HEADER SUGAR BINDING PROTEIN 28-JUN-15 5C9O TITLE CRYSTAL STRUCTURE OF RECOMBINANT PLL LECTIN FROM PHOTORHABDUS TITLE 2 LUMINESCENS AT 1.5 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLL LECTIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTORHABDUS LUMINESCENS; SOURCE 3 ORGANISM_TAXID: 29488; SOURCE 4 GENE: PLU0732; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LECTIN, SEVEN-BLADED BETA-PROPELLER, FUCOSE-SPECIFIC, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,P.SYKOROVA,G.DEMO,P.DOBES,P.HYRSL,M.WIMMEROVA REVDAT 5 10-JAN-24 5C9O 1 REMARK REVDAT 4 07-MAR-18 5C9O 1 REMARK REVDAT 3 07-DEC-16 5C9O 1 JRNL REVDAT 2 02-NOV-16 5C9O 1 JRNL REVDAT 1 19-OCT-16 5C9O 0 JRNL AUTH A.KUMAR,P.SYKOROVA,G.DEMO,P.DOBES,P.HYRSL,M.WIMMEROVA JRNL TITL A NOVEL FUCOSE-BINDING LECTIN FROM PHOTORHABDUS LUMINESCENS JRNL TITL 2 (PLL) WITH AN UNUSUAL HEPTABLADED BETA-PROPELLER TETRAMERIC JRNL TITL 3 STRUCTURE. JRNL REF J.BIOL.CHEM. V. 291 25032 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27758853 JRNL DOI 10.1074/JBC.M115.693473 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 76120 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) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4023 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5539 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.1480 REMARK 3 BIN FREE R VALUE SET COUNT : 305 REMARK 3 BIN FREE R VALUE : 0.1700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2750 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 405 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.49000 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): 0.046 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.695 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3023 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2746 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4144 ; 2.534 ; 1.902 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6306 ; 1.273 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 8.464 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;33.875 ;24.275 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;11.987 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.268 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 474 ; 0.188 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3450 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 750 ; 0.002 ; 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): 1460 ; 1.837 ; 1.126 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1459 ; 1.792 ; 1.124 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1833 ; 2.787 ; 1.689 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1834 ; 2.789 ; 1.691 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1561 ; 2.967 ; 1.322 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1561 ; 2.952 ; 1.323 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2296 ; 4.170 ; 1.896 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3768 ; 5.927 ;11.106 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3529 ; 5.588 ;10.109 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5C9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000211267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.967 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80153 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 79.