HEADER UNKNOWN FUNCTION 21-DEC-01 1KON TITLE CRYSTAL STRUCTURE OF E.COLI YEBC COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN YEBC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YEBC; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YEBC; 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 KEYWDS ALPHA/BETA, TWO-DOMAINS, MONTREAL-KINGSTON BACTERIAL STRUCTURAL KEYWDS 2 GENOMICS INITIATIVE, BSGI, STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.JIA,C.SMITH,V.V.LUNIN,A.MATTE,M.CYGLER,MONTREAL-KINGSTON BACTERIAL AUTHOR 2 STRUCTURAL GENOMICS INITIATIVE (BSGI) REVDAT 4 14-FEB-24 1KON 1 SEQADV REVDAT 3 31-JAN-18 1KON 1 REMARK REVDAT 2 24-FEB-09 1KON 1 VERSN REVDAT 1 17-JUL-02 1KON 0 JRNL TITL UNPUBLISHED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS.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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 11468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.273 REMARK 3 FREE R VALUE : 0.317 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 115 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 : 1732 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) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.00 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) : 1.331 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1KON COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015177. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96404,0.97927,0.97941,0.97945 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : COLLIMATING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11468 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 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 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-CL, POSTASSIUM CHLORIDE, REMARK 280 DITHIOTHREITOL, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 22K, TEMPERATURE 295.0K 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 36.74000 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 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 39 REMARK 465 GLY A 40 REMARK 465 GLY A 41 REMARK 465 ASP A 42 REMARK 465 PRO A 43 REMARK 465 VAL A 74 REMARK 465 GLY A 75 REMARK 465 GLY A 76 REMARK 465 ASP A 77 REMARK 465 ASP A 78 REMARK 465 ASP A 79 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 14 CG CD CE NZ REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 LEU A 38 CG CD1 CD2 REMARK 470 ASP A 44 CG OD1 OD2 REMARK 470 ASN A 46 CG OD1 ND2 REMARK 470 ARG A 48 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 50 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 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 O ARG A 50 OD2 ASP A 54 2.19 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 THR A 10 -9.05 -150.56 REMARK 500 ARG A 11 -72.39 -62.97 REMARK 500 ARG A 13 -45.85 70.93 REMARK 500 ASP A 18 30.05 -92.77 REMARK 500 PRO A 47 49.47 -68.03 REMARK 500 ARG A 48 -9.67 -156.15 REMARK 500 ALA A 71 31.84 -63.36 REMARK 500 PRO A 92 120.31 -29.74 REMARK 500 LYS A 119 12.46 -67.39 REMARK 500 CYS A 120 27.19 -152.31 REMARK 500 SER A 129 -91.66 -65.67 REMARK 500 ALA A 159 150.57 -41.96 REMARK 500 TRP A 176 -40.39 -27.88 REMARK 500 SER A 199 -168.76 -121.96 REMARK 500 ASP A 207 151.87 -46.02 REMARK 500 ALA A 210 -7.33 -59.74 REMARK 500 ALA A 213 -60.69 -108.79 REMARK 500 ALA A 244 43.18 -98.00 REMARK 500 THR A 245 -35.07 -134.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: YEBC_ECOLI RELATED DB: TARGETDB DBREF 1KON A 1 246 UNP P0A8A0 YEBC_ECOLI 1 246 SEQADV 1KON GLY A -2 UNP P0A8A0 CLONING ARTIFACT SEQADV 1KON SER A -1 UNP P0A8A0 CLONING ARTIFACT SEQADV 1KON HIS A 0 UNP P0A8A0 CLONING ARTIFACT SEQRES 1 A 249 GLY SER HIS MET ALA GLY HIS SER LYS TRP ALA ASN THR SEQRES 2 A 249 ARG HIS ARG LYS ALA ALA GLN ASP ALA LYS ARG GLY LYS SEQRES 3 A 249 ILE PHE THR LYS ILE ILE ARG GLU LEU VAL THR ALA ALA SEQRES 4 A 249 LYS LEU GLY GLY GLY ASP PRO ASP ALA ASN PRO ARG LEU SEQRES 5 A 249 ARG ALA ALA VAL ASP LYS ALA LEU SER ASN ASN MET THR SEQRES 6 A 249 ARG ASP THR LEU ASN ARG ALA ILE ALA ARG GLY VAL GLY SEQRES 7 A 249 GLY ASP ASP ASP ALA ASN MET GLU THR ILE ILE TYR GLU SEQRES 8 A 249 GLY TYR GLY PRO GLY GLY THR ALA ILE MET ILE GLU CYS SEQRES 9 A 249 LEU SER ASP ASN ARG ASN ARG THR VAL ALA GLU VAL ARG SEQRES 10 A 249 HIS ALA PHE SER LYS CYS GLY GLY ASN LEU GLY THR ASP SEQRES 11 A 249 GLY SER VAL ALA TYR LEU PHE SER LYS LYS GLY VAL ILE SEQRES 12 A 249 SER PHE GLU LYS GLY ASP GLU ASP THR ILE MET GLU ALA SEQRES 13 A 249 ALA LEU GLU ALA GLY ALA GLU ASP VAL VAL THR TYR ASP SEQRES 14 A 249 ASP GLY ALA ILE ASP VAL TYR THR ALA TRP GLU GLU MET SEQRES 15 A 249 GLY LYS VAL ARG ASP ALA LEU GLU ALA ALA GLY LEU LYS SEQRES 16 A 249 ALA ASP SER ALA GLU VAL SER MET ILE PRO SER THR LYS SEQRES 17 A 249 ALA ASP MET ASP ALA GLU THR ALA PRO LYS LEU MET ARG SEQRES 18 A 249 LEU ILE ASP MET LEU GLU ASP CYS ASP ASP VAL GLN GLU SEQRES 19 A 249 VAL TYR HIS ASN GLY GLU ILE SER ASP GLU VAL ALA ALA SEQRES 20 A 249 THR LEU HELIX 1 1 LYS A 6 THR A 10 5 5 HELIX 2 2 LYS A 20 LEU A 38 1 19 HELIX 3 3 LEU A 49 ASN A 59 1 11 HELIX 4 4 THR A 62 ALA A 71 1 10 HELIX 5 5 ASN A 105 LYS A 119 1 15 HELIX 6 6 VAL A 130 TYR A 132 5 3 HELIX 7 7 ASP A 146 GLY A 158 1 13 HELIX 8 8 GLU A 178 ALA A 189 1 12 HELIX 9 9 ALA A 213 CYS A 226 1 14 HELIX 10 10 SER A 239 ALA A 244 1 6 SHEET 1 A 4 ASN A 123 LEU A 124 0 SHEET 2 A 4 GLU A 83 GLY A 91 -1 N TYR A 90 O ASN A 123 SHEET 3 A 4 THR A 95 SER A 103 -1 O SER A 103 N GLU A 83 SHEET 4 A 4 VAL A 229 HIS A 234 -1 O GLU A 231 N GLU A 100 SHEET 1 B 4 ASP A 161 THR A 164 0 SHEET 2 B 4 ILE A 170 ALA A 175 -1 O ASP A 171 N VAL A 163 SHEET 3 B 4 PHE A 134 PHE A 142 -1 N PHE A 142 O ILE A 170 SHEET 4 B 4 SER A 195 PRO A 202 -1 O GLU A 197 N VAL A 139 CRYST1 39.560 73.480 39.260 90.00 97.89 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 0.025278 0.000000 0.003503 0.00000 SCALE2 0.000000 0.013609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025715 0.00000