HEADER SUGAR BINDING PROTEIN 28-FEB-00 1EIS TITLE UDA UNCOMPLEXED FORM. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A TITLE 2 SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDA; COMPND 5 OTHER_DETAILS: TWO ISOFORMS ARE PRESENT IN THE CRYSTAL: ISOLECTIN VI COMPND 6 AND ISOLECTIN V SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: URTICA DIOICA; SOURCE 3 ORGANISM_COMMON: GREAT NETTLE; SOURCE 4 ORGANISM_TAXID: 3501; SOURCE 5 OTHER_DETAILS: PURIFIED FROM THE RHIZOMES KEYWDS LECTIN, HEVEIN DOMAIN, UDA, SUPERANTIGEN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.A.SAUL,P.ROVIRA,G.BOULOT,E.J.M.VAN DAMME,W.J.PEUMANS,P.TRUFFA- AUTHOR 2 BACHI,G.A.BENTLEY REVDAT 4 25-DEC-19 1EIS 1 REMARK SEQADV SEQRES LINK REVDAT 3 24-FEB-09 1EIS 1 VERSN REVDAT 2 01-APR-03 1EIS 1 JRNL REVDAT 1 21-JUN-00 1EIS 0 JRNL AUTH F.A.SAUL,P.ROVIRA,G.BOULOT,E.J.DAMME,W.J.PEUMANS, JRNL AUTH 2 P.TRUFFA-BACHI,G.A.BENTLEY JRNL TITL CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A JRNL TITL 2 SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS JRNL TITL 3 II. JRNL REF STRUCTURE FOLD.DES. V. 8 593 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10873861 JRNL DOI 10.1016/S0969-2126(00)00142-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.P.DOES,D.K.NG,H.L.DEKKER,W.J.PEUMANS,P.M.HOUTERMAN, REMARK 1 AUTH 2 E.J.VAN DAMME,B.J.C.CORNELISSEN REMARK 1 TITL CHARACTERISATION OF URTICA DIOICA AGGLUTININ ISOLECTINS AND REMARK 1 TITL 2 THE ENCODING GENE FAMILY REMARK 1 REF PLANT MOL.BIOL. V. 39 335 1999 REMARK 1 REFN ISSN 0167-4412 REMARK 1 DOI 10.1023/A:1006134932290 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 11689 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 602 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 626 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.80 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.017 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.016 ; 0.020 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.022 ; 0.030 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.012 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.185 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.149 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.162 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 4.900 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 13.700; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 27.400; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.814 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.864 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.397 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.916 ; 4.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS DETERMINED TO 2.45A REMARK 3 RESOLUTION BY MIR METHODS BASED ON 4 HG DERIVATIVES (ROTATING- REMARK 3 ANODE X-RAY SOURCE) WITH SOLVENT FLATTENING, AND REFINED TO REMARK 3 1.66A RESOLUTION WITH SYNCHROTRON DATA USING A BULK SOLVENT REMARK 3 CORRECTION AND ANISOTROPIC SCALE FACTOR. REMARK 4 REMARK 4 1EIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-98 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : D41A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.375 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, SODIUM ACETATE, SODIUM REMARK 280 CHLORIDE , PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 290.