HEADER SUGAR BINDING PROTEIN 05-APR-17 5NM6 TITLE CHICKEN GRIFIN (CRYSTALLISATION PH: 4.6) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: GRIFIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GALECTIN RELATED PROTEIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.M.RUIZ,A.ROMERO REVDAT 3 17-JAN-24 5NM6 1 REMARK REVDAT 2 21-FEB-18 5NM6 1 JRNL REVDAT 1 14-FEB-18 5NM6 0 JRNL AUTH F.M.RUIZ,U.GILLES,A.K.LUDWIG,C.SEHAD,T.C.SHIAO, JRNL AUTH 2 G.GARCIA CABALLERO,H.KALTNER,I.LINDNER,R.ROY,D.REUSCH, JRNL AUTH 3 A.ROMERO,H.J.GABIUS JRNL TITL CHICKEN GRIFIN: STRUCTURAL CHARACTERIZATION IN CRYSTALS AND JRNL TITL 2 IN SOLUTION. JRNL REF BIOCHIMIE V. 146 127 2018 JRNL REFN ISSN 1638-6183 JRNL PMID 29248541 JRNL DOI 10.1016/J.BIOCHI.2017.12.003 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 39747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1977 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 40.2740 - 3.5124 0.82 2514 114 0.1471 0.1861 REMARK 3 2 3.5124 - 2.7881 0.87 2592 124 0.1555 0.1791 REMARK 3 3 2.7881 - 2.4357 0.89 2646 137 0.1739 0.2392 REMARK 3 4 2.4357 - 2.2131 0.91 2704 150 0.1723 0.2127 REMARK 3 5 2.2131 - 2.0544 0.91 2672 164 0.1633 0.2106 REMARK 3 6 2.0544 - 1.9333 0.93 2740 135 0.1644 0.2014 REMARK 3 7 1.9333 - 1.8365 0.93 2763 161 0.1761 0.2218 REMARK 3 8 1.8365 - 1.7565 0.94 2761 134 0.1983 0.2251 REMARK 3 9 1.7565 - 1.6889 0.94 2796 137 0.2003 0.2593 REMARK 3 10 1.6889 - 1.6306 0.95 2787 152 0.2121 0.2459 REMARK 3 11 1.6306 - 1.5797 0.95 2854 141 0.2137 0.2636 REMARK 3 12 1.5797 - 1.5345 0.95 2797 146 0.2228 0.2713 REMARK 3 13 1.5345 - 1.4941 0.94 2726 159 0.2694 0.2782 REMARK 3 14 1.4941 - 1.4576 0.82 2418 123 0.3199 0.3555 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 2379 REMARK 3 ANGLE : 0.846 3227 REMARK 3 CHIRALITY : 0.094 340 REMARK 3 PLANARITY : 0.006 419 REMARK 3 DIHEDRAL : 3.038 1708 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 5NM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39758 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.458 REMARK 200 RESOLUTION RANGE LOW (A) : 40.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.020 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: 5NLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%PEG4K, NA ACETATE 0.1M PH 4.6, 0.2M REMARK 280 AMM. SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.13700 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -2.33345 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 54.09470 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 2 REMARK 465 MET B 2 REMARK 465 TYR B 140 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 211 O HOH A 242 2.07 REMARK 500 OE2 GLU B 80 O HOH B 201 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 MET A 14 31.76 -96.39 REMARK 500 MET A 14 35.50 -99.01 REMARK 500 SER A 31 -147.88 -100.84 REMARK 500 ASP A 92 -162.26 -117.41 REMARK 500 ASN A 125 -140.20 76.57 REMARK 500 SER B 31 -155.60 -101.76 REMARK 500 ASP B 92 -162.40 -106.82 REMARK 500 ASN B 125 -137.02 80.