PDB Short entry for 1DBP HEADER BINDING PROTEIN 31-JAN-94 1DBP TITLE IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS TITLE 2 PROTEINS WITH NON-IDENTICAL EFFECTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-RIBOSE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.L.MOWBRAY,A.J.JOAKIM BJORKMAN REVDAT 7 07-FEB-24 1DBP 1 HETSYN REVDAT 6 29-JUL-20 1DBP 1 COMPND REMARK SEQADV HETNAM REVDAT 6 2 1 SITE REVDAT 5 29-NOV-17 1DBP 1 HELIX REVDAT 4 24-FEB-09 1DBP 1 VERSN REVDAT 3 01-APR-03 1DBP 1 JRNL REVDAT 2 15-OCT-94 1DBP 1 JRNL REMARK REVDAT 1 31-MAY-94 1DBP 0 JRNL AUTH A.J.BJORKMAN,R.A.BINNIE,L.B.COLE,H.ZHANG,M.A.HERMODSON, JRNL AUTH 2 S.L.MOWBRAY JRNL TITL IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO JRNL TITL 2 HOMOLOGOUS PROTEINS WITH NONIDENTICAL EFFECTS. JRNL REF J.BIOL.CHEM. V. 269 11196 1994 JRNL REFN ISSN 0021-9258 JRNL PMID 8157648 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.L.MOWBRAY,L.B.COLE REMARK 1 TITL THE 1.7 ANGSTROMS X-RAY STRUCTURE OF THE PERIPLASMIC RIBOSE REMARK 1 TITL 2 RECEPTOR FROM ESCHERICHIA COLI REMARK 1 REF J.MOL.BIOL. V. 225 155 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.A.BINNIE,H.ZHANG,S.MOWBRAY,M.A.HERMODSON REMARK 1 TITL FUNCTIONAL MAPPING OF THE SURFACE OF ESCHERICHIA COLI REMARK 1 TITL 2 RIBOSE-BINDING PROTEIN: MUTATIONS WHICH AFFECT CHEMOTAXIS REMARK 1 TITL 3 AND TRANSPORT REMARK 1 REF PROTEIN SCI. V. 1 1642 1992 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.MAHENDROO,L.B.COLE,S.L.MOWBRAY REMARK 1 TITL PRELIMINARY X-RAY DATA FOR THE PERIPLASMIC RIBOSE RECEPTOR REMARK 1 TITL 2 FROM ESCHERICHIA COLI REMARK 1 REF J.MOL.BIOL. V. 211 689 1990 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 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 : 12184 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) : 0.160 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 : 2006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 166 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.070 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 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 1DBP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172723. 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 <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) : 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 37.42000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.42000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.44000 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 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 IN SAME ASYMMETRIC UNIT 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 HZ2 LYS A 20 H1 HOH A 305 1.26 REMARK 500 H VAL A 85 H2 HOH A 290 1.28 REMARK 500 HH22 ARG A 141 HO2 RIP A 272 1.29 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 ASN A 12 49.25 -90.35 REMARK 500 ASN A 13 119.82 -162.32 REMARK 500 ASP A 89 -45.01 73.86 REMARK 500 LYS A 94 -151.94 -126.22 REMARK 500 LYS A 119 -62.56 -101.14 REMARK 500 PHE A 164 19.17 56.55 REMARK 500 ASP A 215 -43.18 125.35 REMARK 500 LEU A 236 73.22 -118.