HEADER SUGAR BINDING PROTEIN 29-JAN-24 8VU8 TITLE WHEAT GERM AGGLUTININ (WGA) DOMAIN D COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGLUTININ ISOLECTIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CHITIN-BINDING TYPE-1 DOMAIN D, RESIDUES 129-171; COMPND 5 SYNONYM: WGA3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRITICUM AESTIVUM; SOURCE 3 ORGANISM_COMMON: BREAD WHEAT; SOURCE 4 ORGANISM_TAXID: 4565; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LECTIN, MULTIDOMAIN PROTEIN, STRUCTURAL STABILITY, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.A.TITAUX-DELGADO,F.DEL RIO-PORTILLA,E.GARCIA-HERNANDEZ REVDAT 1 05-JUN-24 8VU8 0 JRNL AUTH J.L.MEDRANO-CERANO,L.F.COFAS-VARGAS,E.LEYVA,J.A.RAUDA-CEJA, JRNL AUTH 2 M.CALDERON-VARGAS,P.CANO-SANCHEZ,G.TITAUX-DELGADO, JRNL AUTH 3 C.M.MELCHOR-MENESES,A.HERNANDEZ-ARANA,F.DEL RIO-PORTILLA, JRNL AUTH 4 E.GARCIA-HERNANDEZ JRNL TITL DECODING THE MECHANISM GOVERNING THE STRUCTURAL STABILITY OF JRNL TITL 2 WHEAT GERM AGGLUTININ AND ITS ISOLATED DOMAINS: A COMBINED JRNL TITL 3 CALORIMETRIC, NMR, AND MD SIMULATION STUDY. JRNL REF PROTEIN SCI. V. 33 E5020 2024 JRNL REFN ESSN 1469-896X JRNL PMID 38747397 JRNL DOI 10.1002/PRO.5020 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED ALSO FOR SIMULATED ANNEALING REMARK 4 REMARK 4 8VU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000280285. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.74 REMARK 210 IONIC STRENGTH : 0.116 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM WGA_DOMD, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.8, CYANA 2.1, CARA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 16 TYR A 17 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 17 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 20 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.2 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 1 ARG A 11 153.02 -46.36 REMARK 500 1 ASN A 16 38.67 -72.36 REMARK 500 2 ASN A 15 22.15 -71.20 REMARK 500 3 TRP A 22 42.01 -99.43 REMARK 500 4 ASN A 16 44.36 -78.79 REMARK 500 5 ASN A 16 36.36 -71.30 REMARK 500 6 ASN A 16 47.01 -77.77 REMARK 500 6 SER A 38 -175.60 -170.27 REMARK 500 7 ARG A 11 167.36 177.06 REMARK 500 8 ARG A 11 166.11 177.80 REMARK 500 8 ASN A 15 4.63 -69.49 REMARK 500 9 ASN A 16 44.96 -78.06 REMARK 500 11 ASN A 16 32.41 -70.21 REMARK 500 12 ASN A 16 40.04 -73.73 REMARK 500 12 TYR A 31 -61.64 -90.42 REMARK 500 13 ASN A 16 38.41 -78.11 REMARK 500 14 ASN A 16 32.95 -71.10 REMARK 500 15 ARG A 11 164.18 -41.56 REMARK 500 15 VAL A 12 -167.55 -128.53 REMARK 500 15 ASN A 16 30.00 -75.14 REMARK 500 16 ASN A 16 24.15 -68.21 REMARK 500 17 ASN A 16 40.37 -72.66 REMARK 500 18 ASN A 16 46.81 -75.79 REMARK 500 19 ASN A 16 39.98 -74.46 REMARK 500 20 ARG A 11 166.76 179.00 REMARK 500 20 ASN A 16 36.44 -74.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 7 ARG A 11 0.09 SIDE CHAIN REMARK 500 10 ARG A 11 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31143 RELATED DB: BMRB REMARK 900 WHEAT GERM AGGLUTININ (WGA) DOMAIN D DBREF 8VU8 A 1 43 UNP P10969 AGI3_WHEAT 129 171 SEQRES 1 A 43 ASP LYS PRO CYS GLY LYS ASP ALA GLY GLY ARG VAL CYS SEQRES 2 A 43 THR ASN ASN TYR CYS CYS SER LYS TRP GLY SER CYS GLY SEQRES 3 A 43 ILE GLY PRO GLY TYR CYS GLY ALA GLY CYS GLN SER GLY SEQRES 4 A 43 GLY CYS ASP GLY HELIX 1 AA1 CYS A 4 ALA A 8 5 5 HELIX 2 AA2 GLY A 28 GLY A 33 1 6 SHEET 1 AA1 2 CYS A 18 CYS A 19 0 SHEET 2 AA1 2 CYS A 25 GLY A 26 -1 O GLY A 26 N CYS A 18 SSBOND 1 CYS A 4 CYS A 19 1555 1555 2.04 SSBOND 2 CYS A 13 CYS A 25 1555 1555 2.04 SSBOND 3 CYS A 18 CYS A 32 1555 1555 2.04 SSBOND 4 CYS A 36 CYS A 41 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1