HEADER OXIDOREDUCTASE 24-DEC-08 3FNI TITLE CRYSTAL STRUCTURE OF A DIFLAVIN FLAVOPROTEIN A3 (ALL3895) FROM NOSTOC TITLE 2 SP., NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET NSR431A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE DIFLAVIN FLAVOPROTEIN A 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 259-409; COMPND 5 EC: 1.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC SP.; SOURCE 3 ORGANISM_TAXID: 103690; SOURCE 4 STRAIN: PCC 7120; SOURCE 5 GENE: ALL3895, DFA3; 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 ALPHA-BETA PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, ELECTRON KEYWDS 3 TRANSPORT, IRON, METAL-BINDING, OXIDOREDUCTASE, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,S.LEW,J.SEETHARAMAN,S.SAHDEV,R.XIAO,E.L.FOOTE, AUTHOR 2 C.CICCOSANTI,D.WANG,J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST, AUTHOR 3 G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS AUTHOR 4 CONSORTIUM (NESG) REVDAT 3 09-APR-14 3FNI 1 REMARK REVDAT 2 13-JUL-11 3FNI 1 VERSN REVDAT 1 13-JAN-09 3FNI 0 JRNL AUTH F.FOROUHAR,S.LEW,J.SEETHARAMAN,S.SAHDEV,R.XIAO,E.L.FOOTE, JRNL AUTH 2 C.CICCOSANTI,D.WANG,J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST, JRNL AUTH 3 G.T.MONTELIONE,J.F.HUNT,L.TONG JRNL TITL CRYSTAL STRUCTURE OF A DIFLAVIN FLAVOPROTEIN A3 (ALL3895) JRNL TITL 2 FROM NOSTOC SP., NORTHEAST STRUCTURAL GENOMICS CONSORTIUM JRNL TITL 3 TARGET NSR431A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 & XTALVIEW REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 640762.170 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 11425 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) : 0.210 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 586 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1081 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 38 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1148 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.63000 REMARK 3 B22 (A**2) : 19.53000 REMARK 3 B33 (A**2) : -10.90000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.600 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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 : 0.30 REMARK 3 BSOL : 24.46 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 3FNI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB050808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.96863 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 : 12184 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 25.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.16900 REMARK 200 R SYM FOR SHELL (I) : 0.15700 REMARK 200 FOR SHELL : 12.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX THEN SOLVE/RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 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 HEPES (PH 7.5), 40% PEG 4K, AND 100 MM MAGNESIUM ACETATE. , REMARK 280 MICROBATCH 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 14.04800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.57500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.15050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.57500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.04800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.15050 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: MONOMER 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 THR A 1 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 465 HIS A 159 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 224 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH A 228 DISTANCE = 5.43 ANGSTROMS REMARK 525 HOH A 277 DISTANCE = 5.68 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NSR431A RELATED DB: TARGETDB DBREF 3FNI A 1 151 UNP Q8YQD8 DFA3_ANASP 259 409 SEQADV 3FNI LEU A 152 UNP Q8YQD8 EXPRESSION TAG SEQADV 3FNI GLU A 153 UNP Q8YQD8 EXPRESSION TAG SEQADV 3FNI HIS A 154 UNP Q8YQD8 EXPRESSION TAG SEQADV 3FNI HIS A 155 UNP Q8YQD8 EXPRESSION TAG SEQADV 3FNI HIS A 156 UNP Q8YQD8 EXPRESSION TAG SEQADV 3FNI HIS A 157 UNP Q8YQD8 EXPRESSION TAG SEQADV 3FNI HIS A 158 UNP Q8YQD8 EXPRESSION TAG SEQADV 3FNI HIS A 159 UNP Q8YQD8 EXPRESSION TAG SEQRES 1 A 159 THR LYS ALA GLU THR SER ILE GLY VAL PHE TYR VAL SER SEQRES 2 A 159 GLU TYR GLY TYR SER ASP ARG LEU ALA GLN ALA ILE ILE SEQRES 3 A 159 ASN GLY ILE THR LYS THR GLY VAL GLY VAL ASP VAL VAL SEQRES 4 A 159 ASP LEU GLY ALA ALA VAL ASP LEU GLN GLU LEU ARG GLU SEQRES 5 A 159 LEU VAL GLY ARG CYS THR GLY LEU VAL ILE GLY MSE SER SEQRES 6 A 159 PRO ALA ALA SER ALA ALA SER ILE GLN GLY ALA LEU SER SEQRES 7 A 159 THR ILE LEU GLY SER VAL ASN GLU LYS GLN ALA VAL GLY SEQRES 8 A 159 ILE PHE GLU THR GLY GLY GLY ASP ASP GLU PRO ILE ASP SEQRES 9 A 159 PRO LEU LEU SER LYS PHE ARG ASN LEU GLY LEU THR THR SEQRES 10 A 159 ALA PHE PRO ALA ILE ARG ILE LYS GLN THR PRO THR GLU SEQRES 11 A 159 ASN THR TYR LYS LEU CYS GLU GLU ALA GLY THR ASP LEU SEQRES 12 A 159 GLY GLN TRP VAL THR ARG ASP ARG LEU GLU HIS HIS HIS SEQRES 13 A 159 HIS HIS HIS MODRES 3FNI MSE A 64 MET SELENOMETHIONINE HET MSE A 64 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *141(H2 O) HELIX 1 1 TYR A 17 THR A 32 1 16 HELIX 2 2 ASP A 46 ARG A 56 1 11 HELIX 3 3 SER A 69 VAL A 84 1 16 HELIX 4 4 PRO A 102 LEU A 113 1 12 HELIX 5 5 THR A 129 GLU A 153 1 25 SHEET 1 A 5 GLY A 35 ASP A 40 0 SHEET 2 A 5 SER A 6 TYR A 11 1 N VAL A 9 O ASP A 37 SHEET 3 A 5 CYS A 57 GLY A 63 1 O VAL A 61 N PHE A 10 SHEET 4 A 5 ALA A 89 PHE A 93 1 O GLY A 91 N ILE A 62 SHEET 5 A 5 THR A 116 THR A 117 1 O THR A 116 N VAL A 90 LINK C GLY A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N SER A 65 1555 1555 1.33 CRYST1 28.096 66.301 75.150 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 0.035592 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013307 0.00000