PDB Short entry for 2KLF HEADER TRANSPORT PROTEIN 02-JUL-09 2KLF TITLE PERE NMR STRUCTURE OF MALTODEXTRIN-BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MMBP, MALTODEXTRIN-BINDING PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B4034, JW3994, MALE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PMAL-C0 KEYWDS MALTOSE-BINDING PROTEIN, PARAMAGNETIC RELAXATION, GD(DTPA-BMA), SUGAR KEYWDS 2 TRANSPORT, TRANSPORT, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.MADL,W.BERMEL,K.ZANGGER REVDAT 4 10-NOV-21 2KLF 1 SEQADV REVDAT 3 13-JUL-11 2KLF 1 VERSN REVDAT 2 20-OCT-09 2KLF 1 JRNL REVDAT 1 06-OCT-09 2KLF 0 JRNL AUTH T.MADL,W.BERMEL,K.ZANGGER JRNL TITL USE OF RELAXATION ENHANCEMENTS IN A PARAMAGNETIC ENVIRONMENT JRNL TITL 2 FOR THE STRUCTURE DETERMINATION OF PROTEINS USING NMR JRNL TITL 3 SPECTROSCOPY JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 48 8259 2009 JRNL REFN ISSN 1433-7851 JRNL PMID 19774576 JRNL DOI 10.1002/ANIE.200902561 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PERE RESTRAINTS WERE INCORPORATED USING REMARK 3 LAB-WRITTEN SCRIPTS REMARK 4 REMARK 4 2KLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101266. 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 : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20MM POTASSIUM PHOSPHATE-1, 2MM REMARK 210 BETA-CYCLODEXTRIN-2, 3MM SODIUM REMARK 210 AZIDE-3, 100MM EDTA-4, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 CON; COCA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 PARAMAGNETIC ENVIRONMENT REMARK 210 RELAXATION ENHANCEMENT REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 H ALA A 77 O ASN A 267 1.32 REMARK 500 O LYS A 170 HA TYR A 176 1.34 REMARK 500 O GLU A 172 H GLY A 174 1.44 REMARK 500 O VAL A 293 H LYS A 297 1.49 REMARK 500 H ILE A 108 O LEU A 262 1.59 REMARK 500 O PHE A 149 O ASN A 150 1.76 REMARK 500 O TYR A 155 CG PRO A 159 1.89 REMARK 500 O GLU A 153 OG1 THR A 157 1.90 REMARK 500 N ALA A 77 O ASN A 267 1.98 REMARK 500 O GLU A 44 CD PRO A 48 2.03 REMARK 500 O TYR A 155 CD PRO A 159 2.05 REMARK 500 O ASN A 118 O LEU A 122 2.06 REMARK 500 O GLU A 172 N GLY A 174 2.07 REMARK 500 O PRO A 154 N PHE A 156 2.12 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 5 ILE A 266 C - N - CA ANGL. DEV. = 17.6 DEGREES REMARK 500 5 ILE A 266 N - CA - C ANGL. DEV. = -18.8 DEGREES REMARK 500 5 ILE A 266 CA - C - N ANGL. DEV. = 16.4 DEGREES REMARK 500 7 PRO A 123 C - N - CA ANGL. DEV. = 11.1 DEGREES REMARK 500 10 THR A 356 N - CA - C ANGL. DEV. = -16.5 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 ASP A 14 68.82 65.92 REMARK 500 1 LYS A 15 -172.28 162.64 REMARK 500 1 THR A 31 38.28 160.00 REMARK 500 1 LEU A 43 -45.97 -21.57 REMARK 500 1 ASP A 55 -64.94 -96.37 REMARK 500 1 PRO A 57 109.56 -49.83 REMARK 500 1 ASP A 58 113.36 159.27 REMARK 500 1 ALA A 63 151.64 -34.95 REMARK 500 1 LEU A 75 63.82 -179.02 REMARK 500 1 GLU A 78 100.09 -47.36 REMARK 500 1 ILE A 79 159.82 -47.66 REMARK 500 1 LYS A 83 -78.18 -120.10 REMARK 500 1 VAL A 97 54.13 -108.62 REMARK 500 1 ASN A 100 94.00 -48.05 