PDB Short entry for 2D21 HEADER SUGAR BINDING PROTEIN 02-SEP-05 2D21 TITLE NMR STRUCTURE OF STEREO-ARRAY ISOTOPE LABELLED (SAIL) MALTODEXTRIN- TITLE 2 BINDING PROTEIN (MBP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MALTODEXTRIN-BINDING PROTEIN, MMBP, MBP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS STEREO-ARRAY ISOTOPE LABELLING, SAIL, SUGAR BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.KAINOSHO,T.TORIZAWA,Y.IWASHITA,T.TERAUCHI,A.M.ONO,P.GUNTERT REVDAT 3 09-MAR-22 2D21 1 REMARK REVDAT 2 24-FEB-09 2D21 1 VERSN REVDAT 1 07-MAR-06 2D21 0 JRNL AUTH M.KAINOSHO,T.TORIZAWA,Y.IWASHITA,T.TERAUCHI,A.MEI ONO, JRNL AUTH 2 P.GUNTERT JRNL TITL OPTIMAL ISOTOPE LABELLING FOR NMR PROTEIN STRUCTURE JRNL TITL 2 DETERMINATIONS. JRNL REF NATURE V. 440 52 2006 JRNL REFN ISSN 0028-0836 JRNL PMID 16511487 JRNL DOI 10.1038/NATURE04525 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP 1.4 REMARK 3 AUTHORS : R.KORADI,M.BILLETER,P.GUNTERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D21 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000024890. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 20MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.33MM SAIL-MBP, 3.3MM BETA REMARK 210 -CYCLODEXTRIN, 20MM SODIUM REMARK 210 PHOSPHATE, 3MM NAN3, REMARK 210 COMPLETEMINI PROTEASE INHIBITOR REMARK 210 MIX REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, SPARKY 3.110 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 : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 OD2 ASP A 30 HH TYR A 283 1.59 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 3 ARG A 66 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 15 ARG A 354 NE - CZ - NH1 ANGL. DEV. = 3.1 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 THR A 80 75.73 60.08 REMARK 500 1 ALA A 96 0.75 -63.80 REMARK 500 1 ASN A 100 99.90 -68.21 REMARK 500 1 ILE A 108 -55.53 -121.58 REMARK 500 1 ALA A 112 71.82 -102.67 REMARK 500 1 ASN A 118 171.79 -58.04 REMARK 500 1 LEU A 121 36.16 -74.47 REMARK 500 1 ASN A 173 34.43 -67.02 REMARK 500 1 LYS A 202 9.80 59.22 REMARK 500 1 LYS A 251 102.38 -51.65 REMARK 500 1 PRO A 257 -77.51 -75.21 REMARK 500 1 ASN A 282 -35.51 -135.31 REMARK 500 1 TYR A 283 -39.19 -130.17 REMARK 500 2 ALA A 77 -161.57 -69.02 REMARK 500 2 THR A 80 82.20 61.77 REMARK 500 2 ILE A 108 -53.01 -130.07 REMARK 500 2 SER A 114 127.03 -179.57 REMARK 500 2 LEU A 122 70.24 -112.36 REMARK 500 2 PRO A 123 94.59 -67.64 REMARK 500 2 ALA A 146 -71.01 -91.89 REMARK 500 2 LYS A 202 1.56 55.38 REMARK 500 2 VAL A 244 117.18 -35.02 REMARK 500 2 MET A 330 83.96 38.58 REMARK 500 2 PRO A 331 85.71 -66.44 REMARK 500 3 LYS A 15 172.11 -58.35 REMARK 500 3 THR A 31 -35.16 -130.45 REMARK 500 3 THR A 80 93.91 56.22 REMARK 500 3 ILE A 108 -52.08 -134.42 REMARK 500 3 SER A 114 160.59 177.59 REMARK 500 3 LYS A 119 3.62 -69.36 REMARK 500 3 LEU A 122 71.61 45.22 REMARK 500 3 LYS A 142 11.27 -140.56 REMARK 500 3 ASN A 173 47.60 33.60 REMARK 500 3 LYS A 202 14.51 56.65 REMARK 500 3 THR A 225 -179.72 -173.23 REMARK 500 3 PRO A 229 -72.43 -70.11 REMARK 500 3 ALA A 231 -1.34 74.94 REMARK 500 3 ILE A 235 -49.82 -133.86 REMARK 500 3 THR A 237 -6.95 69.80 REMARK 500 3 TYR A 283 -32.37 -139.23 REMARK 500 3 LYS A 305 1.87 -61.10 REMARK 500 3 SER A 306 -67.75 -95.97 REMARK 500 3 MET A 330 75.84 35.40 REMARK 500 4 GLU A 3 89.93 -68.88 REMARK 500 4 ASP A 14 37.64 70.12 REMARK 500 4 THR A 31 -38.79 -130.60 REMARK 500 4 PRO A 57 -178.41 -65.23 REMARK 500 4 THR A 80 82.58 50.87 REMARK 500 4 ASN A 100 97.77 -63.43 REMARK 500 4 ILE A 108 -55.21 -133.05 REMARK 500 REMARK 500 THIS ENTRY HAS 327 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 TYR A 106 0.07 SIDE CHAIN REMARK 500 1 TYR A 117 0.09 SIDE CHAIN REMARK 500 2 ARG A 66 0.11 SIDE CHAIN REMARK 500 2 TYR A 242 0.07 SIDE CHAIN REMARK 500 2 ARG A 354 0.08 SIDE CHAIN REMARK 500 2 ARG A 367 0.10 SIDE CHAIN REMARK 500 4 PHE A 47 0.08 SIDE CHAIN REMARK 500 4 ARG A 66 0.10 SIDE CHAIN REMARK 500 4 TYR A 171 0.07 SIDE CHAIN REMARK 500 5 TYR A 167 0.07 SIDE CHAIN REMARK 500 6 TYR A 176 0.09 SIDE CHAIN REMARK 500 6 TYR A 210 0.09 SIDE CHAIN REMARK 500 6 ARG A 316 0.10 SIDE CHAIN REMARK 500 6 ARG A 344 0.08 SIDE CHAIN REMARK 500 6 ARG A 367 0.11 SIDE CHAIN REMARK 500 8 TYR A 155 0.08 SIDE CHAIN