HEADER SUGAR BINDING PROTEIN 10-DEC-19 6LI7 TITLE CRYSTAL STRUCTURE OF LECTIN FROM PLEUROTUS OSTREATUS IN COMPLEX WITH TITLE 2 GALNAC CAVEAT 6LI7 NAG D 2 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LECTIN 1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS OSTREATUS; SOURCE 3 ORGANISM_COMMON: OYSTER MUSHROOM; SOURCE 4 ORGANISM_TAXID: 5322 KEYWDS MUSHROOM LECTIN, PLEUROTUS OSTREATUS LECTIN, CARBOHYDRATE BINDING KEYWDS 2 MODULE, C-TYPE LETIN, CALCIUM BINDING PROTEIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VAJRAVIJAYAN,S.PLETNEV,Z.LUO,T.ANKUR,K.GUNASEKARAN,N.NANDHAGOPAL REVDAT 2 22-NOV-23 6LI7 1 REMARK REVDAT 1 05-AUG-20 6LI7 0 JRNL AUTH S.VAJRAVIJAYAN,S.PLETNEV,Z.LUO,V.Z.PLETNEV,N.NANDHAGOPAL, JRNL AUTH 2 K.GUNASEKARAN JRNL TITL CRYSTALLOGRAPHIC AND CALORIMETRIC ANALYSIS ON PLEUROTUS JRNL TITL 2 OSTREATUS LECTIN AND ITS SUGAR COMPLEXES - PROMISCUOUS JRNL TITL 3 BINDING DRIVEN BY GEOMETRY. JRNL REF INT.J.BIOL.MACROMOL. V. 152 862 2020 JRNL REFN ISSN 0141-8130 JRNL PMID 32112837 JRNL DOI 10.1016/J.IJBIOMAC.2020.02.294 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 58628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.411 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4130 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2505 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00600 REMARK 3 B22 (A**2) : 0.00600 REMARK 3 B33 (A**2) : -0.01900 REMARK 3 B12 (A**2) : 0.00300 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): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.054 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2695 ; 0.016 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2402 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3699 ; 2.098 ; 1.690 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5582 ; 1.469 ; 1.610 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ;10.495 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;34.148 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;12.688 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;22.108 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 389 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3001 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 544 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 449 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 30 ; 0.144 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1351 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 166 ; 0.207 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.100 ; 0.200 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): 1347 ; 2.922 ; 3.120 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1346 ; 2.921 ; 3.121 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1682 ; 3.861 ; 4.667 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1683 ; 3.860 ; 4.667 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1348 ; 4.601 ; 3.649 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1349 ; 4.600 ; 3.650 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2017 ; 6.244 ; 5.302 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2018 ; 6.242 ; 5.303 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 : NULL 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6LI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : SI 111. ROSENBAUM-ROCK DOUBLE REMARK 200 -CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58637 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.098 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: 3W5N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9M NA2HPO4/K2HPO4, PH 5.5, 33% REMARK 280 GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.65833 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.31667 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 72.98750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 121.64583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.32917 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.65833 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 97.31667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 121.64583 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 