PDB Short entry for 3F2Z 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 5 27-DEC-23 3F2Z 1 LINK 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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