HEADER SUGAR BINDING PROTEIN 28-MAY-08 2K46 TITLE XENOPUS LAEVIS MALECTIN COMPLEXED WITH NIGEROSE (GLCALPHA1-3GLC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MGC80075 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 27-213; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 GENE: MGC80075; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET-24D KEYWDS CARBOHYDRATE RECOGNITION DOMAIN, GLC2-HIGH-MANNOSE-N-GLYCAN, KEYWDS 2 NIGEROSE, SUGAR BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SCHALLUS REVDAT 4 01-MAY-24 2K46 1 HETSYN REVDAT 3 29-JUL-20 2K46 1 COMPND REMARK SEQADV HET REVDAT 3 2 1 HETNAM FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 24-FEB-09 2K46 1 VERSN REVDAT 1 12-AUG-08 2K46 0 JRNL AUTH T.SCHALLUS,C.JAECKH,K.FEHER,A.S.PALMA,Y.LIU,J.C.SIMPSON, JRNL AUTH 2 M.MACKEEN,G.STIER,T.J.GIBSON,T.FEIZI,T.PIELER,C.MUHLE-GOLL JRNL TITL MALECTIN: A NOVEL CARBOHYDRATE-BINDING PROTEIN OF THE JRNL TITL 2 ENDOPLASMIC RETICULUM AND A CANDIDATE PLAYER IN THE EARLY JRNL TITL 3 STEPS OF PROTEIN N-GLYCOSYLATION JRNL REF MOL.CELL.BIOL. V. 19 3404 2008 JRNL REFN ISSN 0270-7306 JRNL PMID 18524852 JRNL DOI 10.1091/MBC.E08-04-0354 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, ARIA 1.2, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA), BRUNGER, ADAMS, REMARK 3 CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ALPHA-NIGEROSE WAS ATTACHED TO MALECTIN REMARK 3 THROUGH 31 NOES IN THE COURSE OF THE CALCULATION. REMARK 4 REMARK 4 2K46 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000100653. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 MALECTIN, 90% H2O/10% D2O; 0.8 REMARK 210 MM [U-100% 13C; U-100% 15N] REMARK 210 MALECTIN, 100% D2O; 0.8 MM REMARK 210 MALECTIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 3D 1H-13C NOESY; 3D 1H-15N REMARK 210 NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 2 TYR A 61 CE1 TYR A 61 CZ 0.125 REMARK 500 2 TYR A 61 CZ TYR A 61 CE2 -0.136 REMARK 500 2 TYR A 83 CE1 TYR A 83 CZ -0.094 REMARK 500 2 TYR A 83 CZ TYR A 83 CE2 0.086 REMARK 500 5 TYR A 61 CE1 TYR A 61 CZ 0.083 REMARK 500 5 TYR A 61 CZ TYR A 61 CE2 -0.091 REMARK 500 9 TYR A 83 CE1 TYR A 83 CZ -0.099 REMARK 500 9 TYR A 83 CZ TYR A 83 CE2 0.089 REMARK 500 9 PHE A 89 CZ PHE A 89 CE2 0.139 REMARK 500 11 TYR A 61 CE1 TYR A 61 CZ 0.116 REMARK 500 11 TYR A 61 CZ TYR A 61 CE2 -0.128 REMARK 500 13 TYR A 83 CE1 TYR A 83 CZ -0.085 REMARK 500 13 TYR A 83 CZ TYR A 83 CE2 0.079 REMARK 500 14 TYR A 61 CE1 TYR A 61 CZ 0.154 REMARK 500 14 TYR A 61 CZ TYR A 61 CE2 -0.166 REMARK 500 15 TYR A 61 CE1 TYR A 61 CZ 0.146 REMARK 500 15 TYR A 61 CZ TYR A 61 CE2 -0.157 REMARK 500 15 TYR A 83 CE1 TYR A 83 CZ -0.097 REMARK 500 15 TYR A 83 CZ TYR A 83 CE2 0.089 REMARK 500 18 TYR A 61 CE1 TYR A 61 CZ 0.109 REMARK 500 18 TYR A 61 CZ TYR A 61 CE2 -0.120 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 ALA A 2 109.68 -166.26 REMARK 500 1 MET A 3 -52.55 -120.38 REMARK 500 1 TRP A 12 134.24 -173.00 REMARK 500 1 GLU A 19 119.36 -162.70 REMARK 500 1 SER A 20 90.25 33.19 REMARK 500 1 LYS A 31 140.49 -16.30 REMARK 500 1 ASP A 32 90.02 -18.71 REMARK 500 1 ARG A 37 24.89 43.46 REMARK 500 1 ASP A 43 54.32 37.27 REMARK 500 1 LEU A 48 64.54 69.20 REMARK 500 1 ARG A 52 36.42 -77.82 REMARK 500 1 TYR A 61 -7.03 -53.81 REMARK 500 1 GLN A 62 -130.65 -115.45 REMARK 500 1 THR A 63 158.38 49.59 REMARK 500 1 ASN A 67 -75.35 -104.96 REMARK 500 1 GLU A 68 -58.55 179.50 REMARK 500 1 ASP A 69 145.08 -175.98 REMARK 500 1 SER A 70 76.09 46.31 REMARK 500 1 GLU A 91 159.34 57.72 REMARK 500 1 VAL A 92 -4.44 -172.25 REMARK 500 1 TYR A 93 140.04 67.04 REMARK 500 1 PHE A 94 127.49 70.42 REMARK 500 1 GLN A 98 25.17 49.11 REMARK 500 1 LYS A 113 79.16 -105.29 REMARK 500 1 ASP A 114 35.44 156.49 REMARK 500 1 LEU A 115 93.28 -63.36 REMARK 500 1 SER A 124 -80.78 -35.26 REMARK 500 1 THR A 125 -164.14 44.02 REMARK 500 1 GLN A 143 -86.62 55.06 REMARK 500 1 TYR A 162 154.19 64.96 REMARK 500 1 ASP A 163 77.83 57.37 REMARK 500 1 PRO A 165 103.60 -29.86 REMARK 500 1 LYS A 166 -73.10 -53.00 REMARK 500 1 LEU A 170 129.86 -33.52 REMARK 500 1 THR A 176 158.73 178.21 REMARK 500 1 VAL A 180 100.24 -37.37 REMARK 500 1 PRO A 187 -158.06 -83.93 REMARK 500 2 TRP A 12 136.26 -173.26 REMARK 500 2 GLU A 19 119.15 -163.72 REMARK 500 2 SER A 20 96.58 38.73 REMARK 500 2 LYS A 31 139.44 -15.47 REMARK 500 2 ASP A 32 89.22 -15.54 REMARK 500 2 LEU A 34 -12.14 -142.91 REMARK 500 2 ARG A 40 -67.13 -144.55 REMARK 500 2 ALA A 41 86.28 -170.79 REMARK 500 2 ASP A 43 36.26 -85.56 REMARK 500 2 TYR A 44 108.08 -58.42 REMARK 500 2 LYS A 47 157.41 -38.25 REMARK 500 2 LEU A 48 62.28 66.66 REMARK 500 2 ARG A 52 32.66 -82.66 REMARK 500 REMARK 500 THIS ENTRY HAS 693 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 2 TYR A 29 0.06 SIDE CHAIN REMARK 500 2 PHE A 71 