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5C9L REMARK 200 REMARK 200 REMARK: PRISM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 2.5 % ETHANOL, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.89350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.91250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.16800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.89350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.91250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.16800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.89350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.91250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.16800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.89350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.91250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.16800 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C2). 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 25080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 638 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 ASN A 3 REMARK 465 PRO A 4 REMARK 465 ASP A 5 REMARK 465 ASN A 6 REMARK 465 THR A 7 REMARK 465 GLU A 8 REMARK 465 ALA A 9 REMARK 465 HIS A 10 REMARK 465 VAL A 11 REMARK 465 ALA A 12 REMARK 465 GLY A 13 REMARK 465 GLU A 14 REMARK 465 VAL A 15 REMARK 465 GLU A 16 REMARK 465 HIS A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 HIS A 375 REMARK 465 HIS A 376 REMARK 465 TRP A 377 REMARK 465 ARG A 378 REMARK 465 SER A 379 REMARK 465 GLY A 380 REMARK 465 CYS A 381 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 OG SER A 252 OG SER A 254 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 SER A 29 CB SER A 29 OG -0.093 REMARK 500 SER A 142 CA SER A 142 CB 0.099 REMARK 500 ASP A 228 CA ASP A 228 CB -0.140 REMARK 500 ASP A 228 CB ASP A 228 CG -0.143 REMARK 500 SER A 246 CA SER A 246 CB -0.100 REMARK 500 SER A 297 CB SER A 297 OG 0.090 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 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 LYS A 68 CD - CE - NZ ANGL. DEV. = 14.9 DEGREES REMARK 500 PHE A 69 CB - CG - CD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 81 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 CYS A 227 CB - CA - C ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 236 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 262 CB - CG - OD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG A 292 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 PRO A 301 C - N - CA ANGL. DEV. = -9.1 DEGREES REMARK 500 ASP A 364 CB - CG - OD2 ANGL. DEV. = -6.8 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 ASN A 109 56.83 -90.53 REMARK 500 TYR A 118 -153.60 63.21 REMARK 500 ASN A 157 43.26 -84.72 REMARK 500 LYS A 214 -158.55 61.37 REMARK 500 LYS A 214 -34.25 76.66 REMARK 500 SER A 215 127.10 51.65 REMARK 500 SER A 215 -155.28 -59.94 REMARK 500 ASN A 299 12.20 55.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 299 GLY A 300 -142.05 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 A 905 DISTANCE = 6.12 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 417 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5C9L RELATED DB: PDB REMARK 900 5C9L IS THE NATIVE FORM OF THE SAME LECTIN DBREF 5C9O A 1 368 UNP Q7N8J0 Q7N8J0_PHOLL 8 375 SEQADV 5C9O HIS A 10 UNP Q7N8J0 TYR 17 CONFLICT SEQADV 5C9O GLU A 16 UNP Q7N8J0 ALA 23 CONFLICT SEQADV 5C9O GLY A 93 UNP Q7N8J0 SER 100 CONFLICT SEQADV 5C9O VAL A 139 UNP Q7N8J0 ALA 146 CONFLICT SEQADV 5C9O SER A 142 UNP Q7N8J0 THR 149 CONFLICT SEQADV 5C9O LEU A 177 UNP Q7N8J0 ILE 184 CONFLICT SEQADV 5C9O ASN A 225 UNP Q7N8J0 GLY 232 CONFLICT SEQADV 