HEADER SUGAR BINDING PROTEIN 04-SEP-00 1FQB
TITLE STRUCTURE OF MALTOTRIOTOL BOUND TO OPEN-FORM MALTODEXTRIN BINDING
TITLE 2 PROTEIN IN P2(1)CRYSTAL FORM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MALTODEXTRIN-BINDING PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: MALTOSE-BINDING PERIPLASMIC PROTEIN, MMBP;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS SUGAR-BINDING PROTEIN, MALTOTRIOTAL, SUGAR BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR X.DUAN,J.A.HALL,H.NIKAIDO,F.A.QUIOCHO
REVDAT 4 07-FEB-24 1FQB 1 HETSYN
REVDAT 3 29-JUL-20 1FQB 1 COMPND REMARK HETNAM LINK
REVDAT 3 2 1 SITE ATOM
REVDAT 2 24-FEB-09 1FQB 1 VERSN
REVDAT 1 14-MAR-01 1FQB 0
JRNL AUTH X.DUAN,J.A.HALL,H.NIKAIDO,F.A.QUIOCHO
JRNL TITL CRYSTAL STRUCTURES OF THE MALTODEXTRIN/MALTOSE-BINDING
JRNL TITL 2 PROTEIN COMPLEXED WITH REDUCED OLIGOSACCHARIDES: FLEXIBILITY
JRNL TITL 3 OF TERTIARY STRUCTURE AND LIGAND BINDING.
JRNL REF J.MOL.BIOL. V. 306 1115 2001
JRNL REFN ISSN 0022-2836
JRNL PMID 11237621
JRNL DOI 10.1006/JMBI.2001.4456
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 21467
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) : 0.162
REMARK 3 FREE R VALUE : 0.218
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2874
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 34
REMARK 3 SOLVENT ATOMS : 562
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1FQB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-00.
REMARK 100 THE DEPOSITION ID IS D_1000011814.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 200
REMARK 200 PH : 6.6
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 RU200
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21467
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 86.7
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.03700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98
REMARK 200 COMPLETENESS FOR SHELL (%) : 56.4
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.09800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.74
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NAN3, MES, PH 6.6, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 273K
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 32.65000
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, 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: 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 ILE A 2 120.39 51.44
REMARK 500 GLU A 172 -90.38 -74.70
REMARK 500 ASP A 184 60.60 -102.46
REMARK 500 ASP A 209 -167.04 -120.05
REMARK 500 LYS A 239 -6.86 82.34
REMARK 500 TYR A 283 -53.63 -122.59
REMARK 500 ALA A 312 -8.75 -57.57
REMARK 500 ASN A 332 30.27 -95.23
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1OMP RELATED DB: PDB
REMARK 900 STRUCTURE OF UNLIGANDED MALTODEXTRIN-BINDING PROTEIN
REMARK 900 RELATED ID: 1ANF RELATED DB: PDB
REMARK 900 STRUCTURE OF MALTOSE BOUND TO CLOSED-FORM MALTODEXTRIN-BINDING
REMARK 900 PROTEIN
DBREF 1FQB A 1 370 UNP P02928 MALE_ECOLI 27 396
SEQADV 1FQB ALA A 1 UNP P02928 LYS 27 CLONING ARTIFACT
SEQRES 1 A 370 ALA 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
HET SOR B 1 12
HET GLC B 2 11
HET GLC B 3 11
HETNAM SOR SORBITOL
HETNAM GLC ALPHA-D-GLUCOPYRANOSE
HETSYN SOR D-SORBITOL; D-GLUCITOL
HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE
FORMUL 2 SOR C6 H14 O6
FORMUL 2 GLC 2(C6 H12 O6)
FORMUL 3 HOH *562(H2 O)
HELIX 1 1 GLY A 16 GLY A 32 1 17
HELIX 2 2 LYS A 42 ALA A 52 1 11
HELIX 3 3 ASP A 65 SER A 73 1 9
HELIX 4 4 ASP A 82 ASP A 87 1 6
HELIX 5 5 TYR A 90 ALA A 96 1 7
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 ALA A 231 5 4
HELIX 11 11 TRP A 232 THR A 237 1 6
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 GLY A 327 1 14
HELIX 16 16 PRO A 334 GLY A 353 1 20
HELIX 17 17 THR A 356 THR A 369 1 14
SHEET 1 A 5 VAL A 35 GLU A 38 0
SHEET 2 A 5 LEU A 7 TRP A 10 1 O LEU A 7 N THR A 36
SHEET 3 A 5 ILE A 59 ALA A 63 1 O ILE A 59 N TRP A 10
SHEET 4 A 5 LEU A 262 ILE A 266 -1 N SER A 263 O TRP A 62
SHEET 5 A 5 TYR A 106 PRO A 107 -1 N TYR A 106 O ALA A 264
SHEET 1 B 2 ARG A 98 TYR A 99 0
SHEET 2 B 2 LYS A 102 LEU A 103 -1 O LYS A 102 N TYR A 99
SHEET 1 C 2 ALA A 109 VAL A 110 0
SHEET 2 C 2 ALA A 301 VAL A 302 -1 O ALA A 301 N VAL A 110
SHEET 1 D 4 SER A 145 LEU A 147 0
SHEET 2 D 4 THR A 222 ASN A 227 1 N ALA A 223 O SER A 145
SHEET 3 D 4 SER A 114 ASN A 118 -1 N SER A 114 O ASN A 227
SHEET 4 D 4 TYR A 242 THR A 245 -1 N GLY A 243 O TYR A 117
SHEET 1 E 2 LYS A 170 TYR A 171 0
SHEET 2 E 2 TYR A 176 ASP A 177 -1 N ASP A 177 O LYS A 170
SHEET 1 F 2 PHE A 258 VAL A 259 0
SHEET 2 F 2 GLU A 328 ILE A 329 1 O GLU A 328 N VAL A 259
LINK O4 SOR B 1 C1 GLC B 2 1555 1555 1.40
LINK O4 GLC B 2 C1 GLC B 3 1555 1555 1.40
CRYST1 43.800 65.300 57.300 90.00 101.00 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 0.022831 0.000000 0.004438 0.00000
SCALE2 0.000000 0.015314 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017779 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
