HEADER SUGAR BINDING PROTEIN 03-SEP-12 4GWI TITLE HIS 62 MUTANT OF THE LECTIN BINDING DOMAIN OF LECTINOLYSIN COMPLEXED TITLE 2 WITH LEWIS Y COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLATELET AGGREGATION FACTOR SM-HPAF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LECTIN BINDING DOMAIN, UNP RESIDUES 38-190; COMPND 5 SYNONYM: LECTINOLYSIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS MITIS; SOURCE 3 ORGANISM_TAXID: 28037; SOURCE 4 STRAIN: NM-65; SOURCE 5 GENE: SAMHPAF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMSG67 KEYWDS CHOLESTEROL-DEPENDENT CYTOLYSINS, LEWIS ANTIGENS, F-TYPE LECTIN FOLD, KEYWDS 2 GLYCAN BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.C.FEIL REVDAT 5 20-MAR-24 4GWI 1 HETSYN REVDAT 4 29-JUL-20 4GWI 1 COMPND REMARK SEQADV HET REVDAT 4 2 1 HETNAM HETSYN FORMUL LINK REVDAT 4 3 1 SITE ATOM REVDAT 3 15-NOV-17 4GWI 1 REMARK REVDAT 2 12-MAR-14 4GWI 1 JRNL REVDAT 1 21-NOV-12 4GWI 0 JRNL AUTH S.L.LAWRENCE,S.C.FEIL,J.K.HOLIEN,M.J.KUIPER,L.DOUGHTY, JRNL AUTH 2 O.DOLEZAL,T.D.MULHERN,R.K.TWETEN,M.W.PARKER JRNL TITL MANIPULATING THE LEWIS ANTIGEN SPECIFICITY OF THE JRNL TITL 2 CHOLESTEROL-DEPENDENT CYTOLYSIN LECTINOLYSIN JRNL REF FRONT IMMUNOL V. 3 330 2012 JRNL REFN ESSN 1664-3224 JRNL PMID 23181061 JRNL DOI 10.3389/FIMMU.2012.00330 REMARK 2 REMARK 2 RESOLUTION. 1.60 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 28960 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1536 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1885 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58000 REMARK 3 B22 (A**2) : -0.58000 REMARK 3 B33 (A**2) : 1.15000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.065 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.074 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1197 ; 0.027 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1624 ; 2.539 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 143 ; 6.339 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;32.197 ;24.839 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 190 ;11.418 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 7.683 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 191 ; 0.190 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 893 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4GWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30563 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 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: FROM PREVIOUS MODEL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M MGSO4, 0.1M KCL, 0.1M TRIS, PH REMARK 280 8.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 49.71600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.54850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.54850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.57400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.54850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.54850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.85800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.54850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.54850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 74.57400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.54850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.54850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.85800 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 49.71600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLU A 38 REMARK 465 GLN A 39 REMARK 465 GLY A 40 REMARK 465 THR A 185 REMARK 465 THR A 186 REMARK 465 GLN A 187 REMARK 465 VAL A 188 REMARK 465 GLY A 189 REMARK 465 CYS A 190 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 O4 NAG B 1 O5 GAL B 2 2.19 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 45 CD GLU A 45 OE1 0.081 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 71 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 160 NE - CZ - NH2 ANGL. DEV. = -3.3 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 42 -133.61 -122.41 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 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 54 OE1 REMARK 620 2 ASP A 97 OD2 96.5 REMARK 620 3 HOH A1175 O 84.6 167.5 REMARK 620 4 HOH A1177 O 170.8 92.7 86.2 REMARK 620 5 HOH A1193 O 87.8 101.2 91.3 91.