5C9O SER A 240 UNP Q7N8J0 ASN 247 CONFLICT SEQADV 5C9O GLN A 278 UNP Q7N8J0 ARG 285 CONFLICT SEQADV 5C9O HIS A 298 UNP Q7N8J0 GLN 305 CONFLICT SEQADV 5C9O LEU A 369 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O GLU A 370 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O HIS A 371 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O HIS A 372 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O HIS A 373 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O HIS A 374 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O HIS A 375 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O HIS A 376 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O TRP A 377 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O ARG A 378 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O SER A 379 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O GLY A 380 UNP Q7N8J0 EXPRESSION TAG SEQADV 5C9O CYS A 381 UNP Q7N8J0 EXPRESSION TAG SEQRES 1 A 381 MET PRO ASN PRO ASP ASN THR GLU ALA HIS VAL ALA GLY SEQRES 2 A 381 GLU VAL GLU ILE GLU ASN SER ALA ILE ALA LEU SER GLY SEQRES 3 A 381 ILE VAL SER VAL ALA ASN ASN ALA ASP ASN ARG LEU GLU SEQRES 4 A 381 VAL PHE GLY VAL SER THR ASP SER ALA VAL TRP HIS ASN SEQRES 5 A 381 TRP GLN THR ALA PRO LEU PRO ASN SER SER TRP ALA GLY SEQRES 6 A 381 TRP ASN LYS PHE ASN GLY VAL VAL THR SER LYS PRO ALA SEQRES 7 A 381 VAL HIS ARG ASN SER ASP GLY ARG LEU GLU VAL PHE VAL SEQRES 8 A 381 ARG GLY THR ASP ASN ALA LEU TRP HIS ASN TRP GLN THR SEQRES 9 A 381 ALA ALA ASP THR ASN THR TRP SER SER TRP GLN PRO LEU SEQRES 10 A 381 TYR GLY GLY ILE THR SER ASN PRO GLU VAL CYS LEU ASN SEQRES 11 A 381 SER ASP GLY ARG LEU GLU VAL PHE VAL ARG GLY SER ASP SEQRES 12 A 381 ASN ALA LEU TRP HIS ILE TRP GLN THR ALA ALA HIS THR SEQRES 13 A 381 ASN SER TRP SER ASN TRP LYS SER LEU GLY GLY THR LEU SEQRES 14 A 381 THR SER ASN PRO ALA ALA HIS LEU ASN ALA ASP GLY ARG SEQRES 15 A 381 ILE GLU VAL PHE ALA ARG GLY ALA ASP ASN ALA LEU TRP SEQRES 16 A 381 HIS ILE TRP GLN THR ALA ALA HIS THR ASP GLN TRP SER SEQRES 17 A 381 ASN TRP GLN SER LEU LYS SER VAL ILE THR SER ASP PRO SEQRES 18 A 381 VAL VAL ILE ASN ASN CYS ASP GLY ARG LEU GLU VAL PHE SEQRES 19 A 381 ALA ARG GLY ALA ASP SER THR LEU ARG HIS ILE SER GLN SEQRES 20 A 381 ILE GLY SER ASP SER VAL SER TRP SER ASN TRP GLN CYS SEQRES 21 A 381 LEU ASP GLY VAL ILE THR SER ALA PRO ALA ALA VAL LYS SEQRES 22 A 381 ASN ILE SER GLY GLN LEU GLU VAL PHE ALA ARG GLY ALA SEQRES 23 A 381 ASP ASN THR LEU TRP ARG THR TRP GLN THR SER HIS ASN SEQRES 24 A 381 GLY PRO TRP SER ASN TRP SER SER PHE THR GLY ILE ILE SEQRES 25 A 381 ALA SER ALA PRO THR VAL ALA LYS ASN SER ASP GLY ARG SEQRES 26 A 381 ILE GLU VAL PHE VAL LEU GLY LEU ASP LYS ALA LEU TRP SEQRES 27 A 381 HIS LEU TRP GLN THR THR SER SER THR THR SER SER TRP SEQRES 28 A 381 THR THR TRP ALA LEU ILE GLY GLY ILE THR LEU ILE ASP SEQRES 29 A 381 ALA SER VAL ILE LEU GLU HIS HIS HIS HIS HIS HIS TRP SEQRES 30 A 381 ARG SER GLY CYS HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 12 HET GOL A 404 12 HET GOL A 405 6 HET GOL A 406 6 HET GOL A 407 6 HET GOL A 408 6 HET GOL A 409 6 HET GOL A 410 6 HET GOL A 411 6 HET GOL A 412 6 HET GOL A 413 6 HET GOL A 414 6 HET GOL A 415 6 HET GOL A 416 6 HET GOL A 417 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 17(C3 H8 O3) FORMUL 19 HOH *405(H2 O) SHEET 1 AA1 4 SER A 29 ASN A 32 0 SHEET 2 AA1 4 LEU A 38 SER A 44 -1 O PHE A 41 N SER A 29 SHEET 3 AA1 4 ALA A 48 TRP A 53 -1 O ASN A 52 N VAL A 40 SHEET 4 AA1 4 ASN A 67 VAL A 72 -1 O PHE A 