REMARK 500 9 TYR A 17 0.12 SIDE CHAIN REMARK 500 9 ARG A 98 0.09 SIDE CHAIN REMARK 500 9 PHE A 156 0.08 SIDE CHAIN REMARK 500 9 TYR A 171 0.08 SIDE CHAIN REMARK 500 9 TYR A 341 0.07 SIDE CHAIN REMARK 500 10 TYR A 171 0.08 SIDE CHAIN REMARK 500 11 ARG A 66 0.10 SIDE CHAIN REMARK 500 11 TYR A 90 0.07 SIDE CHAIN REMARK 500 11 TYR A 176 0.10 SIDE CHAIN REMARK 500 11 ARG A 316 0.08 SIDE CHAIN REMARK 500 12 ARG A 98 0.09 SIDE CHAIN REMARK 500 12 TYR A 176 0.07 SIDE CHAIN REMARK 500 13 ARG A 66 0.10 SIDE CHAIN REMARK 500 13 TYR A 106 0.08 SIDE CHAIN REMARK 500 13 ARG A 367 0.10 SIDE CHAIN REMARK 500 14 TYR A 17 0.10 SIDE CHAIN REMARK 500 14 ARG A 98 0.07 SIDE CHAIN REMARK 500 15 TYR A 90 0.08 SIDE CHAIN REMARK 500 16 TYR A 167 0.07 SIDE CHAIN REMARK 500 17 ARG A 66 0.08 SIDE CHAIN REMARK 500 17 TYR A 106 0.07 SIDE CHAIN REMARK 500 17 TYR A 117 0.07 SIDE CHAIN REMARK 500 17 TYR A 210 0.09 SIDE CHAIN REMARK 500 18 ARG A 316 0.12 SIDE CHAIN REMARK 500 19 TYR A 70 0.09 SIDE CHAIN REMARK 500 19 TYR A 106 0.09 SIDE CHAIN REMARK 500 20 ARG A 98 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2D21 A 1 370 UNP P0AEX9 MALE_ECOLI 27 396 SEQRES 1 A 370 LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN GLY SEQRES 2 A 370 ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS LYS SEQRES 3 A 370 PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU HIS SEQRES 4 A 370 PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA ALA SEQRES 5 A 370 THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS ASP SEQRES 6 A 370 ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA GLU SEQRES 7 A 370 ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR PRO SEQRES 8 A 370 PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU ILE SEQRES 9 A 370 ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE TYR SEQRES 10 A 370 ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP GLU SEQRES 11 A 370 GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS GLY SEQRES 12 A 370 LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR PHE SEQRES 13 A 370 THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA PHE SEQRES 14 A 370 LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL GLY SEQRES 15 A 370 VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE LEU SEQRES 16 A 370 VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP THR SEQRES 17 A 370 ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY GLU SEQRES 18 A 370 THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER ASN SEQRES 19 A 370 ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL LEU SEQRES 20 A 370 PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL GLY SEQRES 21 A 370 VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN LYS SEQRES 22 A 370 GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU THR SEQRES 23 A 370 ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO LEU SEQRES 24 A 370 GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU ALA SEQRES 25 A 370 LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA GLN SEQRES 26 A 370 LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER ALA SEQRES 27 A 370 PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA ALA SEQRES 28 A 370 SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP ALA SEQRES 29 A 370 GLN THR ARG ILE THR LYS HELIX 1 1 GLY A 16 GLY A 32 1 17 HELIX 2 2 LYS A 42 ALA A 51 1 10 HELIX 3 3 ALA A 52 GLY A 54 5 3 HELIX 4 4 HIS A 64 ALA A 71 1 8 HELIX 5 5 LYS A 83 LYS A 88 1 6 HELIX 6 6 TYR A 90 ALA A 96 1 7 HELIX 7 7 THR A 128 GLU A 130 5 3 HELIX 8 8 GLU A 131 ALA A 141 1 11 HELIX 9 9 GLU A 153 ALA A 162 1 10 HELIX 10 10 ASN A 185 ASN A 201 1 17 HELIX 11 11 ASP A 209 LYS A 219 1 11 HELIX 12 12 LYS A 273 GLU A 281 1 9 HELIX 13 13 GLU A 288 LYS A 297 1 10 HELIX 14 14 LEU A 304 ALA A 312 1 9 HELIX 15 15 ASP A 314 LYS A 326 1 13 HELIX 16 16 GLN A 335 SER A 352 1 18 HELIX 17 17 THR A 356 LYS A 370 1 15 SHEET 1 A 2 LYS A 6 TRP A 10 0 SHEET 2 A 2 LYS A 34 GLU A 38 1 O GLU A 38 N ILE A 9 SHEET 1 B 3 ILE A 59 ALA A 63 0 SHEET 2 B 3 LEU A 262 ILE A 266 -1 O GLY A 265 N ILE A 60 SHEET 3 B 3 TYR A 106 ALA A 109 -1 N ILE A 108 O LEU A 262 SHEET 1 C 2 ILE A 116 TYR A 117 0 SHEET 2 C 2 MET A 224 THR A 225 -1 O THR A 225 N ILE A 116 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