HEADER SUGAR BINDING PROTEIN 28-NOV-12 4I4Q TITLE BEL BETA-TREFOIL APO CRYSTAL FORM 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BEL-BETA TREFOIL; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOLETUS EDULIS; SOURCE 3 ORGANISM_COMMON: KING BOLETE MUSHROOM; SOURCE 4 ORGANISM_TAXID: 36056 KEYWDS LECTIN, FRUITING BODIES, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.BOVI,L.CENCI,M.PERDUCA,S.CAPALDI,M.E.CARRIZO,L.CIVIERO, AUTHOR 2 L.R.CHIARELLI,M.GALLIANO,H.L.MONACO REVDAT 2 20-SEP-23 4I4Q 1 REMARK REVDAT 1 24-APR-13 4I4Q 0 JRNL AUTH M.BOVI,L.CENCI,M.PERDUCA,S.CAPALDI,M.E.CARRIZO,L.CIVIERO, JRNL AUTH 2 L.R.CHIARELLI,M.GALLIANO,H.L.MONACO JRNL TITL BEL {BETA}-TREFOIL: A NOVEL LECTIN WITH ANTINEOPLASTIC JRNL TITL 2 PROPERTIES IN KING BOLETE (BOLETUS EDULIS) MUSHROOMS. JRNL REF GLYCOBIOLOGY V. 23 578 2013 JRNL REFN ISSN 0959-6658 JRNL PMID 23213111 JRNL DOI 10.1093/GLYCOB/CWS164 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 28987 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1467 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 16.8331 - 3.2462 0.98 2857 142 0.2109 0.2766 REMARK 3 2 3.2462 - 2.5796 1.00 2813 150 0.1699 0.1743 REMARK 3 3 2.5796 - 2.2544 1.00 2778 152 0.1715 0.1862 REMARK 3 4 2.2544 - 2.0487 1.00 2729 165 0.1551 0.1696 REMARK 3 5 2.0487 - 1.9021 1.00 2763 143 0.1526 0.1755 REMARK 3 6 1.9021 - 1.7900 1.00 2763 148 0.1485 0.2068 REMARK 3 7 1.7900 - 1.7005 1.00 2747 129 0.1653 0.1925 REMARK 3 8 1.7005 - 1.6265 1.00 2736 158 0.2075 0.2124 REMARK 3 9 1.6265 - 1.5640 1.00 2729 142 0.2749 0.2927 REMARK 3 10 1.5640 - 1.5100 0.95 2605 138 0.3997 0.4317 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.47 REMARK 3 K_SOL : 0.60 REMARK 3 B_SOL : 80.05 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15290 REMARK 3 B22 (A**2) : -0.15290 REMARK 3 B33 (A**2) : 0.30590 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 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 1237 REMARK 3 ANGLE : 1.127 1685 REMARK 3 CHIRALITY : 0.081 171 REMARK 3 PLANARITY : 0.006 225 REMARK 3 DIHEDRAL : 10.921 441 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -4.5321 28.4541 6.7980 REMARK 3 T TENSOR REMARK 3 T11: 0.0526 T22: 0.0566 REMARK 3 T33: 0.0571 T12: 0.0004 REMARK 3 T13: 0.0129 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.2102 L22: 0.9189 REMARK 3 L33: 1.1805 L12: 0.2036 REMARK 3 L13: -0.6338 L23: -0.1792 REMARK 3 S TENSOR REMARK 3 S11: -0.0723 S12: -0.0025 S13: -0.0992 REMARK 3 S21: -0.0560 S22: 0.0030 S23: -0.0548 REMARK 3 S31: 0.0467 S32: 0.0167 S33: -0.0088 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 4I4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : DIAMOND(001) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29039 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 16.832 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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 4I4P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE, 0.2 MAGNESIUM REMARK 280 ACETATE, 20% PEG8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.18133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.59067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.59067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.18133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 35.18133 REMARK 350 REMARK 350 BIOMOLECULE: 2 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 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 330 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 388 LIES ON A SPECIAL POSITION. 