HEADER SUGAR BINDING PROTEIN, PLANT PROTEIN 19-FEB-08 3CA0 TITLE SAMBUCUS NIGRA AGGLUTININ II (SNA-II), HEXAGONAL CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGLUTININ II; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SNA-II SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SAMBUCUS NIGRA; SOURCE 3 ORGANISM_COMMON: EUROPEAN ELDER, ELDERBERRY; SOURCE 4 TISSUE: BARK KEYWDS BETA-TREFOIL, RICIN-B DOMAIN, GLYCOSYLATION, GLYCOPROTEIN, LECTIN, KEYWDS 2 SUGAR BINDING PROTEIN, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.MAVEYRAUD,H.NIWA,V.GUILLET,R.A.PALMER,C.D.REYNOLDS,L.MOUREY REVDAT 7 13-NOV-24 3CA0 1 REMARK REVDAT 6 30-AUG-23 3CA0 1 HETSYN REVDAT 5 29-JUL-20 3CA0 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 13-JUL-11 3CA0 1 VERSN REVDAT 3 17-MAR-09 3CA0 1 JRNL REVDAT 2 24-FEB-09 3CA0 1 VERSN REVDAT 1 25-NOV-08 3CA0 0 JRNL AUTH L.MAVEYRAUD,H.NIWA,V.GUILLET,D.I.SVERGUN,P.V.KONAREV, JRNL AUTH 2 R.A.PALMER,W.J.PEUMANS,P.ROUGE,E.J.VAN DAMME,C.D.REYNOLDS, JRNL AUTH 3 L.MOUREY JRNL TITL STRUCTURAL BASIS FOR SUGAR RECOGNITION, INCLUDING THE TN JRNL TITL 2 CARCINOMA ANTIGEN, BY THE LECTIN SNA-II FROM SAMBUCUS NIGRA JRNL REF PROTEINS V. 75 89 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 18798567 JRNL DOI 10.1002/PROT.22222 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 52296 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 + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2762 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3455 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1980 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 209 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 29.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.78000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : -1.16000 REMARK 3 B12 (A**2) : 0.39000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.696 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2289 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1473 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3153 ; 1.907 ; 2.039 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3546 ; 1.369 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 7.444 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;36.937 ;24.688 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 338 ;12.748 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.639 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 385 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2409 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 411 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 373 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1606 ; 0.216 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1143 ; 0.167 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1175 ; 0.113 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 219 ; 0.156 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.127 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 42 ; 0.393 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.199 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1668 ; 1.323 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 534 ; 0.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2140 ; 1.696 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1103 ; 3.052 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1013 ; 4.648 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 129 REMARK 3 ORIGIN FOR THE GROUP (A): 6.4440 45.1509 11.1775 REMARK 3 T TENSOR REMARK 3 T11: -0.2885 T22: -0.1246 REMARK 3 T33: -0.1965 T12: 0.0133 REMARK 3 T13: -0.0268 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 1.9133 L22: 1.1980 REMARK 3 L33: 1.7421 L12: 0.5446 REMARK 3 L13: 0.1744 L23: 0.2593 REMARK 3 S TENSOR REMARK 3 S11: 0.0244 S12: -0.1053 S13: -0.1334 REMARK 3 S21: 0.1103 S22: -0.0267 S23: 0.0309 REMARK 3 S31: 0.1650 S32: -0.0398 S33: 0.0023 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 130 A 257 REMARK 3 ORIGIN FOR THE GROUP (A): 22.7805 67.6192 16.5410 REMARK 3 T TENSOR REMARK 3 T11: -0.2241 T22: -0.1487 REMARK 3 T33: -0.2036 T12: 0.0150 REMARK 3 T13: 0.0053 T23: 0.0340 REMARK 3 L TENSOR REMARK 3 L11: 2.4262 L22: 1.6397 REMARK 3 L33: 2.6493 L12: -0.2415 REMARK 3 L13: 0.1947 L23: 1.0588 REMARK 3 S TENSOR REMARK 3 S11: -0.0341 S12: 0.0540 S13: 0.2397 REMARK 3 S21: -0.0018 S22: 0.0610 S23: 0.0192 REMARK 3 S31: -0.3039 S32: 0.1021 S33: -0.0269 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3CA0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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) : 0.937 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 51.