HEADER BINDING PROTEIN 12-FEB-92 1DRI OBSLTE 26-JAN-95 1DRI 2DRI TITLE 1.7 ANGSTROMS X-RAY STRUCTURE OF THE PERIPLASMIC RIBOSE TITLE 2 RECEPTOR FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.L.MOWBRAY,L.B.COLE REVDAT 2 26-JAN-95 1DRI 3 OBSLTE REVDAT 1 31-OCT-93 1DRI 0 JRNL AUTH S.L.MOWBRAY,L.B.COLE JRNL TITL 1.7 ANGSTROMS X-RAY STRUCTURE OF THE PERIPLASMIC JRNL TITL 2 RIBOSE RECEPTOR FROM ESCHERICHIA COLI JRNL REF J.MOL.BIOL. V. 225 155 1992 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.L.MOWBRAY REMARK 1 TITL RIBOSE AND GLUCOSE-GALACTOSE RECEPTORS REMARK 1 REF J.MOL.BIOL. V. 227 418 1992 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.MAHENDROO,L.B.COLE,S.L.MOWBRAY REMARK 1 TITL PRELIMINARY X-RAY DATA FOR THE PERIPLASMIC RIBOSE REMARK 1 TITL 2 RECEPTOR FROM ESCHERICHIA COLI REMARK 1 REF J.MOL.BIOL. V. 211 689 1990 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 1DRI REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 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 : 27526 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : NULL 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 : 2465 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 648 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 2.53 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 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 1DRI COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1DRI CORRECTION. THIS ENTRY IS OBSOLETE. 26-JAN-95. 1DRI REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 37.46000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.13500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.13500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.46000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.49500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 THR 203 N - CA - C ANGL. DEV. =-17.1 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ASP 89 -37.85 66.71 REMARK 500 ASP 215 -38.47 132.50 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 88 DISTANCE = 5.23 ANGSTROMS REMARK 525 HOH 194 DISTANCE = 5.75 ANGSTROMS SEQRES 1 271 LYS ASP THR ILE ALA LEU VAL VAL SER THR LEU ASN ASN SEQRES 2 271 PRO PHE PHE VAL SER LEU LYS ASP GLY ALA GLN LYS GLU SEQRES 3 271 ALA ASP LYS LEU GLY TYR ASN LEU VAL VAL LEU ASP SER SEQRES 4 271 GLN ASN ASN PRO ALA LYS GLU LEU ALA ASN VAL GLN ASP SEQRES 5 271 LEU THR VAL ARG GLY THR LYS ILE LEU LEU ILE ASN PRO SEQRES 6 271 THR ASP SER ASP ALA VAL GLY ASN ALA VAL LYS MET ALA SEQRES 7 271 ASN GLN ALA ASN ILE PRO VAL ILE THR LEU ASP ARG GLN SEQRES 8 271 ALA THR LYS GLY GLU VAL VAL SER HIS ILE ALA SER ASP SEQRES 9 271 ASN VAL LEU GLY GLY LYS ILE ALA GLY ASP TYR ILE ALA SEQRES 10 271 LYS LYS ALA GLY GLU GLY ALA LYS VAL ILE GLU LEU GLN SEQRES 11 271 GLY ILE ALA GLY THR SER ALA ALA ARG GLU ARG GLY GLU SEQRES 12 271 GLY PHE GLN GLN ALA VAL ALA ALA HIS LYS PHE ASN VAL SEQRES 13 271 LEU ALA SER GLN PRO ALA ASP PHE ASP ARG ILE LYS GLY SEQRES 14 271 LEU ASN VAL MET GLN ASN LEU LEU THR ALA HIS PRO ASP SEQRES 15 271 VAL GLN ALA VAL PHE ALA GLN ASN ASP GLU MET ALA LEU SEQRES 16 271 GLY ALA LEU ARG ALA LEU GLN THR ALA GLY LYS SER ASP SEQRES 17 271 VAL MET VAL VAL GLY PHE ASP GLY THR PRO ASP GLY GLU SEQRES 18 271 LYS ALA VAL ASN ASP GLY LYS LEU ALA ALA THR ILE ALA SEQRES 19 271 GLN LEU PRO ASP GLN ILE GLY ALA LYS GLY VAL GLU THR SEQRES 20 271 ALA ASP LYS VAL LEU LYS GLY GLU LYS VAL GLN ALA LYS SEQRES 21 271 TYR PRO VAL ASP LEU LYS LEU VAL VAL LYS GLN HET RIP 300 20 HETNAM RIP RIBOSE(PYRANOSE FORM) FORMUL 2 RIP C5 H10 O5 FORMUL 3 HOH *216(H2 O1) HELIX 1 A PRO 14 LEU 30 1 17 HELIX 2 B PRO 43 LEU 53 1 11 HELIX 3 C' ASP 67 VAL 71 1ALPHA TURN 5 HELIX 4 C GLY 72 GLN 80 1 9 HELIX 5 D ASN 105 ALA 120 1 16 HELIX 6 E SER 136 HIS 152 1 17 HELIX 7 F ARG 166 ALA 179 1 14 HELIX 8 G ASP 191 ALA 204 1 14 HELIX 9 H PRO 218 ASN 225 1 8 HELIX 10 I PRO 237 LEU 252 1 16 SHEET 1 1 6 ASN 33 ASP 38 0 SHEET 2 1 6 THR 3 VAL 8 1 N ILE 4 O ASN 33 SHEET 3 1 6 ILE 60 ILE 63 1 N LEU 62 O ALA 5 SHEET 4 1 6 VAL 85 LEU 88 1 N ILE 86 O LEU 61 SHEET 5 1 6 SER 99 SER 103 1 N ILE 101 O THR 87 SHEET 6 1 6 LYS 260 VAL 263 1 N TYR 261 O HIS 100 SHEET 1 2 6 ASN 155 PRO 161 0 SHEET 2 2 6 LYS 125 GLN 130 1 N VAL 126 O ASN 155 SHEET 3 2 6 ALA 185 ALA 188 1 N ALA 185 O LYS 125 SHEET 4 2 6 MET 210 ASP 215 1 N MET 210 O ALA 185 SHEET 5 2 6 ALA 231 ALA 234 1 N ALA 231 O ASP 215 SHEET 6 2 6 LYS 266 VAL 268 -1 N LYS 266 O ALA 234 TURN 1 T1 LEU 11 ASN 13 INVERSE GAMMA CONFORMATION TURN 2 T2 SER 39 ASN 42 III' TURN 3 T3 LEU 88 ARG 90 GAMMA CONFORMATION TURN 4 T4 SER 103 ASN 105 INVERSE GAMMA CONFORMATION TURN 5 T5 GLY 121 ALA 124 II TURN 6 T6 ILE 132 THR 135 MIXTURE OF I AND II TURN 7 T7 ALA 162 ASP 165 III' TURN 8 T8 HIS 180 VAL 183 I TURN 9 T9 LYS 206 VAL 209 I (SOME DISORDER) SITE 1 RIB 10 ASN 13 PHE 15 PHE 16 ASP 89 SITE 2 RIB 10 ARG 90 ARG 141 PHE 164 ASN 190 SITE 3 RIB 10 ASP 215 GLN 235 CRYST1 74.920 88.990 40.270 90.00 90.00 90.00 P 21 21 21 4 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 0.013348 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024832 0.00000