PDB Short entry for 2JWP HEADER SUGAR BINDING PROTEIN 23-OCT-07 2JWP TITLE MALECTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 28-201; COMPND 5 SYNONYM: MGC80075; COMPND 6 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_VECTOR_TYPE: VECTOR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET24D KEYWDS LECTIN, SUGAR BINDING, SUGAR BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.SCHALLUS,C.MUHLE-GOLL REVDAT 3 16-MAR-22 2JWP 1 REMARK REVDAT 2 24-FEB-09 2JWP 1 VERSN REVDAT 1 12-AUG-08 2JWP 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 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JWP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000100385. 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 : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 MALECTIN, 90% H2O/10% D2O; 0.5 REMARK 210 MM [U-100% 13C; U-100% 15N] REMARK 210 MALECTIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 OE2 GLU A 91 HZ3 LYS A 100 1.53 REMARK 500 OD2 ASP A 69 HZ3 LYS A 159 1.56 REMARK 500 HG SER A 53 OD2 ASP A 57 1.60 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 3 TYR A 162 CE1 TYR A 162 CZ -0.082 REMARK 500 4 TYR A 29 CE1 TYR A 29 CZ 0.122 REMARK 500 4 TYR A 29 CZ TYR A 29 CE2 -0.115 REMARK 500 7 TYR A 29 CE1 TYR A 29 CZ 0.097 REMARK 500 7 TYR A 29 CZ TYR A 29 CE2 -0.082 REMARK 500 8 TYR A 61 CE1 TYR A 61 CZ 0.092 REMARK 500 8 TYR A 61 CZ TYR A 61 CE2 -0.098 REMARK 500 9 PHE A 71 CE1 PHE A 71 CZ 0.128 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 TRP A 12 146.07 -170.54 REMARK 500 1 SER A 20 90.09 35.31 REMARK 500 1 LYS A 31 96.33 -38.96 REMARK 500 1 ASP A 32 78.25 30.22 REMARK 500 1 ALA A 41 107.53 -56.71 REMARK 500 1 SER A 42 50.10 -102.96 REMARK 500 1 ASP A 43 -74.19 -56.72 REMARK 500 1 TYR A 44 -63.20 68.85 REMARK 500 1 LEU A 48 79.54 -116.51 REMARK 500 1 LEU A 51 -52.99 69.26 REMARK 500 1 ARG A 65 -157.54 -106.22 REMARK 500 1 GLU A 68 -59.93 -143.31 REMARK 500 1 TYR A 93 -69.52 -150.37 REMARK 500 1 GLN A 99 -50.52 -138.08 REMARK 500 1 THR A 110 96.61 -68.52 REMARK 500 1 LYS A 113 76.50 -103.85 REMARK 500 1 ASP A 114 14.03 162.43 REMARK 500 1 LEU A 115 98.29 -66.47 REMARK 500 1 SER A 124 97.50 -59.92 REMARK 500 1 GLN A 143 -82.37 64.17 REMARK 500 1 TYR A 162 -71.58 65.05 REMARK 500 1 ASN A 164 -165.11 -110.14 REMARK 500 1 PRO A 165 96.29 -42.10 REMARK 500 1 ALA A 169 36.49 -80.00 REMARK 500 1 LEU A 170 120.48 -35.92 REMARK 500 2 TRP A 12 119.97 -166.40 REMARK 500 2 SER A 20 86.96 34.61 REMARK 500 2 LYS A 31 103.92 70.18 REMARK 500 2 PRO A 33 -153.23 -107.48 REMARK 500 2 LEU A 34 -71.76 84.18 REMARK 500 2 ARG A 37 66.33 -67.32 REMARK 500 2 PRO A 55 -39.54 -39.22 REMARK 