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: RIB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RIBOSE BINDING SITE REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE REMARK 999 DIFFERENCE BETWEEN SWISS-PROT:RBSB_ECOLI AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT PDB SEQRES COMMENT REMARK 999 REMARK 999 GLY 97 ASP 72 MUTATION POINT DBREF 1DBP A 1 271 UNP P02925 RBSB_ECOLI 26 296 SEQADV 1DBP ASP A 72 UNP P02925 GLY 97 CONFLICT SEQRES 1 A 271 LYS ASP THR ILE ALA LEU VAL VAL SER THR LEU ASN ASN SEQRES 2 A 271 PRO PHE PHE VAL SER LEU LYS ASP GLY ALA GLN LYS GLU SEQRES 3 A 271 ALA ASP LYS LEU GLY TYR ASN LEU VAL VAL LEU ASP SER SEQRES 4 A 271 GLN ASN ASN PRO ALA LYS GLU LEU ALA ASN VAL GLN ASP SEQRES 5 A 271 LEU THR VAL ARG GLY THR LYS ILE LEU LEU ILE ASN PRO SEQRES 6 A 271 THR ASP SER ASP ALA VAL ASP ASN ALA VAL LYS MET ALA SEQRES 7 A 271 ASN GLN ALA ASN ILE PRO VAL ILE THR LEU ASP ARG GLN SEQRES 8 A 271 ALA THR LYS GLY GLU VAL VAL SER HIS ILE ALA SER ASP SEQRES 9 A 271 ASN VAL LEU GLY GLY LYS ILE ALA GLY ASP TYR ILE ALA SEQRES 10 A 271 LYS LYS ALA GLY GLU GLY ALA LYS VAL ILE GLU LEU GLN SEQRES 11 A 271 GLY ILE ALA GLY THR SER ALA ALA ARG GLU ARG GLY GLU SEQRES 12 A 271 GLY PHE GLN GLN ALA VAL ALA ALA HIS LYS PHE ASN VAL SEQRES 13 A 271 LEU ALA SER GLN PRO ALA ASP PHE ASP ARG ILE LYS GLY SEQRES 14 A 271 LEU ASN VAL MET GLN ASN LEU LEU THR ALA HIS PRO ASP SEQRES 15 A 271 VAL GLN ALA VAL PHE ALA GLN ASN ASP GLU MET ALA LEU SEQRES 16 A 271 GLY ALA LEU ARG ALA LEU GLN THR ALA GLY LYS SER ASP SEQRES 17 A 271 VAL MET VAL VAL GLY PHE ASP GLY THR PRO ASP GLY GLU SEQRES 18 A 271 LYS ALA VAL ASN ASP GLY LYS LEU ALA ALA THR ILE ALA SEQRES 19 A 271 GLN LEU PRO ASP GLN ILE GLY ALA LYS GLY VAL GLU THR SEQRES 20 A 271 ALA ASP LYS VAL LEU LYS GLY GLU LYS VAL GLN ALA LYS SEQRES 21 A 271 TYR PRO VAL ASP LEU LYS LEU VAL VAL LYS GLN HET RIP A 272 20 HETNAM RIP BETA-D-RIBOPYRANOSE HETSYN RIP BETA-D-RIBOSE; D-RIBOSE; RIBOSE; RIBOSE(PYRANOSE FORM) FORMUL 2 RIP C5 H10 O5 FORMUL 3 HOH *166(H2 O) HELIX 1 A PRO A 14 LEU A 30 1 17 HELIX 2 B PRO A 43 LEU A 53 1 11 HELIX 3 C' ASP A 67 VAL A 71 1ALPHA TURN 5 HELIX 4 C ASP A 72 GLN A 80 1 9 HELIX 5 D ASN A 105 ALA A 120 1 16 HELIX 6 E SER A 136 HIS A 152 1 17 HELIX 7 F ARG A 166 ALA A 179 1 14 HELIX 8 G ASP A 191 ALA A 204 1 14 HELIX 9 H PRO A 218 ASN A 225 1 8 HELIX 10 I PRO A 237 LEU A 252 1 16 SHEET 1 S1 6 ASN A 33 ASP A 38 0 SHEET 2 S1 6 THR A 3 VAL A 8 1 N ILE A 4 O ASN A 33 SHEET 3 S1 6 ILE A 60 ILE A 63 1 N LEU A 62 O ALA A 5 SHEET 4 S1 6 VAL A 85 LEU A 88 1 N ILE A 86 O LEU A 61 SHEET 5 S1 6 SER A 99 SER A 103 1 N ILE A 101 O THR A 87 SHEET 6 S1 6 LYS A 260 VAL A 263 1 N TYR A 261 O HIS A 100 SHEET 1 S2 6 ASN A 155 PRO A 161 0 SHEET 2 S2 6 LYS A 125 GLN A 130 1 N VAL A 126 O ASN A 155 SHEET 3 S2 6 GLN A 184 ALA A 188 1 N ALA A 185 O LYS A 125 SHEET 4 S2 6 MET A 210 ASP A 215 1 N MET A 210 O GLN A 184 SHEET 5 S2 6 ALA A 231 GLN A 235 1 N GLN A 235 O ASP A 215 SHEET 6 S2 6 LYS A 266 VAL A 268 -1 N LYS A 266 O ALA A 234 SITE 1 RIB 10 ASN A 13 PHE A 15 PHE A 16 ASP A 89 SITE 2 RIB 10 ARG A 90 ARG A 141 PHE A 164 ASN A 190 SITE 3 RIB 10 ASP A 215 GLN A 235 CRYST1 74.840 88.880 39.860 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 0.013362 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025088 0.00000