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 30 109.12 78.00 REMARK 500 TRP A 35 -168.63 -164.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4I4O RELATED DB: PDB REMARK 900 RELATED ID: 4I4P RELATED DB: PDB REMARK 900 RELATED ID: 4I4R RELATED DB: PDB REMARK 900 RELATED ID: 4I4S RELATED DB: PDB REMARK 900 RELATED ID: 4I4U RELATED DB: PDB REMARK 900 RELATED ID: 4I4V RELATED DB: PDB REMARK 900 RELATED ID: 4I4X RELATED DB: PDB REMARK 900 RELATED ID: 4I4Y RELATED DB: PDB DBREF 4I4Q A 1 146 PDB 4I4Q 4I4Q 1 146 SEQRES 1 A 146 VAL ASN PHE PRO ASN ILE PRO ALA GLU GLY VAL ARG PHE SEQRES 2 A 146 ARG LEU ARG ALA ARG ASP SER GLY TYR VAL ILE TYR SER SEQRES 3 A 146 ARG THR GLU ASN ASP PRO LEU VAL TRP HIS TYR ASN GLY SEQRES 4 A 146 PRO PRO TYR ASP ASP GLN LEU PHE THR LEU ILE HIS GLY SEQRES 5 A 146 THR GLY SER ARG LEU ASN LEU TYR ALA ILE LYS SER VAL SEQRES 6 A 146 PRO ASN GLY ARG VAL LEU PHE SER ARG ASN SER ALA SER SEQRES 7 A 146 PRO THR VAL GLY ASN ILE VAL GLY ASP GLY THR TYR ASN SEQRES 8 A 146 ASP ASN TRP PHE GLN PHE ILE GLN ASP ASP ASN ASP ALA SEQRES 9 A 146 ASN SER PHE ARG ILE TYR SER LEU ALA SER ASP SER VAL SEQRES 10 A 146 LEU TYR SER ARG THR THR GLY ALA PRO GLN PHE GLY ASN SEQRES 11 A 146 TYR THR GLY PRO LYS PHE ASP ASP GLN LEU TRP HIS PHE SEQRES 12 A 146 GLU ILE VAL HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *168(H2 O) HELIX 1 1 TYR A 42 GLN A 45 5 4 HELIX 2 2 THR A 53 LEU A 57 5 5 HELIX 3 3 TYR A 90 ASN A 93 5 4 HELIX 4 4 PHE A 136 GLN A 139 5 4 SHEET 1 A 2 PHE A 13 ALA A 17 0 SHEET 2 A 2 TRP A 141 ILE A 145 -1 O GLU A 144 N ARG A 14 SHEET 1 B 2 VAL A 23 SER A 26 0 SHEET 2 B 2 VAL A 34 TYR A 37 -1 O TYR A 37 N VAL A 23 SHEET 1 C 2 PHE A 47 HIS A 51 0 SHEET 2 C 2 TYR A 60 SER A 64 -1 O LYS A 63 N THR A 48 SHEET 1 D 2 VAL A 70 SER A 73 0 SHEET 2 D 2 VAL A 81 ILE A 84 -1 O ILE A 84 N VAL A 70 SHEET 1 E 4 PHE A 95 GLN A 99 0 SHEET 2 E 4 PHE A 107 SER A 111 -1 O TYR A 110 N GLN A 96 SHEET 3 E 4 SER A 116 SER A 120 -1 O SER A 116 N SER A 111 SHEET 4 E 4 PHE A 128 TYR A 131 -1 O GLY A 129 N TYR A 119 CISPEP 1 ASP A 31 PRO A 32 0 -5.75 CISPEP 2 SER A 78 PRO A 79 0 0.22 CISPEP 3 ALA A 125 PRO A 126 0 -5.75 SITE 1 AC1 9 TYR A 25 ARG A 27 TYR A 37 TYR A 42 SITE 2 AC1 9 ASP A 44 GLN A 45 PHE A 136 ASP A 137 SITE 3 AC1 9 HOH A 343 SITE 1 AC2 7 PHE A 72 ARG A 74 TYR A 90 ASP A 92 SITE 2 AC2 7 ASN A 93 HOH A 443 HOH A 455 SITE 1 AC3 7 TYR A 37 TYR A 119 ARG A 121 PHE A 136 SITE 2 AC3 7 ASP A 138 GLN A 139 HOH A 422 CRYST1 77.744 77.744 52.772 90.00 90.00 120.00 P 32 2 1 6 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 0.012863 0.007426 0.000000 0.00000 SCALE2 0.000000 0.014853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018949 0.00000