HEADER SUGAR BINDING PROTEIN 22-JUL-04 1WMY TITLE CRYSTAL STRUCTURE OF C-TYPE LECTIN CEL-I FROM CUCUMARIA ECHINATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN CEL-I, N-ACETYL-D-GALACTOSAMINE-SPECIFIC C-TYPE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: C-TYPE LECTIN, CEL-I SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CUCUMARIA ECHINATA; SOURCE 3 ORGANISM_TAXID: 40245 KEYWDS C-TYPE LECTIN, N-ACETYLGALACTOSAMINE, INVERTEBRATE, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.SUGAWARA,M.KUSUNOKI,G.KURISU,T.FUJIMOTO,H.AOYAGI,T.HATAKEYAMA REVDAT 5 25-OCT-23 1WMY 1 REMARK LINK REVDAT 4 13-JUL-11 1WMY 1 VERSN REVDAT 3 24-FEB-09 1WMY 1 VERSN REVDAT 2 02-NOV-04 1WMY 1 JRNL REVDAT 1 07-SEP-04 1WMY 0 JRNL AUTH H.SUGAWARA,M.KUSUNOKI,G.KURISU,T.FUJIMOTO,H.AOYAGI, JRNL AUTH 2 T.HATAKEYAMA JRNL TITL CHARACTERISTIC RECOGNITION OF N-ACETYLGALACTOSAMINE BY AN JRNL TITL 2 INVERTEBRATE C-TYPE LECTIN, CEL-I, REVEALED BY X-RAY JRNL TITL 3 CRYSTALLOGRAPHIC ANALYSIS JRNL REF J.BIOL.CHEM. V. 279 45219 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15319425 JRNL DOI 10.1074/JBC.M408840200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.HATAKEYAMA,N.MATSUO,H.AOYAGI,H.SUGAWARA,T.UCHIDA,G.KURISU, REMARK 1 AUTH 2 M.KUSUNOKI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC STUDY OF AN REMARK 1 TITL 2 INVERTEBRATE C-TYPE LECTIN, CEL-I, FROM THE MARINE REMARK 1 TITL 3 INVERTEBRATE CUCUMARIA ECHINATA REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 143 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11752793 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19924 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1012 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1207 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1690 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2268 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 12.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.20000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : -0.93000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.157 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2361 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1832 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3220 ; 1.702 ; 1.877 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4268 ; 0.904 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.159 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 306 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2742 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 538 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 501 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2129 ; 0.264 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1198 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 192 ; 0.161 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 13 ; 0.086 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 50 ; 0.301 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.225 ; 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): 1380 ; 1.150 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2186 ; 1.804 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 981 ; 3.073 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1034 ; 4.506 ; 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 203 REMARK 3 ORIGIN FOR THE GROUP (A): 19.1403 -15.5690 53.1360 REMARK 3 T TENSOR REMARK 3 T11: 0.0434 T22: 0.0284 REMARK 3 T33: 0.0396 T12: -0.0266 REMARK 3 T13: -0.0066 T23: 0.0257 REMARK 3 L TENSOR REMARK 3 L11: 0.2596 L22: 0.3676 REMARK 3 L33: 1.6429 L12: -0.0977 REMARK 3 L13: 0.4870 L23: -0.3789 REMARK 3 S TENSOR REMARK 3 S11: 0.0933 S12: -0.0477 S13: -0.0180 REMARK 3 S21: -0.0617 S22: 0.0188 S23: 0.0464 REMARK 3 S31: 0.1590 S32: -0.0602 S33: -0.1121 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 : B 1 B 203 REMARK 3 ORIGIN FOR THE GROUP (A): 4.1096 1.4066 21.4923 REMARK 3 T TENSOR REMARK 3 T11: 0.0381 T22: 0.0379 REMARK 3 T33: 0.0501 T12: 0.0002 REMARK 3 T13: 0.0038 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.3712 L22: 0.0870 REMARK 3 L33: 0.7475 L12: -0.1474 REMARK 3 L13: 0.2634 L23: 0.0004 REMARK 3 S TENSOR REMARK 3 S11: -0.0128 S12: -0.0159 S13: 0.0204 REMARK 3 S21: 0.0086 S22: -0.0062 S23: -0.0107 REMARK 3 S31: -0.0047 S32: -0.0263 S33: 0.0190 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DPS REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20936 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 52.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 (%) : 82.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1LIT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60% 2-METHYL-2,4-PENTANEDIOL, 10MM REMARK 280 CALCIUM CHLORIDE, 0.1M TRIS-HCL, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 46.19000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.19000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.97000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -207.0 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 -1.000000 0.000000 0.000000 36.78791 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.82874 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 B 378 LIES ON A SPECIAL POSITION. 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 O HOH B 340 O HOH B 383 1.77 REMARK 500 O HOH A 387 O HOH A 423 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 TYR B 15 CD1 TYR B 15 CE1 -0.093 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 65 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 110 CB - CG - OD2 ANGL. DEV. = 5.8 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 LYS A 96 55.48 -145.04 REMARK 500 ALA A 108 30.01 -143.39 REMARK 500 GLU B 10 115.92 -163.91 REMARK 500 ASN B 80 86.55 -169.23 REMARK 500 VAL B 92 48.48 -92.97 REMARK 500 ALA B 108 23.00 -142.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 77 OD1 REMARK 620 2 ASP A 77 OD2 50.6 REMARK 620 3 GLU A 81 OE1 118.5 70.1 REMARK 620 4 GLU A 81 OE2 99.3 80.6 51.5 REMARK 620 5 ASN A 104 OD1 157.9 148.1 78.0 79.2 REMARK 620 6 GLU A 109 O 96.2 134.4 141.9 142.1 73.7 REMARK 620 7 ASP A 110 OD2 74.5 112.2 122.6 71.7 84.3 79.5 REMARK 620 8 HOH A 320 O 108.9 86.0 78.0 129.4 88.1 76.0 155.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 81 OE2 REMARK 620 2 ASP A 110 OD1 117.5 REMARK 620 3 ASP A 110 OD2 72.4 52.2 REMARK 620 4 HOH A 321 O 83.8 87.6 108.0 REMARK 620 5 HOH A 354 O 91.1 99.4 75.2 172.7 REMARK 620 6 HOH A 376 O 155.7 84.0 131.8 86.3 96.4 REMARK 620 7 GLY B 93 O 83.9 158.5 145.4 93.8 80.5 74.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 101 OE1 REMARK 620 2 ASP A 103 OD2 76.3 REMARK 620 3 GLU A 109 OE1 145.8 73.9 REMARK 620 4 ASN A 123 OD1 67.1 143.1 142.1 REMARK 620 5 ASP A 124 O 122.3 132.8 70.0 74.5 REMARK 620 6 ASP A 124 OD1 71.2 80.5 87.4 91.7 68.5 REMARK 620 7 MPD A 301 O2 135.3 125.8 77.2 80.8 74.1 142.5 REMARK 620 8 MPD A 301 O4 80.6 73.7 106.5 95.3 145.7 145.6 71.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 77 OD1 REMARK 620 2 ASP B 77 OD2 49.8 REMARK 620 3 GLU B 81 OE1 123.5 75.2 REMARK 620 4 GLU B 81 OE2 100.2 80.6 52.9 REMARK 620 5 ASN B 104 OD1 157.9 150.9 75.7 82.5 REMARK 620 6 GLU B 109 O 91.8 128.6 139.4 147.2 75.6 REMARK 620 7 ASP B 110 OD1 72.0 113.2 131.5 80.5 86.9 74.5 REMARK 620 8 HOH B 322 O 106.8 83.4 74.4 127.1 88.1 76.6 151.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 81 OE2 REMARK 620 2 ASP B 110 OD1 73.5 REMARK 620 3 ASP B 110 OD2 118.7 50.2 REMARK 620 4 HOH B 323 O 80.5 103.3 89.9 REMARK 620 5 HOH B 355 O 82.7 75.5 101.8 162.7 REMARK 620 6 HOH B 421 O 88.0 152.9 153.1 92.6 82.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 101 OE1 REMARK 620 2 ASP B 103 OD2 74.7 REMARK 620 3 GLU B 109 OE1 150.9 79.2 REMARK 620 4 ASN B 123 OD1 65.5 139.4 141.4 REMARK 620 5 ASP B 124 O 121.2 140.0 72.9 72.7 REMARK 620 6 ASP B 124 OD1 71.7 80.4 91.5 94.4 72.4 REMARK 620 7 MPD B 302 O2 84.7 70.4 98.7 97.2 141.1 146.5 REMARK 620 8 MPD B 302 O4 130.4 133.7 77.7 73.2 67.0 139.4 74.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BCH RELATED DB: PDB REMARK 900 C-TYPE LECTIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE REMARK 900 RELATED ID: 1BCJ RELATED DB: PDB REMARK 900 C-TYPE LECTIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE REMARK 900 RELATED ID: 1BYF RELATED DB: PDB REMARK 900 INVERTEBRATE C-TYPE LECTIN REMARK 900 RELATED ID: 1TLG RELATED DB: PDB REMARK 900 INVERTEBRATE C-TYPE LECTIN REMARK 900 RELATED ID: 1WMZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE DBREF 1WMY A 1 140 UNP Q7M462 Q7M462_9ECHN 1 140 DBREF 1WMY B 1 140 UNP Q7M462 Q7M462_9ECHN 1 140 SEQRES 1 A 140 ASN GLN CYS PRO THR ASP TRP GLU ALA GLU GLY ASP HIS SEQRES 2 A 140 CYS TYR ARG PHE PHE ASN THR LEU THR THR TRP GLU ASN SEQRES 3 A 140 ALA HIS HIS GLU CYS VAL SER TYR SER CYS SER THR LEU SEQRES 4 A 140 ASN VAL ARG SER ASP LEU VAL SER VAL HIS SER ALA ALA SEQRES 5 A 140 GLU GLN ALA TYR VAL PHE ASN TYR TRP ARG GLY ILE ASP SEQRES 6 A 140 SER GLN