69 N VAL A 49 SHEET 1 AA2 3 SER A 29 ASN A 32 0 SHEET 2 AA2 3 LEU A 38 SER A 44 -1 O PHE A 41 N SER A 29 SHEET 3 AA2 3 LEU A 362 ILE A 363 -1 O ILE A 363 N VAL A 43 SHEET 1 AA3 4 ALA A 78 ARG A 81 0 SHEET 2 AA3 4 LEU A 87 ARG A 92 -1 O PHE A 90 N ALA A 78 SHEET 3 AA3 4 LEU A 98 TRP A 102 -1 O TRP A 99 N VAL A 91 SHEET 4 AA3 4 GLN A 115 TYR A 118 -1 O LEU A 117 N LEU A 98 SHEET 1 AA4 4 GLU A 126 LEU A 129 0 SHEET 2 AA4 4 LEU A 135 ARG A 140 -1 O PHE A 138 N GLU A 126 SHEET 3 AA4 4 LEU A 146 TRP A 150 -1 O TRP A 147 N VAL A 139 SHEET 4 AA4 4 LYS A 163 GLY A 166 -1 O LEU A 165 N LEU A 146 SHEET 1 AA5 4 ALA A 174 LEU A 177 0 SHEET 2 AA5 4 ILE A 183 ARG A 188 -1 O PHE A 186 N ALA A 174 SHEET 3 AA5 4 ALA A 193 TRP A 198 -1 O ILE A 197 N VAL A 185 SHEET 4 AA5 4 GLN A 211 VAL A 216 -1 O LEU A 213 N LEU A 194 SHEET 1 AA6 4 VAL A 222 ASN A 225 0 SHEET 2 AA6 4 LEU A 231 ARG A 236 -1 O PHE A 234 N VAL A 222 SHEET 3 AA6 4 THR A 241 SER A 246 -1 O ARG A 243 N ALA A 235 SHEET 4 AA6 4 GLN A 259 VAL A 264 -1 O LEU A 261 N LEU A 242 SHEET 1 AA7 4 ALA A 270 LYS A 273 0 SHEET 2 AA7 4 LEU A 279 ARG A 284 -1 O PHE A 282 N ALA A 270 SHEET 3 AA7 4 THR A 289 TRP A 294 -1 O TRP A 291 N ALA A 283 SHEET 4 AA7 4 SER A 306 ILE A 311 -1 O SER A 306 N ARG A 292 SHEET 1 AA8 4 THR A 317 LYS A 320 0 SHEET 2 AA8 4 ILE A 326 LEU A 331 -1 O PHE A 329 N THR A 317 SHEET 3 AA8 4 LEU A 337 TRP A 341 -1 O LEU A 340 N VAL A 328 SHEET 4 AA8 4 ALA A 355 ILE A 357 -1 O ILE A 357 N LEU A 337 SSBOND 1 CYS A 260 CYS A 260 1555 3555 2.22 SITE 1 AC1 9 ASN A 130 ARG A 134 GLU A 136 HIS A 148 SITE 2 AC1 9 TRP A 150 GLN A 199 TRP A 207 HOH A 506 SITE 3 AC1 9 HOH A 683 SITE 1 AC2 8 GLN A 54 PRO A 59 SER A 61 TRP A 63 SITE 2 AC2 8 ASN A 321 ARG A 325 GLU A 327 TRP A 341 SITE 1 AC3 12 ASN A 33 ARG A 37 GLU A 39 HIS A 51 SITE 2 AC3 12 TRP A 53 GLN A 103 ASP A 107 THR A 108 SITE 3 AC3 12 ASN A 109 TRP A 111 GOL A 407 HOH A 686 SITE 1 AC4 9 GLY A 119 GLY A 120 GLY A 141 SER A 142 SITE 2 AC4 9 TRP A 147 TRP A 162 GOL A 412 HOH A 543 SITE 3 AC4 9 HOH A 763 SITE 1 AC5 8 GLY A 167 THR A 168 GLY A 189 ALA A 190 SITE 2 AC5 8 TRP A 195 HOH A 518 HOH A 596 HOH A 606 SITE 1 AC6 5 ARG A 292 SER A 306 SER A 307 PHE A 308 SITE 2 AC6 5 HOH A 729 SITE 1 AC7 6 ARG A 37 THR A 55 ASP A 107 GOL A 403 SITE 2 AC7 6 HOH A 561 HOH A 621 SITE 1 AC8 7 GLY A 71 VAL A 72 GLY A 93 THR A 94 SITE 2 AC8 7 HOH A 605 HOH A 607 HOH A 654 SITE 1 AC9 11 ASN A 82 ARG A 86 GLU A 88 HIS A 100 SITE 2 AC9 11 TRP A 102 GLN A 151 THR A 156 ASN A 157 SITE 3 AC9 11 TRP A 159 HOH A 552 HOH A 704 SITE 1 AD1 7 ASN A 178 ARG A 182 GLU A 184 HIS A 196 SITE 2 AD1 7 GLN A 247 VAL A 253 TRP A 255 SITE 1 AD2 6 GLY A 310 ILE A 311 GLY A 332 LEU A 333 SITE 2 AD2 6 HOH A 627 HOH A 670 SITE 1 AD3 9 TRP A 66 GLY A 119 TRP A 162 GLY A 358 SITE 2 AD3 9 GLY A 359 GOL A 404 HOH A 516 HOH A 541 SITE 3 AD3 9 HOH A 551 SITE 1 AD4 8 THR A 74 ARG A 92 ALA A 365 SER A 366 SITE 2 AD4 8 ILE A 368 HOH A 509 HOH A 652 HOH A 713 SITE 1 AD5 7 LEU A 213 LYS A 214 TRP A 255 SER A 256 SITE 2 AD5 7 ASN A 304 GOL A 417 HOH A 501 SITE 1 AD6 6 TRP A 291 TRP A 305 SER A 307 GOL A 417 SITE 2 AD6 6 HOH A 528 HOH A 797 SITE 1 AD7 8 LEU A 117 TRP A 159 SER A 160 ASN A 161 SITE 2 AD7 8 TRP A 162 GLY A 359 HOH A 508 HOH A 548 SITE 1 AD8 7 ASN A 257 ASP A 262 ASN A 304 TRP A 305 SITE 2 AD8 7 GOL A 414 GOL A 415 HOH A 574 CRYST1 71.787 87.825 158.336 90.00 90.00 90.00 I 2 2 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 0.013930 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006316 0.00000