HEADER SUGAR BINDING PROTEIN 17-MAY-02 1GZC TITLE HIGH-RESOLUTION CRYSTAL STRUCTURE OF ERYTHRINA CRISTAGALLI LECTIN IN TITLE 2 COMPLEX WITH LACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERYTHRINA CRISTA-GALLI LECTIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ERYTHRINA CRISTA-GALLI; SOURCE 3 ORGANISM_COMMON: COCKSPUR CORAL TREE; SOURCE 4 ORGANISM_TAXID: 49817 KEYWDS LECTIN, CARBOHYDRATE, SUGAR BINDING PROTEIN, SACCHARIDE, PROTEIN- KEYWDS 2 CARBOHYDRATE INTERACTIONS, LACTOSE, GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SVENSSON,U.KRENGEL REVDAT 7 13-DEC-23 1GZC 1 HETSYN REVDAT 6 29-JUL-20 1GZC 1 COMPND REMARK HET HETNAM REVDAT 6 2 1 FORMUL LINK SITE ATOM REVDAT 5 17-JAN-18 1GZC 1 REMARK REVDAT 4 06-OCT-09 1GZC 1 HEADER KEYWDS REMARK HETNAM REVDAT 3 24-FEB-09 1GZC 1 VERSN REVDAT 2 01-AUG-02 1GZC 1 JRNL REVDAT 1 21-JUN-02 1GZC 0 JRNL AUTH C.SVENSSON,S.TENEBERG,C.NILSSON,A.KJELLBERG,F.SCHWARZ, JRNL AUTH 2 N.SHARON,U.KRENGEL JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF ERYTHRINA CRISTAGALLI JRNL TITL 2 LECTIN IN COMPLEX WITH LACTOSE AND 2'-ALPHA-L-FUCOSYLLACTOSE JRNL TITL 3 AND CORRELATION WITH THERMODYNAMIC BINDING DATA JRNL REF J.MOL.BIOL. V. 321 69 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12139934 JRNL DOI 10.1016/S0022-2836(02)00554-5 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.90 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) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 58614 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) : 0.208 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 936 REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 60 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 : 1853 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.56600 REMARK 3 B22 (A**2) : -4.56600 REMARK 3 B33 (A**2) : 9.13300 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.016 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.616 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.979 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.975 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 51.53 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ALTERNATIVE CONFORMATIONS REFINED FOR REMARK 3 RESIDUES 9, 10, 12, 95, 159, 173, 180, 234 LACTOSE ARE DEPOSITED: REMARK 3 LAT_XPLOR_TOP.TXT LAT_XPLOR_PAR.TXT. INITIAL STAGES OF REMARK 3 REFINEMENT WITH SIMULATED ANNEALING. REMARK 4 REMARK 4 1GZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1290009509. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 49.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.60800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: 1AX1 REMARK 200 REMARK 200 REMARK: THE DATA SET INCLUDED REFLECTIONS TO 1.45 A RESOLUTION, REMARK 200 BUT THE DATA WERE CUT TO 1.58 A RESOLUTION IN THE FINAL REMARK 200 REFINEMENT CYCLE DUE TO CONSIDERABLE INCREASE IN R-FACTORS REMARK 200 BEYOND THAT RESOLUTION. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.1M TRIS PH 7.5, REMARK 280 10% GLYCEROL, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 63.05000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.90000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 94.57500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.90000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.90000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.52500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.90000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.90000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 94.57500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.90000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.90000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.52500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.05000 