HEADER UNKNOWN FUNCTION 16-SEP-11 3TUA TITLE CRYSTAL STRUCTURE OF THE BURKHOLDERIA LETHAL FACTOR 1 (BLF1) C94S TITLE 2 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BURKHOLDERIA LETHAL FACTOR 1 (BLF1); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI; SOURCE 3 ORGANISM_TAXID: 28450; SOURCE 4 GENE: BPSL1549; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.CRUZ,G.M.HAUTBERGUE,P.J.ARTYMIUK,P.J.BAKER,C.T.CHANG,N.M.MAHADI, AUTHOR 2 G.W.MOBBS,R.MOHAMED,S.NATHAN,L.J.PARTRIDGE,M.F.RAIH,S.N.RUZHEINIKOV, AUTHOR 3 S.E.SEDELNIKOVA,S.A.WILSON,D.W.RICE REVDAT 3 13-SEP-23 3TUA 1 SEQADV REVDAT 2 30-NOV-11 3TUA 1 REVDAT 1 30-NOV-11 3TUA 0 JRNL AUTH A.CRUZ-MIGONI,G.M.HAUTBERGUE,P.J.ARTYMIUK,P.J.BAKER, JRNL AUTH 2 M.BOKORI-BROWN,C.T.CHANG,M.J.DICKMAN,A.ESSEX-LOPRESTI, JRNL AUTH 3 S.V.HARDING,N.M.MAHADI,L.E.MARSHALL,G.W.MOBBS,R.MOHAMED, JRNL AUTH 4 S.NATHAN,S.A.NGUGI,C.ONG,W.F.OOI,L.J.PARTRIDGE,H.L.PHILLIPS, JRNL AUTH 5 M.F.RAIH,S.RUZHEINIKOV,M.SARKAR-TYSON,S.E.SEDELNIKOVA, JRNL AUTH 6 S.J.SMITHER,P.TAN,R.W.TITBALL,S.A.WILSON,D.W.RICE JRNL TITL A BURKHOLDERIA PSEUDOMALLEI TOXIN INHIBITS HELICASE ACTIVITY JRNL TITL 2 OF TRANSLATION FACTOR EIF4A. JRNL REF SCIENCE V. 334 821 2011 JRNL REFN ISSN 0036-8075 JRNL PMID 22076380 JRNL DOI 10.1126/SCIENCE.1211915 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.CRUZ-MIGONI,S.N.RUZHEINIKOV,S.E.SEDELNIKOVA,B.OBENG, REMARK 1 AUTH 2 S.CHIENG,R.MOHAMED,S.NATHAN,P.J.BAKER,D.W.RICE REMARK 1 TITL CLONING, PURIFICATION AND CRYSTALLOGRAPHIC ANALYSIS OF A REMARK 1 TITL 2 HYPOTHETICAL PROTEIN, BPSL1549, FROM BURKHOLDERIA REMARK 1 TITL 3 PSEUDOMALLEI REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.141 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.141 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3889 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 73637 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.127 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 60543 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 294 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1932.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1555.5 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 16 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 18544 REMARK 3 NUMBER OF RESTRAINTS : 24324 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.088 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.021 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.052 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.103 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REMARK 4 REMARK 4 3TUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000067927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 3TU8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 3350, 0.2M SODIUM BROMIDE, REMARK 280 0.1M BIS-TRIS PROPANE PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K 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 18.48500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.84500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.84500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.48500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.61000 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 47 CD - NE - CZ ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 GLU A 70 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 ASP A 128 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES 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 LEU A 19 101.69 -160.47 REMARK 500 ASN A 43 107.05 -55.47 REMARK 500 ASN A 54 60.16 32.35 REMARK 500 ASN A 54 65.77 32.35 REMARK 500 SER A 80 -40.71 -148.59 REMARK 500 ASP A 83 -3.08 77.19 REMARK 500 TRP A 150 -23.96 -144.