ALA GLY GLN LEU TRP ILE GLY LEU TYR ASP LYS SEQRES 7 A 140 TYR ASN GLU GLY ASP PHE ILE TRP THR ASP GLY SER LYS SEQRES 8 A 140 VAL GLY TYR THR LYS TRP ALA GLY GLY GLN PRO ASP ASN SEQRES 9 A 140 TRP ASN ASN ALA GLU ASP TYR GLY GLN PHE ARG HIS THR SEQRES 10 A 140 GLU GLY GLY ALA TRP ASN ASP ASN SER ALA ALA ALA GLN SEQRES 11 A 140 ALA LYS TYR MET CYS LYS LEU THR PHE GLU SEQRES 1 B 140 ASN GLN CYS PRO THR ASP TRP GLU ALA GLU GLY ASP HIS SEQRES 2 B 140 CYS TYR ARG PHE PHE ASN THR LEU THR THR TRP GLU ASN SEQRES 3 B 140 ALA HIS HIS GLU CYS VAL SER TYR SER CYS SER THR LEU SEQRES 4 B 140 ASN VAL ARG SER ASP LEU VAL SER VAL HIS SER ALA ALA SEQRES 5 B 140 GLU GLN ALA TYR VAL PHE ASN TYR TRP ARG GLY ILE ASP SEQRES 6 B 140 SER GLN ALA GLY GLN LEU TRP ILE GLY LEU TYR ASP LYS SEQRES 7 B 140 TYR ASN GLU GLY ASP PHE ILE TRP THR ASP GLY SER LYS SEQRES 8 B 140 VAL GLY TYR THR LYS TRP ALA GLY GLY GLN PRO ASP ASN SEQRES 9 B 140 TRP ASN ASN ALA GLU ASP TYR GLY GLN PHE ARG HIS THR SEQRES 10 B 140 GLU GLY GLY ALA TRP ASN ASP ASN SER ALA ALA ALA GLN SEQRES 11 B 140 ALA LYS TYR MET CYS LYS LEU THR PHE GLU HET CA A 201 1 HET CA A 202 1 HET CA A 203 1 HET MPD A 301 8 HET CA B 201 1 HET CA B 202 1 HET CA B 203 1 HET MPD B 302 8 HETNAM CA CALCIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 CA 6(CA 2+) FORMUL 6 MPD 2(C6 H14 O2) FORMUL 11 HOH *247(H2 O) HELIX 1 1 THR A 23 TYR A 34 1 12 HELIX 2 2 SER A 35 SER A 35 5 1 HELIX 3 3 CYS A 36 LEU A 39 5 4 HELIX 4 4 SER A 50 ASP A 65 1 16 HELIX 5 5 ASN A 104 ALA A 108 5 5 HELIX 6 6 THR B 23 SER B 33 1 11 HELIX 7 7 TYR B 34 SER B 35 5 2 HELIX 8 8 CYS B 36 LEU B 39 5 4 HELIX 9 9 SER B 50 ASP B 65 1 16 HELIX 10 10 ASN B 104 ASN B 107 5 4 HELIX 11 11 THR B 117 GLY B 120 5 4 SHEET 1 A 5 GLU A 8 GLU A 10 0 SHEET 2 A 5 HIS A 13 THR A 22 -1 O TYR A 15 N GLU A 8 SHEET 3 A 5 ALA A 131 PHE A 139 -1 O TYR A 133 N PHE A 18 SHEET 4 A 5 GLN A 70 TYR A 76 1 N TRP A 72 O LYS A 132 SHEET 5 A 5 ILE A 85 TRP A 86 -1 O ILE A 85 N TYR A 76 SHEET 1 B 5 VAL A 41 LEU A 45 0 SHEET 2 B 5 ALA A 131 PHE A 139 -1 O THR A 138 N ARG A 42 SHEET 3 B 5 GLN A 70 TYR A 76 1 N TRP A 72 O LYS A 132 SHEET 4 B 5 TYR A 111 ARG A 115 -1 O GLY A 112 N LEU A 75 SHEET 5 B 5 TRP A 122 ASN A 125 -1 O ASN A 125 N TYR A 111 SHEET 1 C 5 GLU B 8 GLU B 10 0 SHEET 2 C 5 HIS B 13 THR B 22 -1 O TYR B 15 N GLU B 8 SHEET 3 C 5 ALA B 131 PHE B 139 -1 O LEU B 137 N CYS B 14 SHEET 4 C 5 LEU B 71 TYR B 76 1 N TRP B 72 O LYS B 132 SHEET 5 C 5 ILE B 85 TRP B 86 -1 O ILE B 85 N TYR B 76 SHEET 1 D 5 VAL B 41 LEU B 45 0 SHEET 2 D 5 ALA B 131 PHE B 139 -1 O THR B 138 N ARG B 42 SHEET 3 D 5 LEU B 71 TYR B 76 1 N TRP B 72 O LYS B 132 SHEET 4 D 5 GLU B 109 PHE B 114 -1 O GLY B 112 N LEU B 75 SHEET 5 D 5 TRP B 122 SER B 126 -1 O ASN B 123 N GLN B 113 SSBOND 1 CYS A 3 CYS A 14 1555 1555 2.03 SSBOND 2 CYS A 31 CYS A 135 1555 1555 2.03 SSBOND 3 CYS A 36 CYS B 36 1555 1555 2.00 SSBOND 4 CYS B 3 CYS B 14 1555 1555 2.03 SSBOND 5 CYS B 31 CYS B 135 1555 1555 2.02 LINK OD1 ASP A 77 CA CA A 201 