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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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