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.8 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 0.000000 -1.000000 0.000000 81.80000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 81.80000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.05000 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 GLU A 79 CD OE1 OE2 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 A 2019 O HOH A 2043 1.76 REMARK 500 NE2 HIS A 180 O HOH A 2217 2.11 REMARK 500 CD2 HIS A 180 O HOH A 2217 2.16 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 GLU A 10 CG GLU A 10 CD 0.239 REMARK 500 GLU A 10 CG GLU A 10 CD 0.093 REMARK 500 GLU A 10 CD GLU A 10 OE2 1.116 REMARK 500 GLU A 10 CD GLU A 10 OE2 2.060 REMARK 500 MET A 95 SD MET A 95 CE -0.872 REMARK 500 MET A 95 SD MET A 95 CE -0.876 REMARK 500 ASP A 173 CG ASP A 173 OD2 1.561 REMARK 500 ASP A 173 CG ASP A 173 OD2 2.023 REMARK 500 GLN A 234 CG GLN A 234 CD 1.038 REMARK 500 GLN A 234 CG GLN A 234 CD 1.964 REMARK 500 GLN A 234 CD GLN A 234 NE2 3.079 REMARK 500 GLN A 234 CD GLN A 234 NE2 2.353 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 GLU A 10 OE1 - CD - OE2 ANGL. DEV. = -39.3 DEGREES REMARK 500 GLU A 10 OE1 - CD - OE2 ANGL. DEV. = 45.3 DEGREES REMARK 500 GLU A 10 CG - CD - OE2 ANGL. DEV. = -49.3 DEGREES REMARK 500 GLU A 10 CG - CD - OE2 ANGL. DEV. = -76.5 DEGREES REMARK 500 MET A 95 CG - SD - CE ANGL. DEV. = -9.7 DEGREES REMARK 500 MET A 95 CG - SD - CE ANGL. DEV. = 15.2 DEGREES REMARK 500 ASP A 173 OD1 - CG - OD2 ANGL. DEV. = -37.5 DEGREES REMARK 500 ASP A 173 CB - CG - OD2 ANGL. DEV. = -60.6 DEGREES REMARK 500 ASP A 173 CB - CG - OD2 ANGL. DEV. = -74.2 DEGREES REMARK 500 GLN A 234 CB - CG - CD ANGL. DEV. = -36.0 DEGREES REMARK 500 GLN A 234 CB - CG - CD ANGL. DEV. = -70.2 DEGREES REMARK 500 GLN A 234 OE1 - CD - NE2 ANGL. DEV. = -24.2 DEGREES REMARK 500 GLN A 234 CG - CD - OE1 ANGL. DEV. = 16.9 DEGREES REMARK 500 GLN A 234 CG - CD - NE2 ANGL. DEV. = -90.0 DEGREES REMARK 500 GLN A 234 CG - CD - NE2 ANGL. DEV. = -77.1 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 ASN A 40 0.41 -68.82 REMARK 500 PRO A 85 -165.38 -75.55 REMARK 500 ALA A 103 -139.62 -95.46 REMARK 500 TYR A 106 -130.67 50.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 10 0.29 SIDE CHAIN REMARK 500 ASP A 173 0.28 SIDE CHAIN REMARK 500 GLN A 234 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2034 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A2088 DISTANCE = 6.28 ANGSTROMS 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 MN A 289 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 127 OE2 REMARK 620 2 ASP A 129 OD2 95.8 REMARK 620 3 ASP A 136 OD1 170.9 90.8 REMARK 620 4 HIS A 142 NE2 89.8 88.1 96.6 REMARK 620 5 HOH A2259 O 84.6 87.0 89.6 172.1 REMARK 620 6 HOH A2260 O 89.8 174.3 83.7 91.3 94.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 290 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 129 OD1 REMARK 620 2 ASP A 129 OD2 52.7 REMARK 620 3 PHE A 131 O 78.5 107.7 REMARK 620 4 ASN A 133 OD1 149.5 157.5 87.1 REMARK 620 5 ASP A 136 OD2 118.0 82.0 78.4 84.5 REMARK 620 6 HOH A2132 O 73.1 114.9 91.6 80.7 162.5 REMARK 620 7 HOH A2146 O 109.8 76.5 171.2 86.8 94.8 93.5 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GZ9 RELATED DB: PDB REMARK 900 HIGH-RESOLUTION CRYSTAL STRUCTURE OF ERYTHRINA CRISTAGALLI LECTIN REMARK 900 IN COMPLEX WITH 2'-ALPHA-L-FUCOSYLLACTOSE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THE CRYSTALLIZED PROTEIN WAS CONFIRMED BY REMARK 999 MASS SPECTROMETRY, BUT THERE ARE DISCREPANCIES BETWEEN THE REMARK 999 SEQUENCE THAT WAS BUILT INTO ELECTRON DENSITY AND THE MASS REMARK 999 SPEC. SEQUENCE, WHICH ARE PROBABLY DUE TO PREFERENTIAL REMARK 999 CRYSTALLIZATION OF ONE LECTIN ISOFORM. THE DIFFERENCES REMARK 999 BETWEEN THE MASS SPEC-CONFIRMED SEQUENCE AND