HEADER SUGAR BINDING PROTEIN 16-MAR-09 3A0E TITLE CRYSTAL STRUCTURE OF POLYGONATUM CYRTONEMA LECTIN (PCL) COMPLEXED WITH TITLE 2 DIMANNOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSE/SIALIC ACID-BINDING LECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-138 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POLYGONATUM CYRTONEMA; SOURCE 3 ORGANISM_TAXID: 195526; SOURCE 4 STRAIN: HUA KEYWDS BETA-PRISM II, LECTIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.DING,D.C.WANG REVDAT 6 13-NOV-24 3A0E 1 REMARK REVDAT 5 01-NOV-23 3A0E 1 HETSYN REVDAT 4 29-JUL-20 3A0E 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 FORMUL LINK SITE ATOM REVDAT 3 04-OCT-17 3A0E 1 REMARK REVDAT 2 21-MAR-12 3A0E 1 JRNL VERSN REVDAT 1 16-MAR-10 3A0E 0 JRNL AUTH J.DING,J.BAO,D.ZHU,Y.ZHANG,D.C.WANG JRNL TITL CRYSTAL STRUCTURES OF A NOVEL ANTI-HIV MANNOSE-BINDING JRNL TITL 2 LECTIN FROM POLYGONATUM CYRTONEMA HUA WITH UNIQUE JRNL TITL 3 LIGAND-BINDING PROPERTY AND SUPER-STRUCTURE JRNL REF J.STRUCT.BIOL. V. 171 309 2010 JRNL REFN ISSN 1047-8477 JRNL PMID 20546901 JRNL DOI 10.1016/J.JSB.2010.05.009 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14437 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) : 0.190 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1468 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 140 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 843 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.52800 REMARK 3 B22 (A**2) : -1.52800 REMARK 3 B33 (A**2) : 3.05500 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) : 0.22 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.470 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.66 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3A0E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000028653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 1W2B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR555 FLAT PANEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14437 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26500 REMARK 200 R SYM FOR SHELL (I) : 0.26500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3A0D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M LISO4, 2% PEG8000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 40.93400 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 20.46700 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 20.46700 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 40.93400 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: 5320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -134.0 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 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 -20.46700 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 121 O HOH A 121 6554 2.07 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 ASN A 59 3.54 -67.81 REMARK 500 THR A 78 77.00 -108.77 REMARK 500 ASP A 83 -127.09 -168.13 REMARK 500 ARG A 93 -0.67 75.41 REMARK 500 PRO A 100 -165.68 -76.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A0C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ANTI-HIV MANNOSE-BINDING LECTIN FROM REMARK 900 POLYGONATUM CYRTONEMA HUA REMARK 900 RELATED ID: 3A0D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF POLYGONATUM CYRTONEMA LECTIN (PCL) COMPLEXED REMARK 900 WITH MONOMANNOSIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONFLICT BETWEEN THE SEQUENCE OF THE PROTEIN AND DATABASE (UNP REMARK 999 Q8L568; Q8L568_9ASP) MAY BE ARISED FROM THE NATURAL MUTATION IN THE REMARK 999 PROTEIN OR THE ERRORS IN CDNA SEQEUNCING. DBREF 3A0E A 1 110 UNP Q8L568 Q8L568_9ASPA 29 138 SEQADV 3A0E GLN A 27 UNP Q8L568 PRO 55 SEE REMARK 999 SEQRES 1 A 110 VAL ASN SER LEU SER SER PRO ASN SER LEU PHE THR GLY SEQRES 2 A 110 HIS SER LEU GLU VAL GLY PRO SER TYR ARG LEU ILE MET SEQRES 3 A 110 GLN GLY ASP CYS ASN PHE VAL LEU TYR ASP SER GLY LYS SEQRES 4 A 110 PRO VAL TRP ALA SER ASN THR GLY GLY LEU GLY SER GLY SEQRES 5 A 110 CYS ARG LEU THR LEU HIS ASN ASN GLY ASN LEU VAL ILE SEQRES 6 A 110 TYR ASP GLN SER ASN ARG VAL ILE TRP GLN THR LYS THR SEQRES 7 A 110 ASN GLY LYS GLU ASP HIS TYR VAL LEU VAL LEU GLN GLN SEQRES 8 A 110 ASP ARG ASN VAL VAL ILE TYR GLY PRO VAL VAL TRP ALA SEQRES 9 A 110 THR GLY SER GLY PRO ALA HET MAN B 1 12 HET MAN B 2 11 HET SO4 A 112 5 HET SO4 A 113 5 HET SO4 A 114 5 HET SO4 A 115 5 HET SO4 A 116 5 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM SO4 SULFATE ION HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 MAN 2(C6 H12 O6) FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *136(H2 O) SHEET 1 A 3 SER A 3 SER A 5 0 SHEET 2 A 3 VAL A 86 LEU A 89 -1 O LEU A 87 N LEU A 4 SHEET 3 A 3 VAL A 95 TYR A 98 -1 O VAL A 96 N VAL A 88 SHEET 1 B 4 SER A 9 LEU A 10 0 SHEET 2 B 4 ARG A 54 LEU A 57 -1 O LEU A 55 N LEU A 10 SHEET 3 B 4 LEU A 63 TYR A 66 -1 O VAL A 64 N THR A 56 SHEET 4 B 4 VAL A 72 GLN A 75 -1 O ILE A 73 N ILE A 65 SHEET 1 C 4 SER A 15 VAL A 18 0 SHEET 2 C 4 TYR A 22 MET A 26 -1 O LEU A 24 N LEU A 16 SHEET 3 C 4 PHE A 32 ASP A 36 -1 O TYR A 35 N ARG A 23 SHEET 4 C 4 LYS A 39 ALA A 43 -1 O LYS A 39 N ASP A 36 SSBOND 1 CYS A 30 CYS A 53 1555 1555 2.03 LINK O3 MAN B 1 C1 MAN B 2 1555 1555 1.44 CISPEP 1 SER A 6 PRO A 7 0 0.11 CISPEP 2 GLY A 19 PRO A 20 0 -0.14 CISPEP 3 GLY A 99 PRO A 100 0 0.22 CISPEP 4 GLY A 108 PRO A 109 0 -0.03 CRYST1 76.660 76.660 61.401 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 0.013045 0.007531 0.000000 0.00000 SCALE2 0.000000 0.015063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016286 0.00000