REMARK 500 1 LEU A 103 130.61 168.34 REMARK 500 1 ALA A 105 175.77 165.22 REMARK 500 1 ILE A 108 38.40 -149.32 REMARK 500 1 ALA A 109 124.65 177.33 REMARK 500 1 LYS A 119 -87.98 -98.03 REMARK 500 1 ASP A 120 -63.67 -19.72 REMARK 500 1 LYS A 127 -10.06 -155.63 REMARK 500 1 ASN A 150 -169.77 -20.45 REMARK 500 1 LEU A 151 33.58 -168.64 REMARK 500 1 GLN A 152 33.99 172.05 REMARK 500 1 PRO A 154 -136.26 -77.27 REMARK 500 1 TYR A 155 -68.37 40.88 REMARK 500 1 ALA A 168 -80.07 -61.82 REMARK 500 1 ASN A 173 -64.31 44.28 REMARK 500 1 ASP A 177 -79.48 72.92 REMARK 500 1 ILE A 178 -41.37 168.66 REMARK 500 1 LYS A 202 -70.08 -99.72 REMARK 500 1 MET A 204 -77.10 61.68 REMARK 500 1 ALA A 206 36.44 -155.24 REMARK 500 1 MET A 224 137.28 167.69 REMARK 500 1 PRO A 229 69.73 -61.93 REMARK 500 1 TRP A 230 -59.60 -157.93 REMARK 500 1 ASN A 234 77.22 -100.50 REMARK 500 1 THR A 237 78.42 -64.49 REMARK 500 1 SER A 238 52.58 -113.14 REMARK 500 1 LYS A 239 112.97 61.63 REMARK 500 1 PRO A 248 -165.97 -79.44 REMARK 500 1 LYS A 251 31.11 36.93 REMARK 500 1 ASN A 267 -167.38 -13.52 REMARK 500 1 ALA A 269 -65.80 104.94 REMARK 500 1 SER A 270 103.07 155.46 REMARK 500 1 ASN A 272 74.19 26.76 REMARK 500 1 LEU A 285 42.24 -86.29 REMARK 500 1 LYS A 297 169.06 -47.57 REMARK 500 1 PRO A 298 -72.24 -90.67 REMARK 500 1 LEU A 299 -69.14 -156.31 REMARK 500 REMARK 500 THIS ENTRY HAS 527 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 ARG A 354 11.42 REMARK 500 3 ARG A 354 11.60 REMARK 500 4 ARG A 354 10.77 REMARK 500 5 ARG A 354 11.64 REMARK 500 7 ARG A 354 10.78 REMARK 500 8 ARG A 354 12.16 REMARK 500 9 ARG A 354 11.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KLG RELATED DB: PDB REMARK 900 PERE NMR STRUCTURE OF UBIQUITIN DBREF 2KLF A 1 370 UNP P0AEX9 MALE_ECOLI 27 396 SEQADV 2KLF THR A 2 UNP P0AEX9 ILE 28 ENGINEERED MUTATION SEQRES 1 A 370 LYS THR 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 GLY A 54 1 13 HELIX 3 3 HIS A 64 SER A 73 1 10 HELIX 4 4 LYS A 83 LYS A 88 1 6 HELIX 5 5 GLU A 130 ALA A 141 1 12 HELIX 6 6 PHE A 156 ALA A 163 1 8 HELIX 7 7 ASN A 185 LYS A 202 1 18 HELIX 8 8 ASP A 209 GLY A 220 1 12 HELIX 9 9 ASN A 272 TYR A 283 1 12 HELIX 10 10 GLU A 288 LYS A 297 1 10 HELIX 11 11 LEU A 304 LYS A 313 1 10 HELIX 12 12 ASP A 314 LYS A 326 1 13 HELIX 13 13 GLN A 335 GLY A 353 1 19 HELIX 14 14 THR A 356 LYS A 370 1 15 SHEET 1 A 5 VAL A 35 GLU A 38 0 SHEET 2 A 5 LEU A 7 ILE A 11 1 N LEU A 7 O THR A 36 SHEET 3 A 5 ILE A 59 ALA A 63 1 O ILE A 59 N VAL A 8 SHEET 4 A 5 PHE A 258 GLY A 265 -1 O SER A 263 N TRP A 62 SHEET 5 A 5 TYR A 106 GLU A 111 -1 N ILE A 108 O LEU A 262 SHEET 1 B 5 VAL A 35 GLU A 38 0 SHEET 2 B 5 LEU A 7 ILE A 11 1 N LEU A 7 O THR A 36 SHEET 3 B 5 ILE A 59 ALA A 63 1 O ILE A 59 N VAL A 8 SHEET 4 B 5 PHE A 258 GLY A 265 -1 O SER A 263 N TRP A 62 SHEET 5 B 5 GLU A 328 ILE A 329 1 O GLU A 328 N VAL A 259 SHEET 1 C 3 THR A 225 ASN A 227 0 SHEET 2 C 3 SER A 114 ASN A 118 -1 N SER A 114 O ASN A 227 SHEET 3 C 3 TYR A 242 THR A 245 -1 O THR A 245 N LEU A 115 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