HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 30-OCT-08 3F2Z TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF A CHITOBIASE (BF3579) TITLE 2 FROM BACTEROIDES FRAGILIS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET BFR260B COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN BF3579; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 291-440; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS; SOURCE 3 ORGANISM_TAXID: 272559; SOURCE 4 STRAIN: NCTC 9343; SOURCE 5 GENE: BF3579; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS THE PRESENT C-TERMINAL DOMAIN IS PREDOMINANTLY COMPOSED OF BETA KEYWDS 2 STRANDS., STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,S.LEW,J.SEETHARAMAN,H.JANJUA,R.XIAO,E.L.FOOTE, AUTHOR 2 C.CICCOSANTI,D.LEE,R.NAIR,J.K.EVERETT,T.B.ACTON,B.ROST, AUTHOR 3 G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS AUTHOR 4 CONSORTIUM (NESG) REVDAT 4 25-OCT-17 3F2Z 1 REMARK REVDAT 3 13-JUL-11 3F2Z 1 VERSN REVDAT 2 24-FEB-09 3F2Z 1 VERSN REVDAT 1 18-NOV-08 3F2Z 0 JRNL AUTH F.FOROUHAR,S.LEW,J.SEETHARAMAN,H.JANJUA,R.XIAO,E.L.FOOTE, JRNL AUTH 2 C.CICCOSANTI,D.LEE,R.NAIR,J.K.EVERETT,T.B.ACTON,B.ROST, JRNL AUTH 3 G.T.MONTELIONE,J.F.HUNT,L.TONG JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF A CHITOBIASE JRNL TITL 2 (BF3579) FROM BACTEROIDES FRAGILIS, NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS CONSORTIUM TARGET BFR260B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS & XTALVIEW & REFMAC 5.2.0019 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35268 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) : 0.155 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1854 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2100 REMARK 3 BIN R VALUE (WORKING SET) : 0.1370 REMARK 3 BIN FREE R VALUE : 0.1920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 105 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.003 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1168 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 386 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : 0.38000 REMARK 3 B33 (A**2) : -0.16000 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) : 0.13 REMARK 3 ESD FROM SIGMAA (A) : 0.05 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) : 0.14 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MASK 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3F2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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) : 0.97914 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67612 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 43.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.08100 REMARK 200 R SYM FOR SHELL (I) : 0.08900 REMARK 200 FOR SHELL : 11.54 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 10 MM TRIS (PH 7.5), REMARK 280 100 MM SODIUM CHLORIDE, AND 5 MM DTT. RESERVOIR SOLUTION: 100 MM REMARK 280 NAACETATE (PH 5), 40% PEG 8K, AND 100 MM NH4CL , MICROBATCH REMARK 280 UNDER OIL, TEMPERATURE 277K 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 23.94650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.98000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.84200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.98000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.94650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.84200 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 300 REMARK: THE C-TERMINAL DOMAIN IS MONOMER IN SOLUTION AND CRYSTAL. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 290 REMARK 465 GLY A 291 REMARK 465 LEU A 441 REMARK 465 GLU A 442 REMARK 465 HIS A 443 REMARK 465 HIS A 444 REMARK 465 HIS A 445 REMARK 465 HIS A 446 REMARK 465 HIS A 447 REMARK 465 HIS A 448 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 TRP A 335 -32.99 -130.31 REMARK 500 ASN A 370 67.49 -150.82 REMARK 500 PRO A 371 38.57 -86.62 REMARK 500 ASN A 396 46.95 -79.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BFR260B RELATED DB: TARGETDB DBREF 3F2Z A 291 440 UNP Q5L9G5 Q5L9G5_BACFN 291 440 SEQADV 3F2Z MSE A 290 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z LEU A 441 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z GLU A 442 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z HIS A 443 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z HIS A 444 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z HIS A 445 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z HIS A 446 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z HIS A 447 UNP Q5L9G5 EXPRESSION TAG SEQADV 3F2Z HIS A 448 UNP Q5L9G5 EXPRESSION TAG SEQRES 1 A 159 MSE GLY ASP LYS LEU SER LYS THR ASP TRP LYS ILE VAL SEQRES 2 A 159 SER PHE THR THR GLU GLU ALA SER GLY GLU GLY SER ASN SEQRES 3 A 159 ASN GLY HIS ALA LYS HIS LEU ILE ASP GLY ASN ILE GLU SEQRES 4 A 159 THR PHE TRP HIS SER ARG TRP GLN GLY GLY SER ASP PRO SEQRES 5 A 159 LEU PRO TYR GLU ILE ILE ILE ASP MSE ASN HIS ARG VAL SEQRES 6 A 159 LYS ILE ALA GLN ILE GLU LEU LEU PRO ARG GLY ARG GLY SEQRES 7 A 159 SER ASN ASN PRO ILE LYS VAL VAL ARG PHE GLU ALA SER SEQRES 8 A 159 GLU ASP GLY THR ASN TRP GLU SER ILE GLY GLN PHE GLY SEQRES 9 A 159 PHE THR ASN GLN ASP ALA ALA LEU LYS TYR TYR VAL LYS SEQRES 10 A 159 SER SER THR ALA ARG TYR ILE LYS LEU VAL ILE PRO ASP SEQRES 11 A 159 GLY VAL GLY ASN GLY THR VAL ALA ALA ILE ARG GLU LEU SEQRES 12 A 159 ASP VAL ARG GLY THR VAL VAL ASN LEU GLU HIS HIS HIS SEQRES 13 A 159 HIS HIS HIS MODRES 3F2Z MSE A 350 MET SELENOMETHIONINE HET MSE A 350 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *386(H2 O) HELIX 1 1 HIS A 318 ILE A 323 5 6 SHEET 1 A 5 LYS A 300 PHE A 304 0 SHEET 2 A 5 TYR A 344 PRO A 363 -1 O ASP A 349 N LYS A 300 SHEET 3 A 5 SER A 408 ILE A 417 -1 O ILE A 417 N TYR A 344 SHEET 4 A 5 VAL A 374 SER A 380 -1 N ARG A 376 O VAL A 416 SHEET 5 A 5 GLU A 387 GLY A 393 -1 O PHE A 392 N VAL A 375 SHEET 1 B 4 TRP A 331 HIS A 332 0 SHEET 2 B 4 ALA A 428 VAL A 438 -1 O ILE A 429 N TRP A 331 SHEET 3 B 4 TYR A 344 PRO A 363 -1 N LYS A 355 O THR A 437 SHEET 4 B 4 LEU A 401 TYR A 403 -1 O LEU A 401 N LEU A 361 LINK C ASP A 349 N MSE A 350 1555 1555 1.33 LINK C MSE A 350 N ASN A 351 1555 1555 1.33 CISPEP 1 LEU A 342 PRO A 343 0 -0.34 CRYST1 47.893 51.684 63.960 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 0.020880 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015635 0.00000 MASTER 253 0 1 1 9 0 0 6 0 0 0 13 END