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TU8 RELATED DB: PDB REMARK 900 WILD TYPE PROTEIN DBREF 3TUA A 2 211 UNP Q63UP7 Q63UP7_BURPS 2 211 SEQADV 3TUA SER A 94 UNP Q63UP7 CYS 94 ENGINEERED MUTATION SEQRES 1 A 210 PRO ASN SER LEU GLU ALA GLN ILE ARG GLN ALA MET LYS SEQRES 2 A 210 THR GLY SER THR LEU THR ILE GLU PHE ASP GLN ALA LEU SEQRES 3 A 210 ASN GLN LYS SER PRO GLY THR LEU ASN VAL PHE LEU HIS SEQRES 4 A 210 PRO ALA ASN GLY GLY VAL ARG ILE ASP LEU ASP SER GLY SEQRES 5 A 210 ASN GLN GLY GLU PRO ALA LYS ILE LEU TRP LEU PRO TRP SEQRES 6 A 210 LYS GLN GLY GLU LEU GLN THR LEU GLN PRO GLY SER ILE SEQRES 7 A 210 SER THR VAL ASP MET LEU PHE PHE THR TYR TYR LEU SER SEQRES 8 A 210 GLY SER LYS VAL PHE ALA GLY ASP GLY GLY PRO VAL TRP SEQRES 9 A 210 HIS ILE ASP ALA PRO VAL GLU ALA ASN GLN PHE TRP ARG SEQRES 10 A 210 ARG MET SER SER ASP GLU TRP MET GLU ASP TRP GLU VAL SEQRES 11 A 210 GLY THR ASP ARG GLN VAL ALA TYR LEU HIS ARG ALA GLY SEQRES 12 A 210 GLN SER ASP SER LEU TRP ASN LEU SER ALA TYR LEU GLU SEQRES 13 A 210 GLY ALA ALA PRO SER THR TYR GLY ARG ASP ASN LEU GLY SEQRES 14 A 210 GLN ALA VAL VAL GLY GLY ILE VAL THR GLY ARG GLN GLN SEQRES 15 A 210 MET SER LEU TYR GLN TYR ALA THR THR SER SER GLY SER SEQRES 16 A 210 SER ALA TRP SER PRO LEU THR TYR THR LEU GLN GLN ARG SEQRES 17 A 210 LYS GLN FORMUL 2 HOH *294(H2 O) HELIX 1 1 SER A 4 GLY A 16 1 13 HELIX 2 2 GLN A 25 LYS A 30 5 6 HELIX 3 3 GLN A 75 ILE A 79 5 5 HELIX 4 4 GLU A 112 SER A 121 1 10 HELIX 5 5 ASP A 123 ASP A 128 1 6 HELIX 6 6 SER A 146 TRP A 150 5 5 SHEET 1 A 8 THR A 20 PHE A 23 0 SHEET 2 A 8 GLY A 45 ASP A 49 1 O ILE A 48 N GLU A 22 SHEET 3 A 8 GLY A 33 ALA A 42 -1 N PHE A 38 O ASP A 49 SHEET 4 A 8 GLU A 57 LEU A 64 -1 O ALA A 59 N VAL A 37 SHEET 5 A 8 LEU A 85 THR A 88 1 O LEU A 85 N LEU A 62 SHEET 6 A 8 GLN A 171 GLY A 180 -1 O GLY A 176 N PHE A 86 SHEET 7 A 8 GLN A 183 THR A 192 -1 O THR A 191 N GLN A 171 SHEET 8 A 8 GLY A 195 SER A 196 -1 O GLY A 195 N THR A 192 SHEET 1 B 8 THR A 20 PHE A 23 0 SHEET 2 B 8 GLY A 45 ASP A 49 1 O ILE A 48 N GLU A 22 SHEET 3 B 8 GLY A 33 ALA A 42 -1 N PHE A 38 O ASP A 49 SHEET 4 B 8 GLU A 57 LEU A 64 -1 O ALA A 59 N VAL A 37 SHEET 5 B 8 LEU A 85 THR A 88 1 O LEU A 85 N LEU A 62 SHEET 6 B 8 GLN A 171 GLY A 180 -1 O GLY A 176 N PHE A 86 SHEET 7 B 8 GLN A 183 THR A 192 -1 O THR A 191 N GLN A 171 SHEET 8 B 8 SER A 200 LEU A 202 -1 O SER A 200 N GLN A 188 SHEET 1 C 6 LEU A 71 LEU A 74 0 SHEET 2 C 6 VAL A 104 ILE A 107 -1 O VAL A 104 N LEU A 74 SHEET 3 C 6 LYS A 95 GLY A 99 -1 N PHE A 97 O TRP A 105 SHEET 4 C 6 ASP A 134 ARG A 142 -1 O ALA A 138 N ALA A 98 SHEET 5 C 6 THR A 205 ARG A 209 -1 O GLN A 207 N ARG A 135 SHEET 6 C 6 LEU A 156 GLY A 158 -1 N GLU A 157 O GLN A 208 SHEET 1 D 5 LEU A 71 LEU A 74 0 SHEET 2 D 5 VAL A 104 ILE A 107 -1 O VAL A 104 N LEU A 74 SHEET 3 D 5 LYS A 95 GLY A 99 -1 N PHE A 97 O TRP A 105 SHEET 4 D 5 ASP A 134 ARG A 142 -1 O ALA A 138 N ALA A 98 SHEET 5 D 5 SER A 162 TYR A 164 1 O SER A 162 N TYR A 139 CRYST1 36.970 45.220 115.690 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 0.027049 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008644 0.00000