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 5NM6 A 2 140 UNP F1NZ18 F1NZ18_CHICK 1 139 DBREF 5NM6 B 2 140 UNP F1NZ18 F1NZ18_CHICK 1 139 SEQRES 1 A 139 MET ALA LEU ARG PHE GLU ALA LEU TYR PRO GLU GLY MET SEQRES 2 A 139 CYS PRO GLY TRP SER VAL VAL VAL LYS GLY LYS THR SER SEQRES 3 A 139 SER ASN THR SER MET PHE GLU ILE ASN PHE LEU SER HIS SEQRES 4 A 139 PRO GLY ASP GLN ILE ALA PHE HIS PHE ASN PRO ARG PHE SEQRES 5 A 139 ALA SER SER ARG ILE VAL CYS ASN SER PHE LEU ALA ASN SEQRES 6 A 139 HIS TRP GLY LYS GLU GLU VAL ASN LYS THR PHE PRO PHE SEQRES 7 A 139 GLU ALA LYS GLU PRO PHE GLN VAL GLU ILE TYR SER ASP SEQRES 8 A 139 GLN ASP TYR PHE HIS ILE PHE ILE ASP GLU ASN LYS ILE SEQRES 9 A 139 LEU GLN TYR LYS HIS ARG GLN LYS GLN LEU SER SER ILE SEQRES 10 A 139 THR LYS LEU GLN ILE LEU ASN ASP ILE GLU ILE SER SER SEQRES 11 A 139 VAL GLU ILE THR LYS ARG GLY LEU TYR SEQRES 1 B 139 MET ALA LEU ARG PHE GLU ALA LEU TYR PRO GLU GLY MET SEQRES 2 B 139 CYS PRO GLY TRP SER VAL VAL VAL LYS GLY LYS THR SER SEQRES 3 B 139 SER ASN THR SER MET PHE GLU ILE ASN PHE LEU SER HIS SEQRES 4 B 139 PRO GLY ASP GLN ILE ALA PHE HIS PHE ASN PRO ARG PHE SEQRES 5 B 139 ALA SER SER ARG ILE VAL CYS ASN SER PHE LEU ALA ASN SEQRES 6 B 139 HIS TRP GLY LYS GLU GLU VAL ASN LYS THR PHE PRO PHE SEQRES 7 B 139 GLU ALA LYS GLU PRO PHE GLN VAL GLU ILE TYR SER ASP SEQRES 8 B 139 GLN ASP TYR PHE HIS ILE PHE ILE ASP GLU ASN LYS ILE SEQRES 9 B 139 LEU GLN TYR LYS HIS ARG GLN LYS GLN LEU SER SER ILE SEQRES 10 B 139 THR LYS LEU GLN ILE LEU ASN ASP ILE GLU ILE SER SER SEQRES 11 B 139 VAL GLU ILE THR LYS ARG GLY LEU TYR FORMUL 3 HOH *304(H2 O) HELIX 1 AA1 GLN A 114 SER A 116 5 3 HELIX 2 AA2 GLN B 114 SER B 116 5 3 SHEET 1 AA1 6 LEU A 4 LEU A 9 0 SHEET 2 AA1 6 ILE A 118 ASN A 125 -1 O ILE A 123 N PHE A 6 SHEET 3 AA1 6 PHE A 33 SER A 39 -1 N ASN A 36 O GLN A 122 SHEET 4 AA1 6 GLN A 44 ARG A 52 -1 O PHE A 47 N PHE A 37 SHEET 5 AA1 6 ARG A 57 ASN A 61 -1 O ARG A 57 N ARG A 52 SHEET 6 AA1 6 GLU A 72 VAL A 73 -1 O GLU A 72 N CYS A 60 SHEET 1 AA2 5 ASN A 103 LYS A 109 0 SHEET 2 AA2 5 TYR A 95 ILE A 100 -1 N ILE A 98 O ILE A 105 SHEET 3 AA2 5 PHE A 85 SER A 91 -1 N TYR A 90 O HIS A 97 SHEET 4 AA2 5 TRP A 18 LYS A 25 -1 N VAL A 22 O VAL A 87 SHEET 5 AA2 5 GLU A 128 LYS A 136 -1 O GLU A 128 N LYS A 25 SHEET 1 AA3 2 PHE A 63 LEU A 64 0 SHEET 2 AA3 2 HIS A 67 TRP A 68 -1 O HIS A 67 N LEU A 64 SHEET 1 AA4 6 LEU B 4 LEU B 9 0 SHEET 2 AA4 6 ILE B 118 ASN B 125 -1 O ILE B 123 N PHE B 6 SHEET 3 AA4 6 PHE B 33 SER B 39 -1 N ASN B 36 O GLN B 122 SHEET 4 AA4 6 GLN B 44 ARG B 52 -1 O GLN B 44 N SER B 39 SHEET 5 AA4 6 ARG B 57 LEU B 64 -1 O ARG B 57 N ARG B 52 SHEET 6 AA4 6 HIS B 67 TRP B 68 -1 O HIS B 67 N LEU B 64 SHEET 1 AA5 6 LEU B 4 LEU B 9 0 SHEET 2 AA5 6 ILE B 118 ASN B 125 -1 O ILE B 123 N PHE B 6 SHEET 3 AA5 6 PHE B 33 SER B 39 -1 N ASN B 36 O GLN B 122 SHEET 4 AA5 6 GLN B 44 ARG B 52 -1 O GLN B 44 N SER B 39 SHEET 5 AA5 6 ARG B 57 LEU B 64 -1 O ARG B 57 N ARG B 52 SHEET 6 AA5 6 GLU B 72 ASN B 74 -1 O ASN B 74 N ILE B 58 SHEET 1 AA6 5 ASN B 103 LYS B 109 0 SHEET 2 AA6 5 TYR B 95 ILE B 100 -1 N ILE B 98 O ILE B 105 SHEET 3 AA6 5 PHE B 85 SER B 91 -1 N TYR B 90 O HIS B 97 SHEET 4 AA6 5 TRP B 18 LYS B 25 -1 N VAL B 20 O ILE B 89 SHEET 5 AA6 5 GLU B 128 LYS B 136 -1 O GLU B 128 N LYS B 25 CISPEP 1 CYS A 15 PRO A 16 0 -7.23 CISPEP 2 CYS A 15 PRO A 16 0 -7.89 CISPEP 3 HIS A 40 PRO A 41 0 0.48 CISPEP 4 CYS B 15 PRO B 16 0 -9.27 CISPEP 5 CYS B 15 PRO B 16 0 -10.02 CISPEP 6 HIS B 40 PRO B 41 0 0.58 CRYST1 38.943 60.274 54.145 90.00 92.47 90.00 P 1 21 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 0.025679 0.000000 0.001108 0.00000 SCALE2 0.000000 0.016591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018486 0.00000