HEADER UNKNOWN FUNCTION 19-AUG-01 1JSX TITLE CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI GLUCOSE-INHIBITED DIVISION TITLE 2 PROTEIN B (GIDB) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE-INHIBITED DIVISION PROTEIN B; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: GIDB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS METHYLTRANSFERASE FOLD, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 NYSGXRC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR M.J.ROMANOWSKI,J.B.BONANNO,S.K.BURLEY,NEW YORK SGX RESEARCH CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 6 07-FEB-24 1JSX 1 REMARK REVDAT 5 03-FEB-21 1JSX 1 AUTHOR JRNL REVDAT 4 21-JUL-09 1JSX 1 REMARK REVDAT 3 24-FEB-09 1JSX 1 VERSN REVDAT 2 25-JAN-05 1JSX 1 AUTHOR KEYWDS REMARK REVDAT 1 08-MAY-02 1JSX 0 JRNL AUTH M.J.ROMANOWSKI,J.B.BONANNO,S.K.BURLEY JRNL TITL CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI GLUCOSE-INHIBITED JRNL TITL 2 DIVISION PROTEIN B (GIDB) REVEALS A METHYLTRANSFERASE FOLD. JRNL REF PROTEINS V. 47 563 2002 JRNL REFN ISSN 0887-3585 JRNL PMID 12001236 JRNL DOI 10.1002/PROT.10121.ABS REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 663404.350 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 9170 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) : 0.240 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 936 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1338 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 144 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.38000 REMARK 3 B22 (A**2) : 1.38000 REMARK 3 B33 (A**2) : -2.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 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) : 1.440 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.380 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.710 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 41.67 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JSX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-00; 28-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 150; 150 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X9A; X9A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97903, 0.97927; 0.98399 REMARK 200 MONOCHROMATOR : SI 111; SI 111 REMARK 200 OPTICS : PRIMARY APERTURE - 7.4 M FROM REMARK 200 SOURCE. BE WINDOWS FRONT END - REMARK 200 0.020" THICK, 7.1 M FROM SOURCE REMARK 200 EXIT WINDOW - 0.010" THICK. REMARK 200 WHITE X-RAY BEAM.; PRIMARY REMARK 200 APERTURE - 7.4 M FROM SOURCE. BE REMARK 200 WINDOWS FRONT END - 0.020" THICK, REMARK 200 7.1 M FROM SOURCE EXIT WINDOW: REMARK 200 0.010" THICK. WHITE X-RAY BEAM. REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9170 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 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: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG4000, 10% ISOPROPANOL, 0.1M REMARK 280 SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.29600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.64800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.94400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.29600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 112.94400 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 37.64800 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 36 REMARK 465 ALA A 37 REMARK 465 TYR A 38 REMARK 465 ASN A 39 REMARK 465 LEU A 40 REMARK 465 THR A 41 REMARK 465 SER A 42 REMARK 465 VAL A 43 REMARK 465 ARG A 44 REMARK 465 ASP A 45 REMARK 465 PRO A 46 REMARK 465 ASN A 47 REMARK 465 ALA A 192 REMARK 465 LEU A 193 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 11 -7.34 -57.47 REMARK 500 ALA A 12 92.47 -48.16 REMARK 500 SER A 122 158.16 168.32 REMARK 500 GLU A 126 -16.83 -44.80 REMARK 500 PRO A 132 159.41 -44.85 REMARK 500 VAL A 190 -56.74 -121.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T35 RELATED DB: TARGETDB DBREF 1JSX A 1 207 UNP P0A6U5 GIDB_ECOLI 1 207 SEQRES 1 A 207 MET LEU ASN LYS LEU SER LEU LEU LEU LYS ASP ALA GLY SEQRES 2 A 207 ILE SER LEU THR ASP HIS GLN LYS ASN GLN LEU ILE ALA SEQRES 3 A 207 TYR VAL ASN MET LEU HIS LYS TRP ASN LYS ALA TYR ASN SEQRES 4 A 207 LEU THR SER VAL ARG ASP PRO ASN GLU MET LEU VAL ARG SEQRES 5 A 207 HIS ILE LEU ASP SER ILE VAL VAL ALA PRO TYR LEU GLN SEQRES 6 A 207 GLY GLU ARG PHE ILE ASP VAL GLY THR GLY PRO GLY LEU SEQRES 7 A 207 PRO GLY ILE PRO LEU SER ILE VAL ARG PRO GLU ALA HIS SEQRES 8 A 207 PHE THR LEU LEU ASP SER LEU GLY LYS ARG VAL ARG PHE SEQRES 9 A 207 LEU ARG GLN VAL GLN HIS GLU LEU LYS LEU GLU ASN ILE SEQRES 10 A 207 GLU PRO VAL GLN SER ARG VAL GLU GLU PHE PRO SER GLU SEQRES 11 A 207 PRO PRO PHE ASP GLY VAL ILE SER ARG ALA PHE ALA SER SEQRES 12 A 207 LEU ASN ASP MET VAL SER TRP CYS HIS HIS LEU PRO GLY SEQRES 13 A 207 GLU GLN GLY ARG PHE TYR ALA LEU LYS GLY GLN MET PRO SEQRES 14 A 207 GLU ASP GLU ILE ALA LEU LEU PRO GLU GLU TYR GLN VAL SEQRES 15 A 207 GLU SER VAL VAL LYS LEU GLN VAL PRO ALA LEU ASP GLY SEQRES 16 A 207 GLU ARG HIS LEU VAL VAL ILE LYS ALA ASN LYS ILE FORMUL 2 HOH *127(H2 O) HELIX 1 1 MET A 1 ASP A 11 1 11 HELIX 2 2 THR A 17 ASN A 35 1 19 HELIX 3 3 GLU A 48 ALA A 61 1 14 HELIX 4 4 PRO A 62 LEU A 64 5 3 HELIX 5 5 PRO A 79 ARG A 87 1 9 HELIX 6 6 LEU A 98 LEU A 112 1 15 HELIX 7 7 SER A 143 HIS A 152 1 10 HELIX 8 8 PRO A 169 LEU A 175 1 7 SHEET 1 A 7 ILE A 117 GLN A 121 0 SHEET 2 A 7 HIS A 91 ASP A 96 1 N LEU A 94 O VAL A 120 SHEET 3 A 7 ARG A 68 VAL A 72 1 N PHE A 69 O HIS A 91 SHEET 4 A 7 PHE A 133 ILE A 137 1 O ILE A 137 N ILE A 70 SHEET 5 A 7 PRO A 155 LYS A 165 1 O TYR A 162 N VAL A 136 SHEET 6 A 7 GLU A 196 ALA A 204 -1 O HIS A 198 N LYS A 165 SHEET 7 A 7 TYR A 180 GLN A 189 -1 N GLN A 181 O LYS A 203 CISPEP 1 LEU A 78 PRO A 79 0 -0.02 CRYST1 53.914 53.914 150.592 90.00 90.00 90.00 P 41 2 2 8 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 0.018548 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006640 0.00000