72.98750 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 24.32917 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 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 KCAL/MOL 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 VAL A 2 REMARK 465 LEU A 3 REMARK 465 LEU A 4 REMARK 465 VAL A 5 REMARK 465 ILE A 6 REMARK 465 GLY A 7 REMARK 465 LEU A 8 REMARK 465 PRO A 9 REMARK 465 LEU A 10 REMARK 465 VAL A 11 REMARK 465 SER A 12 REMARK 465 LEU A 13 REMARK 465 VAL A 14 REMARK 465 VAL A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 VAL A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 ALA A 21 REMARK 465 ALA A 22 REMARK 465 PRO A 23 REMARK 465 ASP A 24 REMARK 465 SER A 25 REMARK 465 GLN A 26 REMARK 465 VAL A 27 REMARK 465 CYS A 28 REMARK 465 ASP A 29 REMARK 465 VAL A 30 REMARK 465 ASP A 31 REMARK 465 SER A 32 REMARK 465 THR A 33 REMARK 465 ALA A 34 REMARK 465 THR A 35 REMARK 465 CYS A 36 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 NAG B 2 1.14 REMARK 500 O4 NAG C 1 O5 NAG C 2 1.97 REMARK 500 O HOH A 593 O HOH A 690 2.01 REMARK 500 O HOH A 647 O HOH A 691 2.05 REMARK 500 O4 NAG D 1 O5 NAG D 2 2.12 REMARK 500 NH1 ARG A 239 OE2 GLU A 347 2.16 REMARK 500 O HOH A 590 O HOH A 664 2.17 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 ALA A 373 C ALA A 373 O 0.173 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 108 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 239 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ALA A 373 CA - C - O ANGL. DEV. = -20.5 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 TRP A 57 -155.75 -150.90 REMARK 500 PRO A 82 165.64 -48.79 REMARK 500 ARG A 173 48.57 -92.26 REMARK 500 ASN A 243 83.07 -153.17 REMARK 500 VAL A 250 -65.83 -122.40 REMARK 500 ASP A 260 -30.52 -133.33 REMARK 500 SER A 275 36.49 -143.27 REMARK 500 MET A 368 128.68 -37.38 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 ASP A 259 ASP A 260 54.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 259 14.56 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 722 DISTANCE = 6.20 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 CA A 408 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 97 OD1 REMARK 620 2 ASP A 98 OD2 80.3 REMARK 620 3 ASN A 138 OD1 122.5 71.9 REMARK 620 4 SER A 143 OG 159.9 115.3 76.1 REMARK 620 5 PRO A 144 O 87.3 141.4 84.9 87.2 REMARK 620 6 GOL A 410 O3 92.5 74.1 124.5 80.6 143.3 REMARK 620 7 GOL A 410 O2 77.6 132.4 153.5 82.4 78.7 65.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 407 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 259 OD1 REMARK 620 2 ASP A 260 OD2 78.9 REMARK 620 3 ASN A 301 OD1 117.3 75.2 REMARK 620 4 GLY A 303 O 166.1 101.5 75.8 REMARK 620 5 PRO A 305 O 88.5 144.6 81.8 98.4 REMARK 620 6 NGA A 411 O4 74.6 129.9 154.9 95.3 76.2 REMARK 620 7 NGA A 411 O3 86.7 69.3 132.0 80.6 143.3 67.4 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6KBQ RELATED DB: PDB REMARK 900 STRUCTURE OF GLYCEROL BOUND PLEUROTUS OSTREATUS LECTIN DBREF 6LI7 A 1 373 UNP E7E2M2 E7E2M2_PLEOS 1 373 SEQRES 1 A 373 MET VAL LEU LEU VAL ILE GLY LEU PRO LEU VAL SER LEU SEQRES 2 A 373 VAL VAL ALA LEU VAL ALA ALA ALA ALA PRO ASP SER GLN SEQRES 3 A 373 VAL CYS ASP VAL ASP SER THR ALA THR CYS LYS ILE THR SEQRES 4 A 373 ALA THR PRO SER GLN PHE GLN PRO ALA LEU LEU ASN ALA SEQRES 5 A 373 SER LYS TRP ILE TRP THR GLY GLU ASN PRO ILE PRO GLY SEQRES 6 A 373 GLY SER ASN ILE ILE SER THR ARG PRO PHE ARG LYS ASN SEQRES 7 A 373 ILE THR ALA PRO CYS GLY LYS CYS SER VAL CYS ALA THR SEQRES 8 A 373 ILE VAL VAL ALA SER ASP ASP ALA HIS THR PHE TYR VAL SEQRES 9 A 373 ASN GLY VAL ARG ILE GLY THR GLY ALA GLY PHE ARG GLN SEQRES 10 A 373 GLY GLN ALA LEU PHE VAL ALA LEU GLN PRO THR TRP ASN SEQRES 11 A 373 LEU PHE ALA ILE ALA GLY GLN ASN LEU VAL ALA ASN SER SEQRES 12 A 373 PRO ALA GLY ILE MET ALA SER ILE LEU VAL HIS PHE SER SEQRES 13 A 373 ASP GLY THR SER GLU THR PHE VAL THR ASP GLU SER TRP SEQRES 14 A 373 LYS THR LEU ARG ALA ALA PRO PRO GLU ASN PHE GLN LEU SEQRES 15 A 373 PRO SER THR ASN ASP SER ASN TRP PRO SER ALA ALA VAL SEQRES 16 A 373 GLN GLY ALA TYR GLN ASN SER VAL TRP GLY PRO PRO VAL SEQRES 17 A 373 LEU PRO