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.65000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.55000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.55000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.80000 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: MONOMERIC 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 400 REMARK 400 COMPOUND REMARK 400 THE STRUCTURE COMPRISES TWO HEVEIN-LIKE DOMAINS, REMARK 400 EACH HOMOLOGOUS TO THOSE OF WHEAT GERM AGGLUTININ REMARK 400 (PDB CODE: 9WGA). EACH DOMAIN CONTAINS A REMARK 400 SACCHARIDE-BINDING SITE. THE N-TERMINAL RESIDUE IS REMARK 400 PYRROLIDONE CARBOXYLIC ACID (PCA). A DUAL CONFORMATION REMARK 400 IS SEEN AT GLY79, GLY80. NO ELECTRON DENSITY IS SEEN REMARK 400 FOR THE SIDE CHAIN OF ARG33 BEYOND THE CB ATOM. NO REMARK 400 INTERPRETABLE DENSITY IS SEEN FOR C-TERMINAL RESIDUES REMARK 400 SER87, SER88, AND SER89. 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 SER A 87 REMARK 465 SER A 88 REMARK 465 SER A 89 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 33 CD NE CZ NH1 NH2 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 OG SER A 10 O HOH A 97 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EN2 RELATED DB: PDB REMARK 900 UDA TETRASACCHARIDE COMPLEX REMARK 900 RELATED ID: 1ENM RELATED DB: PDB REMARK 900 UDA TRISACCHARIDE COMPLEX DBREF 1EIS A 1 89 UNP Q9SYR5 Q9SYR5_URTDI 24 112 SEQADV 1EIS GLY A 10 UNP Q9SYR5 SER 33 MICROHETEROGENEITY SEQRES 1 A 89 PCA ARG CYS GLY SER GLN GLY GLY GLY SER THR CYS PRO SEQRES 2 A 89 GLY LEU ARG CYS CYS SER ILE TRP GLY TRP CYS GLY ASP SEQRES 3 A 89 SER GLU PRO TYR CYS GLY ARG THR CYS GLU ASN LYS CYS SEQRES 4 A 89 TRP SER GLY GLU ARG SER ASP HIS ARG CYS GLY ALA ALA SEQRES 5 A 89 VAL GLY ASN PRO PRO CYS GLY GLN ASP ARG CYS CYS SER SEQRES 6 A 89 VAL HIS GLY TRP CYS GLY GLY GLY ASN ASP TYR CYS SER SEQRES 7 A 89 GLY GLY ASN CYS GLN TYR ARG CYS SER SER SER MODRES 1EIS PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 FORMUL 2 HOH *49(H2 O) HELIX 1 1 CYS A 12 ARG A 16 5 5 HELIX 2 2 SER A 27 GLY A 32 1 6 HELIX 3 3 CYS A 39 GLU A 43 5 5 HELIX 4 4 GLY A 50 GLY A 54 5 5 HELIX 5 5 GLY A 73 SER A 78 1 6 SHEET 1 A 3 CYS A 24 GLY A 25 0 SHEET 2 A 3 CYS A 17 SER A 19 -1 O CYS A 17 N GLY A 25 SHEET 3 A 3 CYS A 35 ASN A 37 -1 N GLU A 36 O CYS A 18 SHEET 1 B 3 CYS A 70 GLY A 71 0 SHEET 2 B 3 CYS A 63 SER A 65 -1 N CYS A 63 O GLY A 71 SHEET 3 B 3 CYS A 82 TYR A 84 -1 N GLN A 83 O CYS A 64 SSBOND 1 CYS A 3 CYS A 18 1555 1555 2.01 SSBOND 2 CYS A 12 CYS A 24 1555 1555 2.03 SSBOND 3 CYS A 17 CYS A 31 1555 1555 2.03 SSBOND 4 CYS A 35 CYS A 39 1555 1555 2.01 SSBOND 5 CYS A 49 CYS A 64 1555 1555 2.04 SSBOND 6 CYS A 58 CYS A 70 1555 1555 2.02 SSBOND 7 CYS A 63 CYS A 77 1555 1555 2.04 SSBOND 8 CYS A 82 CYS A 86 1555 1555 2.03 LINK C PCA A 1 N ARG A 2 1555 1555 1.36 CRYST1 31.300 41.600 77.100 90.00 90.00 90.00 P 21 21 21 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 0.031950 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012970 0.00000 HETATM 1 N PCA A 1 -19.501 -14.128 -6.905 1.00 32.30 N HETATM 2 CA PCA A 1 -18.324 -14.762 -6.001 1.00 29.73 C HETATM 3 CB PCA A 1 -17.032 -14.921 -6.810 1.00 32.45 C HETATM 4 CG PCA A 1 -17.396 -14.297 -8.011 1.00 33.86 C HETATM 5 CD PCA A 1 -18.753 -14.026 -8.106 1.00 35.80 C HETATM 6 OE PCA A 1 -19.491 -13.345 -8.947 1.00 35.96 O HETATM 7 C PCA A 1 -17.956 -13.926 -4.879 1.00 26.90 C HETATM 8 O PCA A 1 -18.737 -12.881 -4.619 1.00 24.57 O