0.06 SIDE CHAIN REMARK 500 4 TYR A 29 0.05 SIDE CHAIN REMARK 500 5 TYR A 29 0.05 SIDE CHAIN REMARK 500 6 TYR A 29 0.06 SIDE CHAIN REMARK 500 8 PHE A 157 0.06 SIDE CHAIN REMARK 500 10 TYR A 29 0.07 SIDE CHAIN REMARK 500 13 TYR A 29 0.07 SIDE CHAIN REMARK 500 17 TYR A 29 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JWP RELATED DB: PDB DBREF 2K46 A 4 190 UNP Q6INX3 Q6INX3_XENLA 27 213 SEQADV 2K46 GLY A 1 UNP Q6INX3 EXPRESSION TAG SEQADV 2K46 ALA A 2 UNP Q6INX3 EXPRESSION TAG SEQADV 2K46 MET A 3 UNP Q6INX3 EXPRESSION TAG SEQRES 1 A 190 GLY ALA MET SER GLY LEU ALA ASP LYS VAL ILE TRP ALA SEQRES 2 A 190 VAL ASN ALA GLY GLY GLU SER HIS VAL ASP VAL HIS GLY SEQRES 3 A 190 ILE HIS TYR ARG LYS ASP PRO LEU GLU GLY ARG VAL GLY SEQRES 4 A 190 ARG ALA SER ASP TYR GLY MET LYS LEU PRO ILE LEU ARG SEQRES 5 A 190 SER ASN PRO GLU ASP GLN VAL LEU TYR GLN THR GLU ARG SEQRES 6 A 190 TYR ASN GLU ASP SER PHE GLY TYR ASP ILE PRO ILE LYS SEQRES 7 A 190 GLU GLU GLY GLU TYR VAL LEU VAL LEU LYS PHE ALA GLU SEQRES 8 A 190 VAL TYR PHE ALA GLN SER GLN GLN LYS VAL PHE ASP VAL SEQRES 9 A 190 ARG VAL ASN GLY HIS THR VAL VAL LYS ASP LEU ASP ILE SEQRES 10 A 190 PHE ASP ARG VAL GLY HIS SER THR ALA HIS ASP GLU ILE SEQRES 11 A 190 ILE PRO ILE SER ILE LYS LYS GLY LYS LEU SER VAL GLN SEQRES 12 A 190 GLY GLU VAL SER THR PHE THR GLY LYS LEU SER VAL GLU SEQRES 13 A 190 PHE VAL LYS GLY TYR TYR ASP ASN PRO LYS VAL CYS ALA SEQRES 14 A 190 LEU PHE ILE MET LYS GLY THR ALA ASP ASP VAL PRO MET SEQRES 15 A 190 LEU GLN PRO HIS PRO GLY LEU GLU HET GLC B 1 23 HET GLC B 2 22 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 2(C6 H12 O6) HELIX 1 1 ASN A 54 GLN A 62 1 9 HELIX 2 2 ASP A 116 GLY A 122 1 7 SHEET 1 A 6 VAL A 10 VAL A 14 0 SHEET 2 A 6 VAL A 167 GLY A 175 -1 O ILE A 172 N TRP A 12 SHEET 3 A 6 GLY A 81 ALA A 90 -1 N VAL A 86 O PHE A 171 SHEET 4 A 6 HIS A 127 LYS A 136 -1 O ILE A 135 N GLY A 81 SHEET 5 A 6 LYS A 139 VAL A 142 -1 O LYS A 139 N LYS A 136 SHEET 6 A 6 GLU A 145 THR A 148 -1 O SER A 147 N LEU A 140 SHEET 1 B 2 HIS A 21 ASP A 23 0 SHEET 2 B 2 ILE A 27 TYR A 29 -1 O TYR A 29 N HIS A 21 SHEET 1 C 4 PHE A 71 PRO A 76 0 SHEET 2 C 4 LYS A 152 VAL A 158 -1 O LEU A 153 N ILE A 75 SHEET 3 C 4 ASP A 103 VAL A 106 -1 N ARG A 105 O GLU A 156 SHEET 4 C 4 THR A 110 LYS A 113 -1 O VAL A 111 N VAL A 104 LINK O3 GLC B 1 C1 GLC B 2 1555 1555 1.44 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