HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 07-APR-03 1OYZ TITLE X-RAY STRUCTURE OF YIBA_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 2 TARGET ET31. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YIBA; 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: YIBA KEYWDS STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.KUZIN,A.SEMESI,T.SKARINA,A.SAVCHENKO,C.ARROWSMITH,L.TONG,NORTHEAST AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 30-OCT-24 1OYZ 1 SEQADV LINK REVDAT 4 18-APR-18 1OYZ 1 REMARK REVDAT 3 24-FEB-09 1OYZ 1 VERSN REVDAT 2 25-JAN-05 1OYZ 1 AUTHOR KEYWDS REMARK REVDAT 1 12-AUG-03 1OYZ 0 JRNL AUTH A.KUZIN,A.SEMESI,T.SKARINA,A.SAVCHENKO,C.ARROWSMITH,L.TONG JRNL TITL X-RAY STRUCTURE OF YIBA_ECOLI NORTHEAST STRUCTURAL GENOMICS JRNL TITL 2 CONSORTIUM TARGET ET31. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 735731.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.3 REMARK 3 NUMBER OF REFLECTIONS : 26922 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) : 0.219 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1327 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 34.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1849 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2180 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.79000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : -1.47000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.090 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 62.30 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 1OYZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.98150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.98150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.62100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.09500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.62100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.09500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.98150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.62100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.09500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.98150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.62100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.09500 REMARK 290 SMTRY3 8 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 MSE A 1 REMARK 465 SER A 2 REMARK 465 ASN A 3 REMARK 465 THR A 4 REMARK 465 ASN A 156 REMARK 465 ASP A 157 REMARK 465 LYS A 158 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ET31 RELATED DB: TARGETDB DBREF 1OYZ A 1 280 UNP P24172 YIBA_ECOLI 1 280 SEQADV 1OYZ MSE A 1 UNP P24172 MET 1 MODIFIED RESIDUE SEQADV 1OYZ MSE A 98 UNP P24172 MET 98 MODIFIED RESIDUE SEQADV 1OYZ MSE A 200 UNP P24172 MET 200 MODIFIED RESIDUE SEQADV 1OYZ MSE A 260 UNP P24172 MET 260 MODIFIED RESIDUE SEQRES 1 A 280 MSE SER ASN THR TYR GLN LYS ARG LYS ALA SER LYS GLU SEQRES 2 A 280 TYR GLY LEU TYR ASN GLN CYS LYS LYS LEU ASN ASP ASP SEQRES 3 A 280 GLU LEU PHE ARG LEU LEU ASP ASP HIS ASN SER LEU LYS SEQRES 4 A 280 ARG ILE SER SER ALA ARG VAL LEU GLN LEU ARG GLY GLY SEQRES 5 A 280 GLN ASP ALA VAL ARG LEU ALA ILE GLU PHE CYS SER ASP SEQRES 6 A 280 LYS ASN TYR ILE ARG ARG ASP ILE GLY ALA PHE ILE LEU SEQRES 7 A 280 GLY GLN ILE LYS ILE CYS LYS LYS CYS GLU ASP ASN VAL SEQRES 8 A 280 PHE ASN ILE LEU ASN ASN MSE ALA LEU ASN ASP LYS SER SEQRES 9 A 280 ALA CYS VAL ARG ALA THR ALA ILE GLU SER THR ALA GLN SEQRES 10 A 280 ARG CYS LYS LYS ASN PRO ILE TYR SER PRO LYS ILE VAL SEQRES 11 A 280 GLU GLN SER GLN ILE THR ALA PHE ASP LYS SER THR ASN SEQRES 12 A 280 VAL ARG ARG ALA THR ALA PHE ALA ILE SER VAL ILE ASN SEQRES 13 A 280 ASP LYS ALA THR ILE PRO LEU LEU ILE ASN LEU LEU LYS SEQRES 14 A 280 ASP PRO ASN GLY ASP VAL ARG ASN TRP ALA ALA PHE ALA SEQRES 15 A 280 ILE ASN ILE ASN LYS TYR ASP ASN SER ASP ILE ARG ASP SEQRES 16 A 280 CYS PHE VAL GLU MSE LEU GLN ASP LYS ASN GLU GLU VAL SEQRES 17 A 280 ARG ILE GLU ALA ILE ILE GLY LEU SER TYR ARG LYS ASP SEQRES 18 A 280 LYS ARG VAL LEU SER VAL LEU CYS ASP GLU LEU LYS LYS SEQRES 19 A 280 ASN THR VAL TYR ASP ASP ILE ILE GLU ALA ALA GLY GLU SEQRES 20 A 280 LEU GLY ASP LYS THR LEU LEU PRO VAL LEU ASP THR MSE SEQRES 21 A 280 LEU TYR LYS PHE ASP ASP ASN GLU ILE ILE THR SER ALA SEQRES 22 A 280 ILE ASP LYS LEU LYS ARG SER MODRES 1OYZ MSE A 98 MET SELENOMETHIONINE MODRES 1OYZ MSE A 200 MET SELENOMETHIONINE MODRES 1OYZ MSE A 260 MET SELENOMETHIONINE HET MSE A 98 8 HET MSE A 200 8 HET MSE A 260 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *58(H2 O) HELIX 1 1 GLU A 13 LYS A 22 1 10 HELIX 2 2 ASN A 24 LEU A 32 1 9 HELIX 3 3 ASN A 36 GLY A 51 1 16 HELIX 4 4 GLY A 52 SER A 64 1 13 HELIX 5 5 ASN A 67 ILE A 81 1 15 HELIX 6 6 CYS A 87 ASP A 102 1 16 HELIX 7 7 SER A 104 ASN A 122 1 19 HELIX 8 8 TYR A 125 ALA A 137 1 13 HELIX 9 9 SER A 141 VAL A 154 1 14 HELIX 10 10 THR A 160 LYS A 169 1 10 HELIX 11 11 ASN A 172 LYS A 187 1 16 HELIX 12 12 ASN A 190 LEU A 201 1 12 HELIX 13 13 ASN A 205 ARG A 219 1 15 HELIX 14 14 ASP A 221 ARG A 223 5 3 HELIX 15 15 VAL A 224 LYS A 233 1 10 HELIX 16 16 TYR A 238 GLY A 249 1 12 HELIX 17 17 ASP A 250 THR A 252 5 3 HELIX 18 18 LEU A 253 TYR A 262 1 10 HELIX 19 19 ASN A 267 LYS A 278 1 12 LINK C ASN A 97 N MSE A 98 1555 1555 1.33 LINK C MSE A 98 N ALA A 99 1555 1555 1.32 LINK C GLU A 199 N MSE A 200 1555 1555 1.32 LINK C MSE A 200 N LEU A 201 1555 1555 1.33 LINK C THR A 259 N MSE A 260 1555 1555 1.33 LINK C MSE A 260 N LEU A 261 1555 1555 1.33 CRYST1 71.242 104.190 79.963 90.00 90.00 90.00 C 2 2 21 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 0.014037 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012506 0.00000