PRO VAL LEU PRO LEU ARG GLY SER ASN TRP ILE SEQRES 18 A 373 TRP THR SER ASP ASN VAL ASN GLY ALA ALA PRO VAL GLY SEQRES 19 A 373 SER ARG ALA PHE ARG LYS THR VAL ASN GLN CYS THR LYS SEQRES 20 A 373 VAL ALA VAL CYS ALA THR VAL LEU ILE ALA ALA ASP ASP SEQRES 21 A 373 ARG TYR THR LEU TYR VAL ASN GLY ALA THR VAL GLY SER SEQRES 22 A 373 GLY SER SER TYR THR VAL ALA ASP ALA TYR THR ILE PRO SEQRES 23 A 373 ASN LEU HIS PRO THR PHE ASN THR PHE ALA ILE ASN ALA SEQRES 24 A 373 THR ASN GLY GLY GLY PRO ALA GLY VAL ILE ALA THR ILE SEQRES 25 A 373 LEU ILE THR TYR SER ASP GLY SER ASN GLU THR VAL VAL SEQRES 26 A 373 THR ASP ALA SER TRP LYS ALA ILE GLN THR ILE PRO GLN SEQRES 27 A 373 GLY PHE GLN PRO PRO LEU ILE ASP GLU PHE GLY TRP GLU SEQRES 28 A 373 SER ALA LYS ILE ILE GLY ALA PHE GLY VAL ALA PRO TRP SEQRES 29 A 373 GLY ALA GLY MET VAL ILE PRO SER ALA HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET CA A 407 1 HET CA A 408 1 HET GOL A 409 6 HET GOL A 410 6 HET NGA A 411 15 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM NGA 2-ACETAMIDO-2-DEOXY-BETA-D-GALACTOPYRANOSE 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 GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN NGA N-ACETYL-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NGA BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 NGA ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-D-GALACTOSAMINE FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 5 CA 2(CA 2+) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 NGA C8 H15 N O6 FORMUL 10 HOH *222(H2 O) SHEET 1 AA1 5 SER A 43 GLN A 44 0 SHEET 2 AA1 5 ASP A 281 ILE A 285 -1 O THR A 284 N SER A 43 SHEET 3 AA1 5 ALA A 249 ASP A 259 -1 N ALA A 252 O ILE A 285 SHEET 4 AA1 5 GLY A 307 TYR A 316 -1 O GLY A 307 N ASP A 259 SHEET 5 AA1 5 ASN A 321 VAL A 325 -1 O GLU A 322 N ILE A 314 SHEET 1 AA2 2 LYS A 54 TRP A 57 0 SHEET 2 AA2 2 ALA A 194 ALA A 198 -1 O GLN A 196 N TRP A 55 SHEET 1 AA3 4 VAL A 107 ALA A 124 0 SHEET 2 AA3 4 SER A 87 VAL A 104 -1 N PHE A 102 O GLY A 110 SHEET 3 AA3 4 GLY A 146 PHE A 155 -1 O HIS A 154 N CYS A 89 SHEET 4 AA3 4 SER A 160 VAL A 164 -1 O PHE A 163 N ILE A 151 SHEET 1 AA4 5 VAL A 107 ALA A 124 0 SHEET 2 AA4 5 SER A 87 VAL A 104 -1 N PHE A 102 O GLY A 110 SHEET 3 AA4 5 TRP A 129 ASN A 138 -1 O ALA A 133 N TYR A 103 SHEET 4 AA4 5 SER A 71 THR A 80 -1 N ILE A 79 O ASN A 130 SHEET 5 AA4 5 LYS A 170 THR A 171 -1 O LYS A 170 N ARG A 76 SHEET 1 AA5 2 ASN A 219 TRP A 222 0 SHEET 2 AA5 2 LYS A 354 ALA A 358 -1 O LYS A 354 N TRP A 222 SHEET 1 AA6 6 ALA A 269 GLY A 274 0 SHEET 2 AA6 6 ARG A 261 VAL A 266 -1 N LEU A 264 O GLY A 272 SHEET 3 AA6 6 ASN A 293 ASN A 301 -1 O ALA A 296 N TYR A 265 SHEET 4 AA6 6 GLY A 234 VAL A 242 -1 N GLY A 234 O ASN A 301 SHEET 5 AA6 6 LYS A 331 ILE A 333 -1 O LYS A 331 N ARG A 239 SHEET 6 AA6 6 GLU A 351 SER A 352 -1 O GLU A 351 N ALA A 332 SSBOND 1 CYS A 89 CYS A 251 1555 1555 2.31 SSBOND 2 CYS A 245 CYS A 245 1555 7556 2.66 LINK ND2 ASN A 78 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 298 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 321 C1 NAG B 1 1555 1555 1.48 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.34 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.36 LINK OD1 ASP A 97 CA CA A 408 1555 1555 2.31 LINK OD2 ASP A 98 CA CA A 408 1555 1555 2.58 LINK OD1 ASN A 138 CA CA A 408 1555 1555 2.35 LINK OG SER A 143 CA CA A 408 1555 1555 2.53 LINK O PRO A 144 CA CA A 408 1555 1555 2.38 LINK OD1 ASP A 259 CA CA A 407 1555 1555 2.35 LINK OD2 ASP A 260 CA CA A 407 1555 1555 2.29 LINK OD1 ASN A 301 CA CA A 407 1555 1555 2.49 LINK O GLY A 303 CA CA A 407 1555 1555 2.38 LINK O PRO A 305 CA CA A 407 1555 1555 2.23 LINK CA CA A 407 O4 NGA A 411 1555 1555 2.42 LINK CA CA A 407 O3 NGA A 411 1555 1555 2.34 LINK CA CA A 408 O3 GOL A 410 1555 1555 2.48 LINK CA CA A 408 O2 GOL A 410 1555 1555 2.41 CISPEP 1 ASP A 97 ASP A 98 0 9.14 CISPEP 2 ALA A 362 PRO A 363 0 0.67 CRYST1 152.273 152.273 145.975 90.00 90.00 120.00 P 61 2 2 12 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 0.006567 0.003792 0.000000 0.00000 SCALE2 0.000000 0.007583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006850 0.00000