HEADER SUGAR BINDING PROTEIN 29-OCT-02 1N3X TITLE LIGAND-FREE HIGH-AFFINITY MALTOSE-BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MALTODEXTRIN-BINDING PROTEIN, MBP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MALE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HS3309; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLH1DEL KEYWDS ENGINEERED MUTANT, MBPDEL-UNLIGANDED, MBPDEL, MBP, HIGH-AFFINITY, KEYWDS 2 CONFORMATIONAL ENGINEERING, MALTOSE-BINDING PROTEIN, SUGAR BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.G.TELMER,B.H.SHILTON REVDAT 5 14-FEB-24 1N3X 1 SEQADV REVDAT 4 11-OCT-17 1N3X 1 REMARK REVDAT 3 24-FEB-09 1N3X 1 VERSN REVDAT 2 09-SEP-03 1N3X 1 JRNL REVDAT 1 12-AUG-03 1N3X 0 JRNL AUTH P.G.TELMER,B.H.SHILTON JRNL TITL INSIGHTS INTO THE CONFORMATIONAL EQUILIBRIA OF JRNL TITL 2 MALTOSE-BINDING PROTEIN BY ANALYSIS OF HIGH AFFINITY JRNL TITL 3 MUTANTS. JRNL REF J.BIOL.CHEM. V. 278 34555 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12794084 JRNL DOI 10.1074/JBC.M301004200 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 8640970.300 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 12434 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1258 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1840 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 193 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2840 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.72000 REMARK 3 B22 (A**2) : 4.68000 REMARK 3 B33 (A**2) : -0.96000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.240 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.280 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.440 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 31.41 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 5 : MALTOSE.PARA REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESOLUTION-DEPENDENT WEIGHTING SCHEME REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1N3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017487. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5479 REMARK 200 MONOCHROMATOR : GRADED MULITLAYER (OSMIC) REMARK 200 OPTICS : OTHER REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 23.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1OMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 35.66500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: 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 ASP A 30 32.00 -94.96 REMARK 500 THR A 31 -30.53 -147.88 REMARK 500 ASP A 55 -164.39 -114.05 REMARK 500 ILE A 108 -64.76 -127.24 REMARK 500 ALA A 168 -84.32 -81.09 REMARK 500 TYR A 171 68.07 9.42 REMARK 500 ASP A 177 104.99 -38.08 REMARK 500 ASP A 209 -167.67 -120.78 REMARK 500 TYR A 283 -57.67 -124.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N3W RELATED DB: PDB REMARK 900 RELATED ID: 1NL5 RELATED DB: PDB REMARK 900 RELATED ID: 1PEB RELATED DB: PDB DBREF 1N3X A 1 370 UNP P02928 MALE_ECOLI 27 396 SEQADV 1N3X A UNP P02928 GLU 198 DELETION SEQADV 1N3X A UNP P02928 ASN 199 DELETION SEQADV 1N3X A UNP P02928 LYS 201 DELETION SEQADV 1N3X A UNP P02928 TYR 202 DELETION SEQRES 1 A 366 LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN GLY SEQRES 2 A 366 ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS LYS SEQRES 3 A 366 PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU HIS SEQRES 4 A 366 PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA ALA SEQRES 5 A 366 THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS ASP SEQRES 6 A 366 ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA GLU SEQRES 7 A 366 ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR PRO SEQRES 8 A 366 PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU ILE SEQRES 9 A 366 ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE TYR SEQRES 10 A 366 ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP GLU SEQRES 11 A 366 GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS GLY SEQRES 12 A 366 LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR PHE SEQRES 13 A 366 THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA PHE SEQRES 14 A 366 LYS TYR GLY ASP ILE LYS ASP VAL GLY VAL ASP ASN ALA SEQRES 15 A 366 GLY ALA LYS ALA GLY LEU THR PHE LEU VAL ASP LEU ILE SEQRES 16 A 366 LYS ASN LYS HIS MET ASN ALA ASP THR ASP TYR SER ILE SEQRES 17 A 366 ALA GLU ALA ALA PHE ASN LYS GLY GLU THR ALA MET THR SEQRES 18 A 366 ILE ASN GLY PRO TRP ALA TRP SER ASN ILE ASP THR SER SEQRES 19 A 366 LYS VAL ASN TYR GLY VAL THR VAL LEU PRO THR PHE LYS SEQRES 20 A 366 GLY GLN PRO SER LYS PRO PHE VAL GLY VAL LEU SER ALA SEQRES 21 A 366 GLY ILE ASN ALA ALA SER PRO ASN LYS GLU LEU ALA LYS SEQRES 22 A 366 GLU PHE LEU GLU ASN TYR LEU LEU THR ASP GLU GLY LEU SEQRES 23 A 366 GLU ALA VAL ASN LYS ASP LYS PRO LEU GLY ALA VAL ALA SEQRES 24 A 366 LEU LYS SER TYR GLU GLU GLU LEU ALA LYS ASP PRO ARG SEQRES 25 A 366 ILE ALA ALA THR MET GLU ASN ALA GLN LYS GLY GLU ILE SEQRES 26 A 366 MET PRO ASN ILE PRO GLN MET SER ALA PHE TRP TYR ALA SEQRES 27 A 366 VAL ARG THR ALA VAL ILE ASN ALA ALA SER GLY ARG GLN SEQRES 28 A 366 THR VAL ASP GLU ALA LEU LYS ASP ALA GLN THR ARG ILE SEQRES 29 A 366 THR LYS HELIX 1 1 GLY A 16 ASP A 30 1 15 HELIX 2 2 LYS A 42 ALA A 52 1 11 HELIX 3 3 ARG A 66 SER A 73 1 8 HELIX 4 4 ASP A 82 ASP A 87 1 6 HELIX 5 5 TYR A 90 ASP A 95 1 6 HELIX 6 6 GLU A 131 ALA A 141 1 11 HELIX 7 7 GLU A 153 ASP A 164 1 12 HELIX 8 8 ASN A 185 ASN A 201 1 17 HELIX 9 9 ASP A 209 LYS A 219 1 11 HELIX 10 10 GLY A 228 TRP A 230 5 3 HELIX 11 11 ALA A 231 SER A 238 1 8 HELIX 12 12 ASN A 272 TYR A 283 1 12 HELIX 13 13 THR A 286 LYS A 297 1 12 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 6 ALA A 301 VAL A 302 0 SHEET 2 A 6 TYR A 106 GLU A 111 -1 N VAL A 110 O ALA A 301 SHEET 3 A 6 PHE A 258 ILE A 266 -1 O GLY A 260 N GLU A 111 SHEET 4 A 6 ILE A 59 ALA A 63 -1 N TRP A 62 O SER A 263 SHEET 5 A 6 LEU A 7 TRP A 10 1 N TRP A 10 O PHE A 61 SHEET 6 A 6 VAL A 35 GLU A 38 1 O THR A 36 N ILE A 9 SHEET 1 B 4 ALA A 301 VAL A 302 0 SHEET 2 B 4 TYR A 106 GLU A 111 -1 N VAL A 110 O ALA A 301 SHEET 3 B 4 PHE A 258 ILE A 266 -1 O GLY A 260 N GLU A 111 SHEET 4 B 4 GLU A 328 ILE A 329 1 O GLU A 328 N VAL A 259 SHEET 1 C 2 ARG A 98 TYR A 99 0 SHEET 2 C 2 LYS A 102 LEU A 103 -1 O LYS A 102 N TYR A 99 SHEET 1 D 4 SER A 145 LEU A 147 0 SHEET 2 D 4 THR A 222 ASN A 227 1 O ALA A 223 N SER A 145 SHEET 3 D 4 SER A 114 ASN A 118 -1 N ILE A 116 O THR A 225 SHEET 4 D 4 TYR A 242 THR A 245 -1 O THR A 245 N LEU A 115 SHEET 1 E 2 TYR A 167 PHE A 169 0 SHEET 2 E 2 VAL A 181 GLY A 182 -1 O GLY A 182 N TYR A 167 SHEET 1 F 2 THR A 249 PHE A 250 0 SHEET 2 F 2 GLN A 253 PRO A 254 -1 O GLN A 253 N PHE A 250 CRYST1 44.590 71.330 59.010 90.00 101.53 90.00 P 1 21 1 2 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 0.022427 0.000000 0.004575 0.00000 SCALE2 0.000000 0.014019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017295 0.00000