HEADER SUGAR BINDING PROTEIN 14-DEC-17 6F9A TITLE SOLUTION STRUCTURE OF THE MRH DOMAIN OF YOS9 COMPLEXED WITH ALPHA3, TITLE 2 ALPHA6-MAN5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ER QUALITY-CONTROL LECTIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: YOS9, SCKG_0443; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MRH DOMAIN, BETA BARREL, LECTIN, SUGAR BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.KNISS,S.KAZEMI,F.LOHR,P.GUNTERT,V.DOTSCH REVDAT 3 14-JUN-23 6F9A 1 REMARK REVDAT 2 08-MAY-19 6F9A 1 REMARK REVDAT 1 30-JAN-19 6F9A 0 JRNL AUTH M.BERGER,A.KNISS JRNL TITL SOLUTION STRUCTURE OF THE MRH DOMAIN OF YOS9 COMPLEXED WITH JRNL TITL 2 ALPHA3,ALPHA6-MAN5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.9, OPAL REMARK 3 AUTHORS : GUNTERT, P. (CYANA), LUGINBUHL, GUNTERT, BILLETER REMARK 3 AND WUTHRICH (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6F9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007970. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT BAR REMARK 210 SAMPLE CONTENTS : 0.55 MM [U-98% 13C; U-98% 15N] REMARK 210 MRH DOMAIN OF YOS9, 8.25 MM REMARK 210 ALPHA3,ALPHA6-MAN5, 95% H2O/5% REMARK 210 D2O; 1 MM [U-98% 13C; U-98% 15N] REMARK 210 MRH DOMAIN OF YOS9, 15 MM ALPHA3, REMARK 210 ALPHA6-MAN5, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-15N HSQC; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(COCA)CB; 3D HCCH- REMARK 210 TOCSY; 3D 1H TOCSY; 3D 13C TOCSY; REMARK 210 2D(HB)CB(CGCD)HD; 2D (H)CB(CGCC) REMARK 210 H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.13 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 6 ARG A 170 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 6 TYR A 229 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 8 ARG A 170 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 17 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 200 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 1 PRO A 131 90.41 -67.96 REMARK 500 1 ILE A 133 -67.17 -127.31 REMARK 500 1 THR A 146 -18.21 -146.47 REMARK 500 1 LEU A 160 -70.20 -120.03 REMARK 500 1 VAL A 179 -74.37 -74.28 REMARK 500 1 SER A 189 47.27 80.69 REMARK 500 1 ARG A 200 29.14 -79.17 REMARK 500 1 ALA A 245 41.40 -77.21 REMARK 500 1 ASN A 247 -179.41 -172.54 REMARK 500 2 PRO A 131 90.90 -61.05 REMARK 500 2 LEU A 160 -72.47 -95.28 REMARK 500 2 VAL A 179 -67.07 -94.07 REMARK 500 2 SER A 189 46.07 74.43 REMARK 500 2 ARG A 200 28.96 -73.46 REMARK 500 2 ASN A 212 35.98 -98.28 REMARK 500 2 SER A 213 33.19 -143.24 REMARK 500 2 ALA A 245 47.64 -79.02 REMARK 500 3 PRO A 131 84.91 -63.67 REMARK 500 3 ILE A 133 -67.25 -106.77 REMARK 500 3 THR A 146 -43.31 -144.86 REMARK 500 3 VAL A 150 -74.18 -86.17 REMARK 500 3 LEU A 160 -62.40 -101.68 REMARK 500 3 SER A 189 31.86 74.44 REMARK 500 3 ARG A 200 28.30 -75.56 REMARK 500 3 ASN A 212 37.44 -72.51 REMARK 500 3 ARG A 222 118.80 -164.34 REMARK 500 3 ALA A 245 38.51 -75.58 REMARK 500 4 PRO A 131 87.10 -65.60 REMARK 500 4 ILE A 133 -66.18 -128.05 REMARK 500 4 SER A 189 58.05 78.16 REMARK 500 4 ASN A 212 23.10 -50.15 REMARK 500 4 SER A 213 47.39 -145.96 REMARK 500 4 ALA A 245 70.26 -68.07 REMARK 500 5 SER A 90 76.19 -67.55 REMARK 500 5 PRO A 131 87.41 -65.69 REMARK 500 5 THR A 146 -30.05 -146.51 REMARK 500 5 LEU A 160 -65.67 -108.25 REMARK 500 5 SER A 189 36.94 74.82 REMARK 500 5 ARG A 200 29.81 -79.05 REMARK 500 5 ASN A 212 28.19 -57.14 REMARK 500 5 ALA A 245 37.97 -78.10 REMARK 500 5 GLU A 248 -22.98 -172.93 REMARK 500 6 PRO A 131 96.34 -67.06 REMARK 500 6 ILE A 133 -68.01 -125.95 REMARK 500 6 LEU A 156 73.45 -110.72 REMARK 500 6 LEU A 160 -75.98 -95.40 REMARK 500 6 VAL A 179 -73.47 -79.16 REMARK 500 6 SER A 189 57.99 72.05 REMARK 500 6 ASN A 212 17.36 -66.42 REMARK 500 6 CYS A 227 -65.05 -108.83 REMARK 500 REMARK 500 THIS ENTRY HAS 178 RAMACHANDRAN OUTLIERS. 