HEADER SUGAR BINDING PROTEIN 27-OCT-13 4NDU TITLE CRYSTAL STRUCTURE OF L. DECASTES ALPHA-GALACTOSYL-BINDING LECTIN IN TITLE 2 COMPLEX WITH ALPHA-METHYLGALACTOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSYL-BINDING LECTIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYOPHYLLUM DECASTES; SOURCE 3 ORGANISM_COMMON: FRIED CHICKEN MUSHROOM; SOURCE 4 ORGANISM_TAXID: 64660; SOURCE 5 ORGAN: FRUITING BODIES KEYWDS LECTIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.VAN EERDE,E.GRAHN,U.KRENGEL REVDAT 5 20-SEP-23 4NDU 1 HETSYN REVDAT 4 29-JUL-20 4NDU 1 COMPND REMARK HETNAM SITE REVDAT 3 08-APR-15 4NDU 1 JRNL REVDAT 2 14-JAN-15 4NDU 1 JRNL REVDAT 1 10-DEC-14 4NDU 0 JRNL AUTH A.VAN EERDE,E.M.GRAHN,H.C.WINTER,I.J.GOLDSTEIN,U.KRENGEL JRNL TITL ATOMIC-RESOLUTION STRUCTURE OF THE ALPHA-GALACTOSYL BINDING JRNL TITL 2 LYOPHYLLUM DECASTES LECTIN REVEALS A NEW PROTEIN FAMILY JRNL TITL 3 FOUND IN BOTH FUNGI AND PLANTS. JRNL REF GLYCOBIOLOGY V. 25 492 2015 JRNL REFN ISSN 0959-6658 JRNL PMID 25504801 JRNL DOI 10.1093/GLYCOB/CWU136 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 50851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2590 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 18.7636 - 3.4040 0.99 2882 163 0.1604 0.1777 REMARK 3 2 3.4040 - 2.7045 1.00 2772 162 0.1871 0.2088 REMARK 3 3 2.7045 - 2.3634 0.99 2748 142 0.1925 0.2241 REMARK 3 4 2.3634 - 2.1476 0.99 2746 141 0.1682 0.2222 REMARK 3 5 2.1476 - 1.9939 0.99 2709 139 0.1604 0.1901 REMARK 3 6 1.9939 - 1.8764 0.99 2685 143 0.1660 0.1943 REMARK 3 7 1.8764 - 1.7825 0.99 2684 149 0.1612 0.2160 REMARK 3 8 1.7825 - 1.7050 0.99 2670 154 0.1549 0.1892 REMARK 3 9 1.7050 - 1.6394 0.99 2655 147 0.1524 0.2123 REMARK 3 10 1.6394 - 1.5828 0.99 2680 138 0.1547 0.2051 REMARK 3 11 1.5828 - 1.5334 0.99 2634 137 0.1520 0.1844 REMARK 3 12 1.5334 - 1.4896 0.98 2667 143 0.1661 0.2195 REMARK 3 13 1.4896 - 1.4504 0.98 2631 132 0.1692 0.2398 REMARK 3 14 1.4504 - 1.4150 0.98 2645 132 0.1824 0.2184 REMARK 3 15 1.4150 - 1.3828 0.98 2655 123 0.1995 0.2969 REMARK 3 16 1.3828 - 1.3534 0.97 2593 151 0.2021 0.2530 REMARK 3 17 1.3534 - 1.3264 0.97 2627 158 0.2147 0.2622 REMARK 3 18 1.3264 - 1.3010 0.97 2578 136 0.2524 0.3048 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.30 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 : 0.011 1642 REMARK 3 ANGLE : 1.486 2233 REMARK 3 CHIRALITY : 0.097 232 REMARK 3 PLANARITY : 0.007 298 REMARK 3 DIHEDRAL : 12.520 590 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 4NDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50868 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.64400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4NDT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M TRIS-HCL, REMARK 280 30% W/V PEG4000, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 31.04900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.51750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.04900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.51750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 HIS A 49 -53.14 75.81 REMARK 500 SER A 81 -24.36 73.60 REMARK 500 HIS B 49 -45.57 77.22 REMARK 500 SER B 81 -23.78 72.