP A 68 ARG A 76 -1 O PHE A 73 N VAL A 55 SHEET 5 B 6 CYS A 82 ILE A 89 -1 O CYS A 82 N ARG A 76 SHEET 6 B 6 LYS A 92 TRP A 93 -1 O LYS A 92 N ILE A 89 SHEET 1 C 6 TYR A 26 THR A 29 0 SHEET 2 C 6 THR A 144 GLY A 149 -1 O LEU A 145 N GLY A 28 SHEET 3 C 6 PHE A 53 ASN A 59 -1 N ASP A 56 O GLY A 146 SHEET 4 C 6 ASP A 68 ARG A 76 -1 O PHE A 73 N VAL A 55 SHEET 5 C 6 CYS A 82 ILE A 89 -1 O CYS A 82 N ARG A 76 SHEET 6 C 6 GLU A 97 THR A 99 -1 O GLU A 97 N CYS A 85 LINK C ILE A 114 N MSE A 115 1555 1555 1.33 LINK C MSE A 115 N VAL A 116 1555 1555 1.33 CISPEP 1 ILE A 24 PRO A 25 0 0.25 CISPEP 2 LYS A 64 PRO A 65 0 -0.10 CRYST1 47.668 50.012 69.363 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 0.020978 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019995 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014417 0.00000