HEADER SUGAR BINDING PROTEIN 24-AUG-11 3ZYR TITLE STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH TITLE 2 HEPTASACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLATYPODIUM ELEGANS; SOURCE 3 ORGANISM_TAXID: 115002; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET29A; SOURCE 10 OTHER_DETAILS: BRASILIAN FLORA KEYWDS SUGAR BINDING PROTEIN, N-GLYCAN, PLANT LECTIN EXPDTA X-RAY DIFFRACTION AUTHOR R.G.BENEVIDES,G.GANNE,B.S.CAVAZZA,A.VARROT,A.IMBERTY REVDAT 6 01-MAY-24 3ZYR 1 HETSYN SHEET REVDAT 5 29-JUL-20 3ZYR 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 08-AUG-12 3ZYR 1 JRNL REVDAT 3 25-JUL-12 3ZYR 1 AUTHOR JRNL REVDAT 2 25-JAN-12 3ZYR 1 REMARK LINK ATOM TER REVDAT 2 2 1 HETATM CONECT MASTER REVDAT 1 11-JAN-12 3ZYR 0 JRNL AUTH R.G.BENEVIDES,G.GANNE,R.D.C.SIMOES,V.SCHUBERT,M.NIEMIETZ, JRNL AUTH 2 C.UNVERZAGT,V.CHAZALET,C.BRETON,A.VARROT,B.S.CAVADA, JRNL AUTH 3 A.IMBERTY JRNL TITL A LECTIN FROM PLATYPODIUM ELEGANS WITH UNUSUAL SPECIFICITY JRNL TITL 2 AND AFFINITY FOR ASYMMETRIC COMPLEX N-GLYCANS. JRNL REF J.BIOL.CHEM. V. 287 26352 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22692206 JRNL DOI 10.1074/JBC.M112.375816 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 52116 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2760 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2514 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 223 REMARK 3 SOLVENT ATOMS : 518 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : -0.65000 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): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.490 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4331 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2848 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5957 ; 1.595 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6872 ; 0.910 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 529 ; 7.292 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;38.693 ;23.768 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 630 ;13.129 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.989 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 703 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4850 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 932 ; 0.001 ; 0.020 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): 2554 ; 0.918 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1014 ; 0.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4182 ; 1.635 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1777 ; 2.328 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1772 ; 3.695 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. U VALUES REFINED INDIVIDUALLY RESIDUES 1 TO 7 AND 250 REMARK 3 TO 265 WERE TOO DISORDERED TO BE MODELLED. REMARK 4 REMARK 4 3ZYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1290048665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH SX-165 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55022 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 47.