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.32400 REMARK 200 R SYM FOR SHELL (I) : 0.32400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: CHAIN B OF RICIN, PDN ENTRY 2AAI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 81.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN 16 MG/ML, AMMONIUM SULFATE 2.0 REMARK 280 M, SODIUM ACETATE 100 MM, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 59.11333 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 118.22667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.11333 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 118.22667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.11333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 118.22667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 59.11333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 118.22667 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, B, C, D, E 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 911 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 912 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1244 LIES ON A SPECIAL POSITION. 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 258 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 130 CD CE NZ REMARK 470 ILE A 132 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 128 CB ASN A 128 CG 0.139 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 ASP A 87 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 87 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 103 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES 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 ARG A 107 -1.71 79.87 REMARK 500 LYS A 193 1.01 80.04 REMARK 500 ARG A 223 -4.13 74.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C9Z RELATED DB: PDB REMARK 900 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM REMARK 900 RELATED ID: 3CA1 RELATED DB: PDB REMARK 900 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED REMARK 900 TO GALACTOSE REMARK 900 RELATED ID: 3CA3 RELATED DB: PDB REMARK 900 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED REMARK 900 TO N-ACETYGALACTOSAMINE REMARK 900 RELATED ID: 3CA4 RELATED DB: PDB REMARK 900 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED REMARK 900 TO LACTOSE REMARK 900 RELATED ID: 3CA5 RELATED DB: PDB REMARK 900 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED REMARK 900 TO METHYL-GALACTOSE REMARK 900 RELATED ID: 3CA6 RELATED DB: PDB REMARK 900 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED REMARK 900 TO TN ANTIGEN REMARK 900 RELATED ID: 3CAH RELATED DB: PDB REMARK 900 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED REMARK 900 TO FUCOSE REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE ELECTRON DENSITY OF THE STRUCTURE INDICATES REMARK 999 CLEARLY THAT THE AMINO ACID AT POSITION 224 IS A LEU AND NOT A HIS. DBREF 3CA0 A 1 258 UNP P33183 NIGB_SAMNI 306 563 SEQADV 3CA0 LEU A 224 UNP P33183 HIS 529 SEE REMARK 999 SEQRES 1 A 258 THR SER PHE THR ARG ASN ILE VAL GLY ARG ASP GLY LEU SEQRES 2 A 258 CYS VAL ASP VAL ARG ASN GLY TYR ASP THR ASP GLY THR SEQRES 3 A 258 PRO LEU GLN LEU TRP PRO CYS GLY THR GLN ARG ASN GLN SEQRES 4 A 258 ARG TRP THR PHE ASP SER ASP ASP THR ILE ARG SER MET SEQRES 5 A 258 GLY LYS CYS MET THR ALA ASN GLY LEU ASN ASN GLY SER SEQRES 6 A 258 ASN ILE VAL ILE PHE ASN CYS SER THR ALA ALA GLU ASN SEQRES 7 A 258 ALA ILE LYS TRP GLU VAL PRO ILE ASP GLY SER ILE ILE SEQRES 8 A 258 ASN PRO SER SER GLY LEU VAL MET