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 68 O REMARK 620 2 ASP A 71 OD1 77.4 REMARK 620 3 ASN A 73 O 164.7 90.3 REMARK 620 4 SER A 82 OG 104.3 70.3 79.7 REMARK 620 5 SER A 82 O 79.6 128.0 115.5 71.3 REMARK 620 6 ALA A 176 O 94.3 154.4 92.9 135.3 72.7 REMARK 620 7 GLU A 177 OE1 88.0 74.2 79.7 138.4 150.2 81.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1125 O REMARK 620 2 HOH A1211 O 88.3 REMARK 620 3 HOH A1213 O 175.6 88.3 REMARK 620 4 HOH A1214 O 89.1 88.1 87.9 REMARK 620 5 HOH A1215 O 91.9 90.8 91.1 178.5 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LEK RELATED DB: PDB REMARK 900 LECTIN BINDING DOMAIN COMPLEXED WITH LEWIS B REMARK 900 RELATED ID: 3LEG RELATED DB: PDB REMARK 900 LECTIN BINDING DOMAIN COMPLEXED WITH LEWIS Y REMARK 900 RELATED ID: 3LEI RELATED DB: PDB REMARK 900 LECTIN BINDING DOMAIN COMPLEXED WITH FUCOSE REMARK 900 RELATED ID: 3LEO RELATED DB: PDB REMARK 900 LECTIN BINDING DOMAIN COMPLEXED WITH GLYCEROL REMARK 900 RELATED ID: 3GWJ RELATED DB: PDB REMARK 900 LECTIN BINDING DOMAIN COMPLEXED WITH LEWIS B REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE WAS DERIVED FROM THE PUBLISHED PROTEIN SEQUENCE REMARK 999 PUBLISHED BY FARRAND ET AL. (BIOCHEMISTRY, VOL. 47, 2008). AMINO REMARK 999 ACIDS 67 AND 158 ARE THREONINE AND ASPARTATE, RESPECTIVELY. DBREF 4GWI A 38 190 UNP Q2PHL4 Q2PHL4_STRMT 38 190 SEQADV 4GWI HIS A 62 UNP Q2PHL4 TYR 62 ENGINEERED MUTATION SEQADV 4GWI THR A 67 UNP Q2PHL4 ALA 67 SEE REMARK 999 SEQADV 4GWI ASP A 158 UNP Q2PHL4 ALA 158 SEE REMARK 999 SEQADV 4GWI CYS A 190 UNP Q2PHL4 GLN 190 ENGINEERED MUTATION SEQRES 1 A 153 GLU GLN GLY ASN ARG PRO VAL GLU THR GLU ASN ILE ALA SEQRES 2 A 153 ARG GLY LYS GLN ALA SER GLN SER SER THR ALA HIS GLY SEQRES 3 A 153 GLY ALA ALA THR ARG ALA VAL ASP GLY ASN VAL ASP SER SEQRES 4 A 153 ASP TYR GLY HIS HIS SER VAL THR HIS THR ASN PHE GLU SEQRES 5 A 153 ASP ASN ALA TRP TRP GLN VAL ASP LEU GLY LYS THR GLU SEQRES 6 A 153 ASN VAL GLY LYS VAL LYS LEU TYR ASN ARG GLY ASP GLY SEQRES 7 A 153 ASN VAL ALA ASN ARG LEU SER ASN PHE ASP VAL VAL LEU SEQRES 8 A 153 LEU ASN GLU ALA LYS GLN GLU VAL ALA ARG GLN HIS PHE SEQRES 9 A 153 ASP SER LEU ASN GLY LYS ALA GLU LEU GLU VAL PHE PHE SEQRES 10 A 153 THR ALA LYS ASP ALA ARG TYR VAL LYS VAL GLU LEU LYS SEQRES 11 A 153 THR LYS ASN THR PRO LEU SER LEU ALA GLU VAL GLU VAL SEQRES 12 A 153 PHE ARG SER ALA THR THR GLN VAL GLY CYS HET NAG B 1 15 HET GAL B 2 11 HET FUC B 3 10 HET FUC B 4 10 HET MG A 201 1 HET GOL A 202 6 HET MG A 203 1 HET CA A 204 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM CA CALCIUM 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 GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG C8 H15 N O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 FUC 2(C6 H12 O5) FORMUL 3 MG 2(MG 2+) FORMUL 4 GOL C3 H8 O3 FORMUL 6 CA CA 2+ FORMUL 7 HOH *140(H2 O) HELIX 1 1 ALA A 65 ASP A 71 5 7 HELIX 2 2 ASP A 77 HIS A 81 5 5 HELIX 3 3 VAL A 117 LEU A 121 5 5 SHEET 1 A 5 GLN A 54 GLN A 57 0 SHEET 2 A 5 TRP A 93 ASN A 111 -1 O GLN A 95 N SER A 56 SHEET 3 A 5 GLU A 149 LEU A 166 -1 O LYS A 157 N VAL A 104 SHEET 4 A 5 PHE A 124 LEU A 129 -1 N VAL A 127 O LYS A 163 SHEET 5 A 5 GLU A 135 PHE A 141 -1 O VAL A 136 N LEU A 128 SHEET 1 B 3 GLN A 54 GLN A 57 0 SHEET 2 B 3 TRP A 93 ASN A 111 -1 O GLN A 95 N SER A 56 SHEET 3 B 3 LEU A 175 ARG A 182 -1 O GLU A 179 N LYS A 108 LINK O4 NAG B 1 C1 GAL B 2 1555 1555 1.39 LINK O3 NAG B 1 C1 FUC B 4 1555 1555 1.39 LINK O2 GAL B 2 C1 FUC B 3 1555 1555 1.43 LINK OE1 GLN A 54 MG MG A 203 1555 1555 2.38 LINK O ARG A 68 CA CA A 204 1555 1555 2.24 LINK OD1 ASP A 71 CA CA A 204 1555 1555 2.48 LINK O ASN A 73 CA CA A 204 1555 1555 2.29 LINK OG SER A 82 CA CA A 204 1555 1555 2.35 LINK O SER A 82 CA CA A 204 1555 1555 2.56 LINK OD2 ASP A 97 MG MG A 203 1555 1555 2.18 LINK O ALA A 176 CA CA A 204 1555 1555 2.34 LINK OE1 GLU A 177 CA CA A 204 1555 1555 2.43 LINK MG MG A 201 O HOH A1125 1555 1555 2.04 LINK MG MG A 201 O HOH A1211 1555 1555 2.11 LINK MG MG A 201 O HOH A1213 1555 1555 2.12 LINK MG MG A 201 O HOH A1214 1555 1555 2.08 LINK MG MG A 201 O HOH A1215 1555 1555 1.99 LINK MG MG A 203 O HOH A1175 1555 1555 2.16 LINK MG MG A 203 O HOH A1177 1555 1555 2.24 LINK MG MG A 203 O HOH A1193 1555 1555 1.86 CRYST1 67.097 67.097 99.432 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 0.014904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010057 0.00000