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY IN30 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG20K, 2% DIOXANE, 100 MM BICINE REMARK 280 PH 9, 30% GLYCEROL ADDED AS CRYOPROTECTANT. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.70000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.79500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.49000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.79500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.70000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.49000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 LEU A 2 REMARK 465 LEU A 3 REMARK 465 ASN A 4 REMARK 465 ARG A 5 REMARK 465 ALA A 6 REMARK 465 ASN A 7 REMARK 465 TYR A 248 REMARK 465 THR A 249 REMARK 465 ALA A 250 REMARK 465 GLN A 251 REMARK 465 LYS A 252 REMARK 465 GLU A 253 REMARK 465 ASP A 254 REMARK 465 GLU A 255 REMARK 465 TYR A 256 REMARK 465 LEU A 257 REMARK 465 ALA A 258 REMARK 465 ARG A 259 REMARK 465 ASP A 260 REMARK 465 MET A 261 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 LEU B 3 REMARK 465 ASN B 4 REMARK 465 ARG B 5 REMARK 465 ALA B 6 REMARK 465 ASN B 7 REMARK 465 THR B 249 REMARK 465 ALA B 250 REMARK 465 GLN B 251 REMARK 465 LYS B 252 REMARK 465 GLU B 253 REMARK 465 ASP B 254 REMARK 465 GLU B 255 REMARK 465 TYR B 256 REMARK 465 LEU B 257 REMARK 465 ALA B 258 REMARK 465 ARG B 259 REMARK 465 ASP B 260 REMARK 465 MET B 261 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 44 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 44 NE - CZ - NH2 ANGL. DEV. = -3.5 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 SER A 54 70.75 55.22 REMARK 500 ASN B 37 32.37 -99.94 REMARK 500 SER B 54 72.33 54.82 REMARK 500 ASN B 152 53.31 -91.55 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 A2017 DISTANCE = 5.90 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG D 1 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 400 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 137 OE2 REMARK 620 2 ASP A 139 OD2 94.8 REMARK 620 3 ASP A 150 OD1 172.7 91.0 REMARK 620 4 HIS A 155 NE2 90.6 87.2 94.1 REMARK 620 5 HOH A2175 O 83.4 93.8 91.8 174.0 REMARK 620 6 HOH A2176 O 87.9 175.8 86.5 89.5 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 139 OD1 REMARK 620 2 ASP A 139 OD2 53.4 REMARK 620 3 PHE A 141 O 75.6 118.6 REMARK 620 4 ASN A 147 OD1 155.3 151.0 86.0 REMARK 620 5 ASP A 150 OD2 105.4 79.3 84.5 88.8 REMARK 620 6 HOH A2137 O 74.3 107.0 86.6 88.5 170.8 REMARK 620 7 HOH A2152 O 113.4 71.0 170.3 84.4 96.1 92.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 400 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 137 OE2 REMARK 620 2 ASP B 139 OD2 92.9 REMARK 620 3 ASP B 150 OD1 173.6 93.5 REMARK 620 4 HIS B 155 NE2 90.0 88.5 90.7 REMARK 620 5 HOH B2113 O 84.3 91.2 95.0 174.3 REMARK 620 6 HOH B2114 O 87.1 178.9 86.5 90.4 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 139 OD1 REMARK 620 2 ASP B 139 OD2 54.1 REMARK 620 3 PHE B 141 O 74.9 120.3 REMARK 620 4 ASN B 147 OD1 153.3 151.9 85.1 REMARK 620 5 ASP B 150 OD2 105.7 81.2 85.6 89.8 REMARK 620 6 HOH B2084 O 75.5 106.1 86.3 85.9 171.2 REMARK 620 7 HOH B2098 O 117.2 71.8 167.5 82.3 93.9 93.2 REMARK 620 N 1 2 3 4 5 6 