THR ALA PRO ARG ALA SEQRES 9 A 258 ALA SER ARG THR ILE LEU LEU LEU GLU ASP ASN ILE TYR SEQRES 10 A 258 ALA ALA SER GLN GLY TRP THR VAL THR ASN ASN VAL LYS SEQRES 11 A 258 PRO ILE VAL ALA SER ILE VAL GLY TYR LYS GLU MET CYS SEQRES 12 A 258 LEU GLN SER ASN GLY GLU ASN ASN GLY VAL TRP MET GLU SEQRES 13 A 258 ASP CYS GLU ALA THR SER LEU GLN GLN GLN TRP ALA LEU SEQRES 14 A 258 TYR GLY ASP ARG THR ILE ARG VAL ASN SER THR ARG GLY SEQRES 15 A 258 LEU CYS VAL THR THR ASN GLY TYR ASN SER LYS ASP LEU SEQRES 16 A 258 ILE ILE ILE LEU LYS CYS GLN GLY LEU PRO SER GLN ARG SEQRES 17 A 258 TRP PHE PHE ASN SER ASP GLY ALA ILE VAL ASN PRO LYS SEQRES 18 A 258 SER ARG LEU VAL MET ASP VAL ARG ALA SER ASN VAL SER SEQRES 19 A 258 LEU ARG GLU ILE ILE ILE PHE PRO ALA THR GLY ASN PRO SEQRES 20 A 258 ASN GLN GLN TRP VAL THR GLN VAL LEU PRO SER MODRES 3CA0 ASN A 63 ASN GLYCOSYLATION SITE MODRES 3CA0 ASN A 71 ASN GLYCOSYLATION SITE MODRES 3CA0 ASN A 178 ASN GLYCOSYLATION SITE MODRES 3CA0 ASN A 232 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET XYP B 4 9 HET MAN B 5 11 HET MAN B 6 11 HET FUC B 7 10 HET NAG C 1 14 HET FUC C 2 10 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET FUC E 2 10 HET NAG E 3 14 HET SO4 A 901 5 HET SO4 A 902 5 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 A 906 5 HET SO4 A 907 5 HET ACT A 910 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 7(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 XYP C5 H10 O5 FORMUL 2 MAN 2(C6 H12 O6) FORMUL 2 FUC 3(C6 H12 O5) FORMUL 6 SO4 7(O4 S 2-) FORMUL 13 ACT C2 H3 O2 1- FORMUL 14 HOH *335(H2 O) HELIX 1 1 GLY A 9 LEU A 13 5 5 HELIX 2 2 ASN A 19 TYR A 21 5 3 HELIX 3 3 GLN A 36 ARG A 40 5 5 HELIX 4 4 ALA A 76 LYS A 81 1 6 HELIX 5 5 ALA A 118 GLY A 122 5 5 HELIX 6 6 GLY A 138 MET A 142 5 5 HELIX 7 7 SER A 162 GLN A 165 5 4 HELIX 8 8 LEU A 204 ARG A 208 5 5 HELIX 9 9 ALA A 230 ARG A 236 5 7 HELIX 10 10 ASN A 246 GLN A 250 5 5 SHEET 1 A 8 VAL A 98 THR A 100 0 SHEET 2 A 8 LEU A 111 GLU A 113 -1 O GLU A 113 N VAL A 98 SHEET 3 A 8 SER A 65 PHE A 70 -1 N SER A 65 O LEU A 112 SHEET 4 A 8 LYS A 54 ALA A 58 -1 N CYS A 55 O PHE A 70 SHEET 5 A 8 ILE A 49 SER A 51 -1 N ILE A 49 O MET A 56 SHEET 6 A 8 TRP A 41 ASP A 44 -1 N THR A 42 O ARG A 50 SHEET 7 A 8 SER A 2 VAL A 8 -1 N PHE A 3 O PHE A 43 SHEET 8 A 8 THR A 124 THR A 126 -1 O THR A 124 N VAL A 8 SHEET 1 B 2 CYS A 14 VAL A 17 0 SHEET 2 B 2 LEU A 28 TRP A 31 -1 O TRP A 31 N CYS A 14 SHEET 1 C 6 ILE A 196 LYS A 200 0 SHEET 2 C 6 THR A 180 THR A 187 -1 N THR A 186 O ILE A 197 SHEET 3 C 6 ILE A 175 VAL A 177 -1 N ILE A 175 O VAL A 185 SHEET 4 C 6 TRP A 167 LEU A 169 -1 N ALA A 168 O ARG A 176 SHEET 5 C 6 ILE A 132 VAL A 137 -1 N ILE A 132 O LEU A 169 SHEET 6 C 6 VAL A 252 VAL A 255 -1 O VAL A 252 N VAL A 137 SHEET 1 D 2 CYS A 143 GLN A 145 0 SHEET 2 D 2 TRP A 154 GLU A 156 -1 O GLU A 156 N CYS A 143 SHEET 1 E 2 PHE A 210 PHE A 211 0 SHEET 2 E 2 ILE A 217 VAL A 218 -1 O VAL A 218 N PHE A 210 SHEET 1 F 2 VAL A 225 VAL A 228 0 SHEET 2 F 2 ILE A 238 PHE A 241 -1 O PHE A 241 N VAL A 225 SSBOND 1 CYS A 14 CYS A 33 1555 1555 2.14 SSBOND 2 CYS A 55 CYS A 72 1555 1555 2.12 SSBOND 3 CYS A 143 CYS A 158 1555 1555 2.15 SSBOND 4 CYS A 184 CYS A 201 1555 1555 2.10 LINK ND2 ASN A 63 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 71 C1 NAG C 1 1555 1555 1.47 LINK ND2 ASN A 178 C1 NAG D 1 1555 1555 1.48 LINK ND2 ASN A 232 C1 NAG E 1 1555 1555 1.46 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.41 LINK O3 NAG B 1 C1 FUC B 7 1555 1555 1.48 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.41 LINK O2 BMA B 3 C1 XYP B 4 1555 1555 1.45 LINK O3 BMA B 3 C1 MAN B 5 1555 1555 1.44 LINK O6 BMA B 3 C1 MAN B 6 1555 1555 1.44 LINK O3 NAG C 1 C1 FUC C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.46 LINK O3 NAG E 1 C1 FUC E 2 1555 1555 1.46 LINK O4 NAG E 1 C1 NAG E 3 1555 1555 1.44 CRYST1 120.204 120.204 177.340 90.00 90.00 120.00 P 64 2 2 12 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 0.008319 0.004803 0.000000 0.00000 SCALE2 0.000000 0.009606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005639 0.00000