HEADER REPLICATION 31-JUL-08 3E0E TITLE CRYSTAL STRUCTURE OF A DOMAIN OF REPLICATION PROTEIN A FROM TITLE 2 METHANOCOCCUS MARIPALUDIS. NORTHEAST STRUCTURAL GENOMICS TITLE 3 TARGE MRR110B COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 173-267; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS MARIPALUDIS; SOURCE 3 ORGANISM_TAXID: 39152; SOURCE 4 GENE: RPA, MMP1032; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET 21 KEYWDS REPLICATION PROTEIN A, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG EXPDTA X-RAY DIFFRACTION AUTHOR J.SEETHARAMAN,Y.CHEN,H.WANG,H.JANJUA,E.L.FOOTE,R.XIAO, AUTHOR 2 R.NAIR,J.K.EVERETT,T.B.ACTON,B.ROST,G.T.MONTELIONE,J.F.HUNT, AUTHOR 3 L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 24-FEB-09 3E0E 1 VERSN REVDAT 1 30-SEP-08 3E0E 0 JRNL AUTH J.SEETHARAMAN,Y.CHEN,H.WANG,H.JANJUA,E.L.FOOTE, JRNL AUTH 2 R.XIAO,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 A DOMAIN OF REPLICATION JRNL TITL 2 PROTEIN A FROM METHANOCOCCUS MARIPALUDIS. JRNL TITL 3 NORTHEAST STRUCTURAL GENOMICS TARGE MRR110B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 146558.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 19559 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) : 0.234 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1146 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2958 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 204 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 687 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : -1.13000 REMARK 3 B33 (A**2) : -0.41000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.74 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 : 0.40 REMARK 3 BSOL : 61.01 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3E0E COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-08. REMARK 100 THE RCSB ID CODE IS RCSB048716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-08; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X4A; X4C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.979; 0.979 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19963 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 21.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.22500 REMARK 200 R SYM FOR SHELL (I) : 0.21300 REMARK 200 FOR SHELL : 19.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE 0.1 M, SODIUM REMARK 280 ACETATE 0.1 M, PEG 4000 40%, PH 5, MICRO BATCH UNDER OIL REMARK 280 METHOD, TEMPERATURE 293K 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 12.63150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.11150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.44800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.11150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.63150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.44800 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 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 ARG A 30 REMARK 465 LYS A 31 REMARK 465 ASP A 32 REMARK 465 GLY A 33 REMARK 465 TYR A 79 REMARK 465 SER A 80 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 THR A 34 OG1 CG2 REMARK 470 LYS A 35 CB CG CD CE NZ REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLN A 77 CG CD OE1 NE2 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 ASN A 56 -120.69 47.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MRR110B RELATED DB: TARGETDB DBREF 3E0E A 1 95 UNP Q6LYF9 Q6LYF9_METMP 173 267 SEQADV 3E0E MSE A 0 UNP Q6LYF9 EXPRESSION TAG SEQADV 3E0E LEU A 96 UNP Q6LYF9 EXPRESSION TAG SEQRES 1 A 97 MSE ASN TYR LYS ILE SER GLU LEU MSE PRO ASN LEU SER SEQRES 2 A 97 GLY THR ILE ASN ALA GLU VAL VAL THR ALA TYR PRO LYS SEQRES 3 A 97 LYS GLU PHE SER ARG LYS ASP GLY THR LYS GLY GLN LEU SEQRES 4 A 97 LYS SER LEU PHE LEU LYS ASP ASP THR GLY SER ILE ARG SEQRES 5 A 97 GLY THR LEU TRP ASN GLU LEU ALA ASP PHE GLU VAL LYS SEQRES 6 A 97 LYS GLY ASP ILE ALA GLU VAL SER GLY TYR VAL LYS GLN SEQRES 7 A 97 GLY TYR SER GLY LEU GLU ILE SER VAL ASP ASN ILE GLY SEQRES 8 A 97 ILE ILE GLU LYS SER LEU MODRES 3E0E MSE A 0 MET SELENOMETHIONINE MODRES 3E0E MSE A 8 MET SELENOMETHIONINE HET MSE A 0 8 HET MSE A 8 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *104(H2 O) HELIX 1 1 LYS A 3 LEU A 7 5 5 HELIX 2 2 GLU A 57 PHE A 61 5 5 SHEET 1 A 4 ASN A 1 TYR A 2 0 SHEET 2 A 4 LEU A 11 ALA A 22 1 O THR A 14 N TYR A 2 SHEET 3 A 4 GLY A 36 ASP A 45 -1 O LYS A 44 N GLU A 18 SHEET 4 A 4 LYS A 26 PHE A 28 -1 N LYS A 26 O LEU A 38 SHEET 1 B 7 ASN A 1 TYR A 2 0 SHEET 2 B 7 LEU A 11 ALA A 22 1 O THR A 14 N TYR A 2 SHEET 3 B 7 ILE A 68 LYS A 76 -1 O VAL A 75 N LEU A 11 SHEET 4 B 7 GLU A 83 GLU A 93 -1 O SER A 85 N TYR A 74 SHEET 5 B 7 GLY A 48 TRP A 55 1 N ARG A 51 O ILE A 84 SHEET 6 B 7 GLY A 36 ASP A 45 -1 N LEU A 41 O GLY A 52 SHEET 7 B 7 LYS A 26 PHE A 28 -1 N LYS A 26 O LEU A 38 LINK C MSE A 0 N ASN A 1 1555 1555 1.33 LINK C LEU A 7 N MSE A 8 1555 1555 1.33 LINK C MSE A 8 N PRO A 9 1555 1555 1.34 CRYST1 25.263 54.896 56.223 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 0.039584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018216 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017786 0.00000 HETATM 1 N MSE A 0 6.561 9.402 -0.858 1.00 33.15 N HETATM 2 CA MSE A 0 5.166 9.919 -0.772 1.00 32.76 C HETATM 3 C MSE A 0 4.350 9.030 0.152 1.00 31.28 C HETATM 4 O MSE A 0 4.706 7.880 0.396 1.00 31.38 O HETATM 5 CB MSE A 0 4.508 9.924 -2.156 1.00 33.72 C HETATM 6 CG MSE A 0 4.302 8.530 -2.745 1.00 38.07 C HETATM 7 SE MSE A 0 3.266 8.492 -4.387 1.00 43.47 SE HETATM 8 CE MSE A 0 1.511 8.201 -3.629 1.00 41.77 C