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 1 ARG A 159 0.12 SIDE CHAIN REMARK 500 1 ARG A 170 0.09 SIDE CHAIN REMARK 500 1 TYR A 182 0.07 SIDE CHAIN REMARK 500 1 ARG A 222 0.08 SIDE CHAIN REMARK 500 5 ARG A 116 0.10 SIDE CHAIN REMARK 500 5 ARG A 152 0.10 SIDE CHAIN REMARK 500 6 TYR A 120 0.08 SIDE CHAIN REMARK 500 6 ARG A 170 0.08 SIDE CHAIN REMARK 500 7 TYR A 182 0.07 SIDE CHAIN REMARK 500 8 ARG A 170 0.08 SIDE CHAIN REMARK 500 10 ARG A 141 0.11 SIDE CHAIN REMARK 500 10 ARG A 159 0.09 SIDE CHAIN REMARK 500 11 TYR A 158 0.08 SIDE CHAIN REMARK 500 13 ARG A 222 0.09 SIDE CHAIN REMARK 500 14 ARG A 170 0.10 SIDE CHAIN REMARK 500 15 ARG A 141 0.10 SIDE CHAIN REMARK 500 17 ARG A 222 0.08 SIDE CHAIN REMARK 500 19 ARG A 152 0.09 SIDE CHAIN REMARK 500 19 ARG A 200 0.09 SIDE CHAIN REMARK 500 20 TYR A 129 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F99 RELATED DB: PDB REMARK 900 FREE FORM REMARK 900 RELATED ID: 34219 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE MRH DOMAIN OF YOS9 COMPLEXED WITH ALPHA3, REMARK 900 ALPHA6-MAN5 DBREF1 6F9A A 90 249 UNP A0A250W9K2_YEASX DBREF2 6F9A A A0A250W9K2 90 249 SEQADV 6F9A GLY A 88 UNP A0A250W9K EXPRESSION TAG SEQADV 6F9A ALA A 89 UNP A0A250W9K EXPRESSION TAG SEQRES 1 A 162 GLY ALA SER ASN SER GLU LYS THR ALA LEU LEU THR LYS SEQRES 2 A 162 THR LEU ASN GLN GLY VAL LYS THR ILE PHE ASP LYS LEU SEQRES 3 A 162 ASN GLU ARG CYS ILE PHE TYR GLN ALA GLY PHE TRP ILE SEQRES 4 A 162 TYR GLU TYR CYS PRO GLY ILE GLU PHE VAL GLN PHE HIS SEQRES 5 A 162 GLY ARG VAL ASN THR LYS THR GLY GLU ILE VAL ASN ARG SEQRES 6 A 162 ASP GLU SER LEU VAL TYR ARG LEU GLY LYS PRO LYS ALA SEQRES 7 A 162 ASN VAL GLU GLU ARG GLU PHE GLU LEU LEU TYR ASP ASP SEQRES 8 A 162 VAL GLY TYR TYR ILE SER GLU ILE ILE GLY SER GLY ASP SEQRES 9 A 162 ILE CYS ASP VAL THR GLY ALA GLU ARG MET VAL GLU ILE SEQRES 10 A 162 GLN TYR VAL CYS GLY GLY SER ASN SER GLY PRO SER THR SEQRES 11 A 162 ILE GLN TRP VAL ARG GLU THR LYS ILE CYS VAL TYR GLU SEQRES 12 A 162 ALA GLN VAL THR ILE PRO GLU LEU CYS ASN LEU GLU LEU SEQRES 13 A 162 LEU ALA LYS ASN GLU ASP HELIX 1 AA1 ASN A 91 GLU A 115 1 25 HELIX 2 AA2 PRO A 236 ALA A 245 5 10 SHEET 1 AA1 4 ILE A 118 ALA A 122 0 SHEET 2 AA1 4 TRP A 125 TYR A 129 -1 O TYR A 129 N ILE A 118 SHEET 3 AA1 4 PHE A 135 HIS A 139 -1 O VAL A 136 N GLU A 128 SHEET 4 AA1 4 VAL A 157 GLY A 161 -1 O TYR A 158 N GLN A 137 SHEET 1 AA2 5 GLU A 173 TYR A 176 0 SHEET 2 AA2 5 TYR A 181 ILE A 187 -1 O SER A 184 N GLU A 173 SHEET 3 AA2 5 VAL A 202 CYS A 208 -1 O VAL A 202 N ILE A 187 SHEET 4 AA2 5 TYR A 229 ILE A 235 1 O VAL A 233 N VAL A 207 SHEET 5 AA2 5 THR A 217 ARG A 222 -1 N GLN A 219 O GLN A 232 SSBOND 1 CYS A 117 CYS A 130 1555 1555 2.05 SSBOND 2 CYS A 193 CYS A 227 1555 1555 2.01 SSBOND 3 CYS A 208 CYS A 239 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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