THE SEQUENCE REMARK 999 THAT WAS BUILT INTO THE ELECTRON DENSITY ARE: REMARK 999 REMARK 999 RES.NUM MS BUILT REMARK 999 A 59 ILE MET REMARK 999 A 62 MET SER (MAY BE DUE TO CRYSTAL DISORDER) DBREF 1GZC A 1 239 PDB 1GZC 1GZC 1 239 SEQRES 1 A 239 VAL GLU THR ILE SER PHE SER PHE SER GLU PHE GLU PRO SEQRES 2 A 239 GLY ASN ASP ASN LEU THR LEU GLN GLY ALA ALA LEU ILE SEQRES 3 A 239 THR GLN SER GLY VAL LEU GLN LEU THR LYS ILE ASN GLN SEQRES 4 A 239 ASN GLY MET PRO ALA TRP ASP SER THR GLY ARG THR LEU SEQRES 5 A 239 TYR THR LYS PRO VAL HIS MET TRP ASP SER THR THR GLY SEQRES 6 A 239 THR VAL ALA SER PHE GLU THR ARG PHE SER PHE SER ILE SEQRES 7 A 239 GLU GLN PRO TYR THR ARG PRO LEU PRO ALA ASP GLY LEU SEQRES 8 A 239 VAL PHE PHE MET GLY PRO THR LYS SER LYS PRO ALA GLN SEQRES 9 A 239 GLY TYR GLY TYR LEU GLY VAL PHE ASN ASN SER LYS GLN SEQRES 10 A 239 ASP ASN SER TYR GLN THR LEU ALA VAL GLU PHE ASP THR SEQRES 11 A 239 PHE SER ASN PRO TRP ASP PRO PRO GLN VAL PRO HIS ILE SEQRES 12 A 239 GLY ILE ASP VAL ASN SER ILE ARG SER ILE LYS THR GLN SEQRES 13 A 239 PRO PHE GLN LEU ASP ASN GLY GLN VAL ALA ASN VAL VAL SEQRES 14 A 239 ILE LYS TYR ASP ALA PRO SER LYS ILE LEU HIS VAL VAL SEQRES 15 A 239 LEU VAL TYR PRO SER SER GLY ALA ILE TYR THR ILE ALA SEQRES 16 A 239 GLU ILE VAL ASP VAL LYS GLN VAL LEU PRO ASP TRP VAL SEQRES 17 A 239 ASP VAL GLY LEU SER GLY ALA THR GLY ALA GLN ARG ASP SEQRES 18 A 239 ALA ALA GLU THR HIS ASP VAL TYR SER TRP SER PHE GLN SEQRES 19 A 239 ALA SER LEU PRO GLU HET BGC B 1 13 HET GAL B 2 11 HET MN A 289 1 HET CA A 290 1 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 MN MN 2+ FORMUL 4 CA CA 2+ FORMUL 5 HOH *266(H2 O) HELIX 1 1 GLY A 105 LEU A 109 5 5 HELIX 2 2 ASP A 118 GLN A 122 5 5 HELIX 3 3 ASP A 199 LEU A 204 1 6 SHEET 1 AA 4 GLU A 2 PHE A 8 0 SHEET 2 AA 4 ASP A 227 LEU A 237 -1 O TRP A 231 N PHE A 8 SHEET 3 AA 4 LEU A 32 GLN A 33 -1 O LEU A 32 N VAL A 228 SHEET 4 AA 4 LEU A 25 ILE A 26 -1 O LEU A 25 N GLN A 33 SHEET 1 AB 6 GLU A 2 PHE A 8 0 SHEET 2 AB 6 ASP A 227 LEU A 237 -1 O TRP A 231 N PHE A 8 SHEET 3 AB 6 SER A 69 SER A 77 -1 O SER A 69 N SER A 236 SHEET 4 AB 6 VAL A 165 ASP A 173 -1 O ALA A 166 N PHE A 76 SHEET 5 AB 6 ILE A 178 VAL A 184 -1 O ILE A 178 N ASP A 173 SHEET 6 AB 6 ILE A 191 ILE A 197 -1 O TYR A 192 N LEU A 183 SHEET 1 AC 4 LEU A 18 GLY A 22 0 SHEET 2 AC 4 THR A 48 TYR A 53 -1 O ARG A 50 N GLN A 21 SHEET 3 AC 4 TRP A 207 THR A 216 -1 O VAL A 210 N TYR A 53 SHEET 4 AC 4 VAL A 57 HIS A 58 -1 O VAL A 57 N VAL A 208 SHEET 1 AD 7 LEU A 18 GLY A 22 0 SHEET 2 AD 7 THR A 48 TYR A 53 -1 O ARG A 50 N GLN A 21 SHEET 3 AD 7 TRP A 207 THR A 216 -1 O VAL A 210 N TYR A 53 SHEET 4 AD 7 ASP A 89 GLY A 96 -1 O GLY A 90 N ALA A 215 SHEET 5 AD 7 LEU A 124 ASP A 129 -1 O LEU A 124 N MET A 95 SHEET 6 AD 7 HIS A 142 VAL A 147 -1 O HIS A 142 N ASP A 129 SHEET 7 AD 7 LYS A 154 PRO A 157 -1 O LYS A 154 N ILE A 145 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.45 LINK OE2 GLU A 127 MN MN A 289 1555 1555 2.18 LINK OD2 ASP A 129 MN MN A 289 1555 1555 2.16 LINK OD1 ASP A 129 CA CA A 290 1555 1555 2.43 LINK OD2 ASP A 129 CA CA A 290 1555 1555 2.46 LINK O PHE A 131 CA CA A 290 1555 1555 2.37 LINK OD1 ASN A 133 CA CA A 290 1555 1555 2.34 LINK OD1 ASP A 136 MN MN A 289 1555 1555 2.18 LINK OD2 ASP A 136 CA CA A 290 1555 1555 2.36 LINK NE2 HIS A 142 MN MN A 289 1555 1555 2.30 LINK MN MN A 289 O HOH A2259 1555 1555 2.24 LINK MN MN A 289 O HOH A2260 1555 1555 2.19 LINK CA CA A 290 O HOH A2132 1555 1555 2.39 LINK CA CA A 290 O HOH A2146 1555 1555 2.42 CISPEP 1 ARG A 84 PRO A 85 0 -2.43 CISPEP 2 ALA A 88 ASP A 89 0 -1.11 CISPEP 3 VAL A 140 PRO A 141 0 -0.18 CRYST1 81.800 81.800 126.100 90.00 90.00 90.00 P 43 21 2 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 0.012225 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007930 0.00000