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZVX RELATED DB: PDB REMARK 900 STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH A REMARK 900 TRIMANNOSIDE DBREF 3ZYR A 1 261 PDB 3ZYR 3ZYR 1 261 DBREF 3ZYR B 1 261 PDB 3ZYR 3ZYR 1 261 SEQRES 1 A 261 MET LEU LEU ASN ARG ALA ASN SER THR ASP SER LEU SER SEQRES 2 A 261 PHE SER PHE ILE ASN PHE ASP ARG ASP GLU ARG ASN LEU SEQRES 3 A 261 ILE PHE GLN GLY ASP ALA HIS THR SER ARG ASN ASN ILE SEQRES 4 A 261 LEU GLN LEU THR ARG THR ASP SER ASN GLY ALA PRO VAL SEQRES 5 A 261 ARG SER THR VAL GLY ARG ILE LEU HIS SER ALA GLN VAL SEQRES 6 A 261 ARG LEU TRP GLU LYS SER THR ASN ARG VAL ALA ASN LEU SEQRES 7 A 261 GLN THR GLN PHE SER PHE PHE LEU SER SER PRO LEU SER SEQRES 8 A 261 ASN PRO ALA ASP GLY ILE ALA PHE PHE ILE ALA PRO PRO SEQRES 9 A 261 ASP THR THR ILE PRO SER GLY SER ALA GLY GLY LEU LEU SEQRES 10 A 261 GLY LEU PHE ASN PRO ARG THR ALA LEU ASN GLU SER ALA SEQRES 11 A 261 ASN GLN VAL LEU ALA VAL GLU PHE ASP THR PHE PHE ALA SEQRES 12 A 261 GLN ASN SER ASN THR TRP ASP PRO ASN TYR GLN HIS ILE SEQRES 13 A 261 GLY ILE ASP VAL ASN SER ILE ARG SER SER LYS VAL VAL SEQRES 14 A 261 ARG TRP GLU ARG ARG GLU GLY LYS THR LEU ASN VAL LEU SEQRES 15 A 261 VAL THR TYR ASN PRO SER THR ARG THR ILE ASP VAL VAL SEQRES 16 A 261 ALA THR TYR PRO ASP GLY GLN ARG TYR GLN LEU SER HIS SEQRES 17 A 261 VAL VAL ASP LEU THR THR ILE LEU PRO GLU TRP VAL ARG SEQRES 18 A 261 VAL GLY PHE SER ALA ALA SER GLY GLU GLN PHE GLN THR SEQRES 19 A 261 HIS ASN LEU GLU SER TRP SER PHE THR SER THR LEU LEU SEQRES 20 A 261 TYR THR ALA GLN LYS GLU ASP GLU TYR LEU ALA ARG ASP SEQRES 21 A 261 MET SEQRES 1 B 261 MET LEU LEU ASN ARG ALA ASN SER THR ASP SER LEU SER SEQRES 2 B 261 PHE SER PHE ILE ASN PHE ASP ARG ASP GLU ARG ASN LEU SEQRES 3 B 261 ILE PHE GLN GLY ASP ALA HIS THR SER ARG ASN ASN ILE SEQRES 4 B 261 LEU GLN LEU THR ARG THR ASP SER ASN GLY ALA PRO VAL SEQRES 5 B 261 ARG SER THR VAL GLY ARG ILE LEU HIS SER ALA GLN VAL SEQRES 6 B 261 ARG LEU TRP GLU LYS SER THR ASN ARG VAL ALA ASN LEU SEQRES 7 B 261 GLN THR GLN PHE SER PHE PHE LEU SER SER PRO LEU SER SEQRES 8 B 261 ASN PRO ALA ASP GLY ILE ALA PHE PHE ILE ALA PRO PRO SEQRES 9 B 261 ASP THR THR ILE PRO SER GLY SER ALA GLY GLY LEU LEU SEQRES 10 B 261 GLY LEU PHE ASN PRO ARG THR ALA LEU ASN GLU SER ALA SEQRES 11 B 261 ASN GLN VAL LEU ALA VAL GLU PHE ASP THR PHE PHE ALA SEQRES 12 B 261 GLN ASN SER ASN THR TRP ASP PRO ASN TYR GLN HIS ILE SEQRES 13 B 261 GLY ILE ASP VAL ASN SER ILE ARG SER SER LYS VAL VAL SEQRES 14 B 261 ARG TRP GLU ARG ARG GLU GLY LYS THR LEU ASN VAL LEU SEQRES 15 B 261 VAL THR TYR ASN PRO SER THR ARG THR ILE ASP VAL VAL SEQRES 16 B 261 ALA THR TYR PRO ASP GLY GLN ARG TYR GLN LEU SER HIS SEQRES 17 B 261 VAL VAL ASP LEU THR THR ILE LEU PRO GLU TRP VAL ARG SEQRES 18 B 261 VAL GLY PHE SER ALA ALA SER GLY GLU GLN PHE GLN THR SEQRES 19 B 261 HIS ASN LEU GLU SER TRP SER PHE THR SER THR LEU LEU SEQRES 20 B 261 TYR THR ALA GLN LYS GLU ASP GLU TYR LEU ALA ARG ASP SEQRES 21 B 261 MET HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET NAG C 5 14 HET MAN C 6 11 HET NAG C 7 14 HET NAG D 1 14 HET NAG D 2 17 HET BMA D 3 11 HET MAN D 4 11 HET NAG D 