HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-MAY-12 4FFD TITLE CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS TITLE 2 CONSORTIUM TARGET OR48 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PF00702 DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, NORTHEAST STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, NESG, PF00702 DOMAIN PROTEIN, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.SEETHARAMAN,S.LEW,L.NIVON,D.BAKER,S.BJELIC,C.CICCOSANTI,S.SAHDEV, AUTHOR 2 R.XIAO,J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,L.TONG,J.F.HUNT, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 13-SEP-23 4FFD 1 REMARK LINK REVDAT 1 13-FEB-13 4FFD 0 JRNL AUTH J.SEETHARAMAN,S.LEW,L.NIVON,D.BAKER,S.BJELIC,C.CICCOSANTI, JRNL AUTH 2 S.SAHDEV,R.XIAO,J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,L.TONG, JRNL AUTH 3 J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST JRNL TITL 2 STRUCTURAL GENOMICS CONSORTIUM TARGET OR48 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 282473.730 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 10102 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) : 0.238 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 535 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1381 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 70 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.042 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1819 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.35000 REMARK 3 B22 (A**2) : 3.32000 REMARK 3 B33 (A**2) : 7.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 9.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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) : 1.390 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.260 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.210 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 47.86 REMARK 3 REMARK 3 NCS MODEL : NONE 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4FFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000072831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-12 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) : 0.979 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10847 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 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 : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3U26 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PBS BUFFER PH 7.5 25% PEG REMARK 280 3350,0.1M CYCLOHEXANONE, MICROBATCH UNDER OIL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.68350 REMARK 290 SMTRY3 2 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 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 GLY A 231 REMARK 465 GLN A 232 REMARK 465 GLY A 233 REMARK 465 SER A 234 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 70 CB CG CD OE1 OE2 REMARK 470 GLU A 77 CG CD OE1 OE2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 LYS A 115 CB CG CD CE NZ REMARK 470 ASP A 210 CB CG OD1 OD2 REMARK 470 LYS A 224 CB CG CD CE NZ 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 SER A 9 -81.58 -106.45 REMARK 500 LEU A 31 -100.76 -93.00 REMARK 500 ASP A 33 -43.84 77.77 REMARK 500 PRO A 35 43.11 -59.74 REMARK 500 ASN A 86 33.33 -84.92 REMARK 500 LYS A 205 23.58 -62.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 LEU A 10 O 69.6 REMARK 620 3 ASP A 180 OD1 64.4 70.3 REMARK 620 4 HOH A 481 O 75.1 75.8 133.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-OR48 RELATED DB: TARGETTRACK DBREF 4FFD A 1 234 PDB 4FFD 4FFD 1 234 SEQRES 1 A 234 MET ILE ARG ALA VAL PHE PHE ASP SER LEU GLY THR LEU SEQRES 2 A 234 ASN SER VAL GLU GLY ALA ALA LYS SER HIS LEU LYS ILE SEQRES 3 A 234 MET GLU GLU VAL LEU GLY ASP TYR PRO LEU ASN PRO LYS SEQRES 4 A 234 THR LEU LEU ASP GLU TYR GLU LYS LEU THR ARG GLU ALA SEQRES 5 A 234 PHE SER ASN TYR ALA GLY LYS PRO TYR ARG PRO LEU ARG SEQRES 6 A 234 ASP ILE LEU GLU GLU VAL MET ARG LYS LEU ALA GLU LYS SEQRES 7 A 234 TYR GLY PHE LYS TYR PRO GLU ASN PHE TRP GLU ILE SER SEQRES 8 A 234 LEU ARG MET SER GLN ARG TYR GLY GLU LEU TYR PRO GLU SEQRES 9 A 234 VAL VAL GLU VAL LEU LYS SER LEU LYS GLY LYS TYR HIS SEQRES 10 A 234 VAL GLY MET ILE THR ASP SER ASP THR GLU GLN ALA MET SEQRES 11 A 234 ALA PHE LEU ASP ALA LEU GLY ILE LYS ASP LEU PHE ASP SEQRES 12 A 234 SER ILE THR THR SER GLU GLU ALA GLY PHE PHE LYS PRO SEQRES 13 A 234 HIS PRO ARG ILE PHE GLU LEU ALA LEU LYS LYS ALA GLY SEQRES 14 A 234 VAL LYS GLY GLU GLU ALA VAL TYR VAL GLY ASP ASN PRO SEQRES 15 A 234 VAL LYS ASP CYS GLY GLY SER LYS ASN LEU GLY MET THR SEQRES 16 A 234 SER ILE LEU LEU ASP ARG LYS GLY GLU LYS ARG GLU PHE SEQRES 17 A 234 TRP ASP LYS CYS ASP PHE ILE VAL SER ASP LEU ARG GLU SEQRES 18 A 234 VAL ILE LYS ILE VAL ASP GLU LEU ASN GLY GLN GLY SER HET MG A 301 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *81(H2 O) HELIX 1 1 SER A 15 LEU A 31 1 17 HELIX 2 2 ASN A 37 ALA A 57 1 21 HELIX 3 3 PRO A 63 GLY A 80 1 18 HELIX 4 4 ASN A 86 GLY A 99 1 14 HELIX 5 5 GLU A 104 TYR A 116 1 13 HELIX 6 6 ASP A 125 LEU A 136 1 12 HELIX 7 7 ILE A 138 PHE A 142 5 5 HELIX 8 8 SER A 148 GLY A 152 1 5 HELIX 9 9 PRO A 158 GLY A 169 1 12 HELIX 10 10 LYS A 171 GLU A 173 5 3 HELIX 11 11 ASP A 185 ASN A 191 1 7 HELIX 12 12 GLU A 204 CYS A 212 5 9 HELIX 13 13 ARG A 220 ASN A 230 1 11 SHEET 1 A 6 SER A 144 THR A 147 0 SHEET 2 A 6 HIS A 117 THR A 122 1 N MET A 120 O THR A 146 SHEET 3 A 6 ALA A 4 PHE A 7 1 N VAL A 5 O HIS A 117 SHEET 4 A 6 ALA A 175 GLY A 179 1 O VAL A 178 N PHE A 6 SHEET 5 A 6 THR A 195 LEU A 199 1 O LEU A 199 N GLY A 179 SHEET 6 A 6 PHE A 214 VAL A 216 1 O PHE A 214 N LEU A 198 LINK OD2 ASP A 8 MG MG A 301 1555 1555 2.55 LINK O LEU A 10 MG MG A 301 1555 1555 2.49 LINK OD1 ASP A 180 MG MG A 301 1555 1555 2.52 LINK MG MG A 301 O HOH A 481 1555 1555 2.31 CISPEP 1 LYS A 155 PRO A 156 0 0.51 SITE 1 AC1 4 ASP A 8 LEU A 10 ASP A 180 HOH A 481 CRYST1 34.334 71.367 52.926 90.00 104.83 90.00 P 1 21 1 2 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 0.029126 0.000000 0.007712 0.00000 SCALE2 0.000000 0.014012 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019545 0.00000