1555 1555 2.52 LINK OD2 ASP A 77 CA CA A 201 1555 1555 2.46 LINK OE1 GLU A 81 CA CA A 201 1555 1555 2.45 LINK OE2 GLU A 81 CA CA A 201 1555 1555 2.49 LINK OE2 GLU A 81 CA CA A 203 1555 1555 2.33 LINK OE1 GLN A 101 CA CA A 202 1555 1555 2.50 LINK OD2 ASP A 103 CA CA A 202 1555 1555 2.51 LINK OD1 ASN A 104 CA CA A 201 1555 1555 2.58 LINK O GLU A 109 CA CA A 201 1555 1555 2.41 LINK OE1 GLU A 109 CA CA A 202 1555 1555 2.36 LINK OD2 ASP A 110 CA CA A 201 1555 1555 2.30 LINK OD1 ASP A 110 CA CA A 203 1555 1555 2.45 LINK OD2 ASP A 110 CA CA A 203 1555 1555 2.42 LINK OD1 ASN A 123 CA CA A 202 1555 1555 2.50 LINK O ASP A 124 CA CA A 202 1555 1555 2.52 LINK OD1 ASP A 124 CA CA A 202 1555 1555 2.35 LINK CA CA A 201 O HOH A 320 1555 1555 2.50 LINK CA CA A 202 O2 MPD A 301 1555 1555 2.57 LINK CA CA A 202 O4 MPD A 301 1555 1555 2.51 LINK CA CA A 203 O HOH A 321 1555 1555 2.26 LINK CA CA A 203 O HOH A 354 1555 1555 2.33 LINK CA CA A 203 O HOH A 376 1555 1555 2.40 LINK CA CA A 203 O GLY B 93 1555 1656 2.39 LINK OD1 ASP B 77 CA CA B 201 1555 1555 2.62 LINK OD2 ASP B 77 CA CA B 201 1555 1555 2.56 LINK OE1 GLU B 81 CA CA B 201 1555 1555 2.58 LINK OE2 GLU B 81 CA CA B 201 1555 1555 2.39 LINK OE2 GLU B 81 CA CA B 203 1555 1555 2.48 LINK OE1 GLN B 101 CA CA B 202 1555 1555 2.46 LINK OD2 ASP B 103 CA CA B 202 1555 1555 2.44 LINK OD1 ASN B 104 CA CA B 201 1555 1555 2.63 LINK O GLU B 109 CA CA B 201 1555 1555 2.48 LINK OE1 GLU B 109 CA CA B 202 1555 1555 2.30 LINK OD1 ASP B 110 CA CA B 201 1555 1555 2.30 LINK OD1 ASP B 110 CA CA B 203 1555 1555 2.58 LINK OD2 ASP B 110 CA CA B 203 1555 1555 2.55 LINK OD1 ASN B 123 CA CA B 202 1555 1555 2.48 LINK O ASP B 124 CA CA B 202 1555 1555 2.55 LINK OD1 ASP B 124 CA CA B 202 1555 1555 2.42 LINK CA CA B 201 O HOH B 322 1555 1555 2.39 LINK CA CA B 202 O2 MPD B 302 1555 1555 2.49 LINK CA CA B 202 O4 MPD B 302 1555 1555 2.67 LINK CA CA B 203 O HOH B 323 1555 1555 2.42 LINK CA CA B 203 O HOH B 355 1555 1555 2.44 LINK CA CA B 203 O HOH B 421 1555 1555 2.50 CISPEP 1 GLN A 101 PRO A 102 0 -1.69 CISPEP 2 GLN B 101 PRO B 102 0 -5.07 SITE 1 AC1 6 ASP A 77 GLU A 81 ASN A 104 GLU A 109 SITE 2 AC1 6 ASP A 110 HOH A 320 SITE 1 AC2 6 GLN A 101 ASP A 103 GLU A 109 ASN A 123 SITE 2 AC2 6 ASP A 124 MPD A 301 SITE 1 AC3 6 GLU A 81 ASP A 110 HOH A 321 HOH A 354 SITE 2 AC3 6 HOH A 376 GLY B 93 SITE 1 AC4 6 ASP B 77 GLU B 81 ASN B 104 GLU B 109 SITE 2 AC4 6 ASP B 110 HOH B 322 SITE 1 AC5 6 GLN B 101 ASP B 103 GLU B 109 ASN B 123 SITE 2 AC5 6 ASP B 124 MPD B 302 SITE 1 AC6 5 GLU B 81 ASP B 110 HOH B 323 HOH B 355 SITE 2 AC6 5 HOH B 421 SITE 1 AC7 6 GLN A 101 ASP A 103 GLU A 109 ASN A 123 SITE 2 AC7 6 ASP A 124 CA A 202 SITE 1 AC8 7 GLN B 101 ASP B 103 TRP B 105 GLU B 109 SITE 2 AC8 7 ASN B 123 ASP B 124 CA B 202 CRYST1 92.380 69.940 76.690 90.00 136.46 90.00 C 1 2 1 8 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 0.010825 0.000000 0.011391 0.00000 SCALE2 0.000000 0.014298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018929 0.00000