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NDS RELATED DB: PDB REMARK 900 L. DECASTES ALPHA-GALACTOSYL-BINDING LECTIN, MONOCLINIC CRYSTAL FORM REMARK 900 RELATED ID: 4NDT RELATED DB: PDB REMARK 900 L. DECASTES ALPHA-GALACTOSYL-BINDING LECTIN, ORTHORHOMBIC CRYSTAL REMARK 900 FORM REMARK 900 RELATED ID: 4NDV RELATED DB: PDB REMARK 900 L. DECASTES ALPHA-GALACTOSYL-BINDING LECTIN IN COMPLEX WITH REMARK 900 GLOBOTRIOSE DBREF 4NDU A 1 94 UNP A7UNK4 AGBL_LYODE 1 94 DBREF 4NDU B 1 94 UNP A7UNK4 AGBL_LYODE 1 94 SEQRES 1 A 94 ALA CYS TRP LYS ALA ASN SER CYS PRO GLY SER ALA PHE SEQRES 2 A 94 GLU SER LYS ASP ARG LEU ARG SER PHE ALA LEU LEU TYR SEQRES 3 A 94 CYS ARG TYR ASN TYR LYS PRO PRO TYR GLY GLN GLY ALA SEQRES 4 A 94 PHE GLY TYR ALA SER ALA VAL SER THR HIS GLY TRP GLU SEQRES 5 A 94 THR GLU ALA GLN CYS ILE ASN THR PHE GLU GLN ILE ILE SEQRES 6 A 94 THR SER CYS HIS GLY GLN SER ASN GLY GLY THR LEU GLU SEQRES 7 A 94 LEU ASN SER GLY ARG LEU SER LEU ALA PHE GLY ASN CYS SEQRES 8 A 94 GLU GLU LEU SEQRES 1 B 94 ALA CYS TRP LYS ALA ASN SER CYS PRO GLY SER ALA PHE SEQRES 2 B 94 GLU SER LYS ASP ARG LEU ARG SER PHE ALA LEU LEU TYR SEQRES 3 B 94 CYS ARG TYR ASN TYR LYS PRO PRO TYR GLY GLN GLY ALA SEQRES 4 B 94 PHE GLY TYR ALA SER ALA VAL SER THR HIS GLY TRP GLU SEQRES 5 B 94 THR GLU ALA GLN CYS ILE ASN THR PHE GLU GLN ILE ILE SEQRES 6 B 94 THR SER CYS HIS GLY GLN SER ASN GLY GLY THR LEU GLU SEQRES 7 B 94 LEU ASN SER GLY ARG LEU SER LEU ALA PHE GLY ASN CYS SEQRES 8 B 94 GLU GLU LEU HET AMG A 101 13 HET AMG B 101 13 HETNAM AMG METHYL ALPHA-D-GALACTOPYRANOSIDE HETSYN AMG ALPHA-METHYL-D-GALACTOSIDE; METHYL ALPHA-D-GALACTOSIDE; HETSYN 2 AMG METHYL D-GALACTOSIDE; METHYL GALACTOSIDE FORMUL 3 AMG 2(C7 H14 O6) FORMUL 5 HOH *319(H2 O) HELIX 1 1 SER A 15 TYR A 31 1 17 HELIX 2 2 THR A 53 HIS A 69 1 17 HELIX 3 3 SER B 15 TYR B 31 1 17 HELIX 4 4 THR B 53 HIS B 69 1 17 SHEET 1 A 4 TYR A 35 PHE A 40 0 SHEET 2 A 4 ALA A 43 THR A 48 -1 O SER A 47 N GLY A 36 SHEET 3 A 4 GLY A 82 ALA A 87 -1 O ALA A 87 N SER A 44 SHEET 4 A 4 GLY A 74 LEU A 79 -1 N LEU A 77 O LEU A 84 SHEET 1 B 4 TYR B 35 PHE B 40 0 SHEET 2 B 4 ALA B 43 THR B 48 -1 O SER B 47 N GLY B 36 SHEET 3 B 4 GLY B 82 ALA B 87 -1 O ALA B 87 N SER B 44 SHEET 4 B 4 GLY B 74 LEU B 79 -1 N LEU B 77 O LEU B 84 SSBOND 1 CYS A 2 CYS A 68 1555 1555 2.04 SSBOND 2 CYS A 8 CYS A 91 1555 1555 2.06 SSBOND 3 CYS A 27 CYS A 57 1555 1555 2.07 SSBOND 4 CYS B 2 CYS B 68 1555 1555 2.03 SSBOND 5 CYS B 8 CYS B 91 1555 1555 2.06 SSBOND 6 CYS B 27 CYS B 57 1555 1555 2.09 CISPEP 1 PRO A 33 PRO A 34 0 7.77 CISPEP 2 PRO B 33 PRO B 34 0 5.92 CRYST1 62.098 75.035 44.412 90.00 90.00 90.00 P 21 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 0.016104 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022516 0.00000