500 2 GLN A 62 -124.55 -124.44 REMARK 500 2 THR A 63 104.05 29.04 REMARK 500 2 TYR A 66 -160.79 57.45 REMARK 500 2 GLU A 68 -164.29 -78.59 REMARK 500 2 GLN A 99 -49.51 -148.63 REMARK 500 2 THR A 110 98.98 -66.64 REMARK 500 2 LYS A 113 71.74 -113.16 REMARK 500 2 ASP A 114 30.20 162.66 REMARK 500 2 SER A 124 -121.63 51.77 REMARK 500 2 THR A 125 -161.41 52.32 REMARK 500 2 GLN A 143 -85.98 58.77 REMARK 500 2 TYR A 161 -72.34 -68.41 REMARK 500 2 TYR A 162 -48.39 -175.47 REMARK 500 2 LYS A 166 -39.82 88.42 REMARK 500 2 ALA A 169 38.59 -87.64 REMARK 500 2 LEU A 170 131.91 -31.00 REMARK 500 3 SER A 20 109.27 36.31 REMARK 500 3 ASP A 32 106.09 -45.80 REMARK 500 REMARK 500 THIS ENTRY HAS 251 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 3 PHE A 71 0.07 SIDE CHAIN REMARK 500 4 TYR A 29 0.07 SIDE CHAIN REMARK 500 4 TYR A 66 0.06 SIDE CHAIN REMARK 500 5 PHE A 157 0.09 SIDE CHAIN REMARK 500 7 TYR A 29 0.08 SIDE CHAIN REMARK 500 7 PHE A 71 0.07 SIDE CHAIN REMARK 500 8 PHE A 71 0.06 SIDE CHAIN REMARK 500 9 PHE A 71 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2JWP A 5 178 UNP Q6INX3 Q6INX3_XENLA 28 201 SEQRES 1 A 174 GLY LEU ALA ASP LYS VAL ILE TRP ALA VAL ASN ALA GLY SEQRES 2 A 174 GLY GLU SER HIS VAL ASP VAL HIS GLY ILE HIS TYR ARG SEQRES 3 A 174 LYS ASP PRO LEU GLU GLY ARG VAL GLY ARG ALA SER ASP SEQRES 4 A 174 TYR GLY MET LYS LEU PRO ILE LEU ARG SER ASN PRO GLU SEQRES 5 A 174 ASP GLN VAL LEU TYR GLN THR GLU ARG TYR ASN GLU ASP SEQRES 6 A 174 SER PHE GLY TYR ASP ILE PRO ILE LYS GLU GLU GLY GLU SEQRES 7 A 174 TYR VAL LEU VAL LEU LYS PHE ALA GLU VAL TYR PHE ALA SEQRES 8 A 174 GLN SER GLN GLN LYS VAL PHE ASP VAL ARG VAL ASN GLY SEQRES 9 A 174 HIS THR VAL VAL LYS ASP LEU ASP ILE PHE ASP ARG VAL SEQRES 10 A 174 GLY HIS SER THR ALA HIS ASP GLU ILE ILE PRO ILE SER SEQRES 11 A 174 ILE LYS LYS GLY LYS LEU SER VAL GLN GLY GLU VAL SER SEQRES 12 A 174 THR PHE THR GLY LYS LEU SER VAL GLU PHE VAL LYS GLY SEQRES 13 A 174 TYR TYR ASP ASN PRO LYS VAL CYS ALA LEU PHE ILE MET SEQRES 14 A 174 LYS GLY THR ALA ASP HELIX 1 1 GLY A 5 LYS A 9 1 5 HELIX 2 2 ASN A 54 LEU A 60 1 7 HELIX 3 3 ASP A 116 GLY A 122 1 7 SHEET 1 A 6 VAL A 10 ALA A 16 0 SHEET 2 A 6 VAL A 167 MET A 173 -1 O LEU A 170 N VAL A 14 SHEET 3 A 6 GLY A 81 ALA A 90 -1 N LYS A 88 O ALA A 169 SHEET 4 A 6 HIS A 127 LYS A 136 -1 O ILE A 133 N TYR A 83 SHEET 5 A 6 LYS A 139 VAL A 142 -1 O SER A 141 N SER A 134 SHEET 6 A 6 GLU A 145 THR A 148 -1 O GLU A 145 N VAL A 142 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 PHE A 102 VAL A 106 -1 N ASP A 103 O VAL A 158 SHEET 4 C 4 HIS A 109 LEU A 115 -1 O HIS A 109 N VAL A 106 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