5 14 HET MAN D 6 11 HET NAG D 7 14 HET ASN A 299 9 HET MN A 400 1 HET CA A 401 1 HET GOL A 402 12 HET URE A 403 4 HET GOL A 405 6 HET GOL A 406 6 HET MN B 400 1 HET CA B 401 1 HET GOL B 403 6 HET URE B 404 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ASN ASPARAGINE HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM URE UREA 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 3 BMA 2(C6 H12 O6) FORMUL 3 MAN 4(C6 H12 O6) FORMUL 5 ASN C4 H8 N2 O3 FORMUL 6 MN 2(MN 2+) FORMUL 7 CA 2(CA 2+) FORMUL 8 GOL 4(C3 H8 O3) FORMUL 9 URE 2(C H4 N2 O) FORMUL 16 HOH *518(H2 O) HELIX 1 1 ASN A 127 ASN A 131 5 5 HELIX 2 2 ASP A 211 ILE A 215 1 5 HELIX 3 3 ASN B 127 ASN B 131 5 5 HELIX 4 4 ASP B 211 ILE B 215 5 5 SHEET 1 AA 7 HIS A 33 SER A 35 0 SHEET 2 AA 7 ILE A 39 GLN A 41 -1 O GLN A 41 N HIS A 33 SHEET 3 AA 7 THR A 234 LEU A 247 1 O LEU A 237 N LEU A 40 SHEET 4 AA 7 ARG A 74 SER A 87 -1 O VAL A 75 N LEU A 247 SHEET 5 AA 7 LEU A 179 ASN A 186 -1 O LEU A 179 N PHE A 84 SHEET 6 AA 7 THR A 191 THR A 197 -1 O THR A 191 N ASN A 186 SHEET 7 AA 7 ARG A 203 VAL A 209 -1 O TYR A 204 N ALA A 196 SHEET 1 AB10 HIS A 33 SER A 35 0 SHEET 2 AB10 ILE A 39 GLN A 41 -1 O GLN A 41 N HIS A 33 SHEET 3 AB10 THR A 234 LEU A 247 1 O LEU A 237 N LEU A 40 SHEET 4 AB10 ASP A 10 PHE A 16 -1 O LEU A 12 N SER A 244 SHEET 5 AB10 ASP B 10 PHE B 16 -1 O SER B 11 N SER A 15 SHEET 6 AB10 THR B 234 LEU B 247 -1 O TRP B 240 N PHE B 16 SHEET 7 AB10 ARG B 74 SER B 87 -1 O VAL B 75 N LEU B 247 SHEET 8 AB10 LEU B 179 ASN B 186 -1 O LEU B 179 N PHE B 84 SHEET 9 AB10 THR B 191 THR B 197 -1 O THR B 191 N ASN B 186 SHEET 10 AB10 ARG B 203 VAL B 209 -1 O TYR B 204 N ALA B 196 SHEET 1 AC 5 HIS A 33 SER A 35 0 SHEET 2 AC 5 ILE A 39 GLN A 41 -1 O GLN A 41 N HIS A 33 SHEET 3 AC 5 THR A 234 LEU A 247 1 O LEU A 237 N LEU A 40 SHEET 4 AC 5 ARG A 74 SER A 87 -1 O VAL A 75 N LEU A 247 SHEET 5 AC 5 LEU A 67 GLU A 69 -1 N GLU A 69 O ARG A 74 SHEET 1 BA 7 HIS B 33 SER B 35 0 SHEET 2 BA 7 ILE B 39 GLN B 41 1 O GLN B 41 N HIS B 33 SHEET 3 BA 7 THR B 234 LEU B 247 1 O LEU B 237 N LEU B 40 SHEET 4 BA 7 ARG B 74 SER B 87 -1 O VAL B 75 N LEU B 247 SHEET 5 BA 7 LEU B 179 ASN B 186 -1 O LEU B 179 N PHE B 84 SHEET 6 BA 7 THR B 191 THR B 197 -1 O THR B 191 N ASN B 186 SHEET 7 BA 7 ARG B 203 VAL B 209 -1 O TYR B 204 N ALA B 196 SHEET 1 AD 8 HIS A 33 SER A 35 0 SHEET 2 AD 8 ILE A 39 GLN A 41 -1 O GLN A 41 N HIS A 33 SHEET 3 AD 8 THR A 234 LEU A 247 1 O LEU A 237 N LEU A 40 SHEET 4 AD 8 ASP A 10 PHE A 16 -1 O LEU A 12 N SER A 244 SHEET 5 AD 8 ASP B 10 PHE B 16 -1 O SER B 11 N SER A 15 SHEET 6 AD 8 THR B 234 LEU B 247 -1 O TRP B 240 N PHE B 16 SHEET 7 AD 8 ILE B 39 GLN B 41 1 O LEU B 40 N LEU B 237 SHEET 8 AD 8 HIS B 33 THR B 34 1 O HIS B 33 N GLN B 41 SHEET 1 AE 8 HIS A 33 SER A 35 0 SHEET 2 AE 8 ILE A 39 GLN A 41 -1 O GLN A 41 N HIS A 33 SHEET 3 AE 8 THR A 234 LEU A 247 1 O LEU A 237 N LEU A 40 SHEET 4 AE 8 ASP A 10 PHE A 16 -1 O LEU A 12 N SER A 244 SHEET 5 AE 8 ASP B 10 PHE B 16 -1 O SER B 11 N SER A 15 SHEET 6 AE 8 THR B 234 LEU B 247 -1 O TRP B 240 N PHE B 16 SHEET 7 AE 8 ARG B 74 SER B 87 -1 O VAL B 75 N LEU B 247 SHEET 8 AE 8 LEU B 67 GLU B 69 -1 O GLU B 69 N ARG B 74 SHEET 1 AF 7 LEU A 26 GLY A 30 0 SHEET 2 AF 7 THR A 55 HIS A 61 -1 O ARG A 58 N GLN A 29 SHEET 3 AF 7 TRP A 219 SER A 228 -1 O VAL A 222 N HIS A 61 SHEET 4 AF 7 GLY A 96 ALA A 102 -1 O GLY A 96 N ALA A 227 SHEET 5 AF 7 LEU A 134 ASP A 139 -1 O LEU A 134 N ILE A 101 SHEET 6 AF 7 HIS A 155 VAL A 160 -1 O HIS A 155 N ASP A 139 SHEET 7 AF 7 LYS A 167 ARG A 170 -1 O LYS A 167 N ILE A 158 SHEET 1 AG 3 LEU A 26 GLY A 30 0 SHEET 2 AG 3 THR A 55 HIS A 61 -1 O ARG A 58 N GLN A 29 SHEET 3 AG 3 TRP A 219 SER A 228 -1 O VAL A 222 N HIS A 61 SHEET 1 BB 7 LEU B 26 GLY B 30 0 SHEET 2 BB 7 THR B 55 HIS B 61 -1 O ARG B 58 N GLN B 29 SHEET 3 BB 7 TRP B 219 SER B 228 -1 O VAL B 222 N HIS B 61 SHEET 4 BB 7 GLY B 96 ALA B 102 -1 O GLY B 96 N ALA B 227 SHEET 5 BB 7 LEU B 134 ASP B 139 -1 O LEU B 134 N ILE B 101 SHEET 6 BB 7 HIS B 155 VAL B 160 -1 O HIS B 155 N ASP B 139 SHEET 7 BB 7 LYS B 167 ARG B 170 -1 O LYS B 167 N ILE B 158 SHEET 1 BC 3 LEU B 26 GLY B 30 0 SHEET 2 BC 3 THR B 55 HIS B 61 -1 O ARG B 58 N GLN B 29 SHEET 3 BC 3 TRP B 219 SER B 228 -1 O VAL B 222 N HIS B 61 LINK ND2 ASN A 299 C1 NAG C 1 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.43 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.46 LINK O6 BMA C 3 C1 MAN C 6 1555 1555 1.44 LINK O2 MAN C 4 C1 NAG C 5 1555 1555 1.43 LINK O2 MAN C 6 C1 NAG C 7 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.43 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.42 LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.44 LINK O6 BMA D 3 C1 MAN D 6 1555 1555 1.44 LINK O2 MAN D 4 C1 NAG D 5 1555 1555 1.42 LINK O2 MAN D 6 C1 NAG D 7 1555 1555 1.42 LINK OE2 GLU A 137 MN MN A 400 1555 1555 2.11 LINK OD2 ASP A 139 MN MN A 400 1555 1555 2.20 LINK OD1 ASP A 139 CA CA A 401 1555 1555 2.48 LINK OD2 ASP A 139 CA CA A 401 1555 1555 2.46 LINK O PHE A 141 CA CA A 401 1555 1555 2.30 LINK OD1 ASN A 147 CA CA A 401 1555 1555 2.31 LINK OD1 ASP A 150 MN MN A 400 1555 1555 2.20 LINK OD2 ASP A 150 CA CA A 401 1555 1555 2.32 LINK NE2 HIS A 155 MN MN A 400 1555 1555 2.24 LINK MN MN A 400 O HOH A2175 1555 1555 2.23 LINK MN MN A 400 O HOH A2176 1555 1555 2.20 LINK CA CA A 401 O HOH A2137 1555 1555 2.35 LINK CA CA A 401 O HOH A2152 1555 1555 2.42 LINK OE2 GLU B 137 MN MN B 400 1555 1555 2.18 LINK OD2 ASP B 139 MN MN B 400 1555 1555 2.22 LINK OD1 ASP B 139 CA CA B 401 1555 1555 2.47 LINK OD2 ASP B 139 CA CA B 401 1555 1555 2.46 LINK O PHE B 141 CA CA B 401 1555 1555 2.35 LINK OD1 ASN B 147 CA CA B 401 1555 1555 2.35 LINK OD1 ASP B 150 MN MN B 400 1555 1555 2.17 LINK OD2 ASP B 150 CA CA B 401 1555 1555 2.33 LINK NE2 HIS B 155 MN MN B 400 1555 1555 2.22 LINK MN MN B 400 O HOH B2113 1555 1555 2.23 LINK MN MN B 400 O HOH B2114 1555 1555 2.19 LINK CA CA B 401 O HOH B2084 1555 1555 2.37 LINK CA CA B 401 O HOH B2098 1555 1555 2.39 CISPEP 1 ALA A 94 ASP A 95 0 6.41 CISPEP 2 ALA B 94 ASP B 95 0 7.72 CRYST1 51.400 76.980 125.590 90.00 90.00 90.00 P 21 21 21 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 0.019455 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012990 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007962 0.00000