HEADER TRANSCRIPTION 04-JUL-05 2CY1 TITLE CRYSTAL STRUCTURE OF APE1850 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUSA PROTEIN HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HYPOTHETICAL PROTEIN APE1850; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 STRAIN: K1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS TRANSCRIPTION TERMINATION, RNA BINDING PROTEIN, ARCHAEAL NUSA, KH KEYWDS 2 DOMAIN, MICROGRAVITY, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT KEYWDS 3 ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.SHIBATA,Y.BESSHO,T.UMEHARA,M.SHIROUZU,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 25-OCT-23 2CY1 1 REMARK REVDAT 4 13-JUL-11 2CY1 1 VERSN REVDAT 3 20-JAN-09 2CY1 1 JRNL VERSN REVDAT 2 04-JUL-06 2CY1 1 AUTHOR JRNL REVDAT 1 04-JAN-06 2CY1 0 JRNL AUTH H.TANAKA,T.UMEHARA,K.INAKA,S.TAKAHASHI,R.SHIBATA,Y.BESSHO, JRNL AUTH 2 M.SATO,S.SUGIYAMA,E.FUSATOMI,T.TERADA,M.SHIROUZU,S.SANO, JRNL AUTH 3 M.MOTOHARA,T.KOBAYASHI,T.TANAKA,A.TANAKA,S.YOKOYAMA JRNL TITL CRYSTALLIZATION OF THE ARCHAEAL TRANSCRIPTION TERMINATION JRNL TITL 2 FACTOR NUSA: A SIGNIFICANT DECREASE IN TWINNING UNDER JRNL TITL 3 MICROGRAVITY CONDITIONS JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 63 69 2007 JRNL REFN ESSN 1744-3091 JRNL PMID 17277442 JRNL DOI 10.1107/S1744309106054625 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 481555.370 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 9904 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) : 0.209 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1027 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 424 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 41 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.054 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1080 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.43000 REMARK 3 B22 (A**2) : -2.43000 REMARK 3 B33 (A**2) : 4.86000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.590 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) : 4.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.090 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.680 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.440 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 36.22 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.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CY1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000024755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI (311) CUT SAGITTAL DOUBLE REMARK 200 -CRYSTAL 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9945 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.875 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.3989 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.058 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2CXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM PHOSPHATE, LIQUID REMARK 280 DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 49.88500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 49.88500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.90600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.45300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.88500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.35900 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 49.88500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.88500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.90600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 49.88500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.35900 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 49.88500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 11.45300 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 ASP A 4 REMARK 465 TYR A 5 REMARK 465 ARG A 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APE001001850.2 RELATED DB: TARGETDB DBREF 2CY1 A 1 144 UNP Q9YAU4 Q9YAU4_AERPE 1 144 SEQRES 1 A 144 MET SER GLY ASP TYR ARG ILE THR LEU GLU GLU LEU ARG SEQRES 2 A 144 TYR ILE SER VAL PHE HIS SER ILE THR GLY VAL THR ALA SEQRES 3 A 144 TYR ARG CYS ILE VAL ASP GLU GLU ASN ASN ARG LEU ILE SEQRES 4 A 144 PHE LEU VAL SER GLU GLY GLU ALA GLY ARG ALA ILE GLY SEQRES 5 A 144 ARG GLY GLY ARG LEU ILE LYS LEU LEU ARG GLU ALA LEU SEQRES 6 A 144 GLY LYS ASN ILE GLU VAL VAL GLU TYR SER SER ASP LEU SEQRES 7 A 144 GLU ARG ILE VAL LYS ASN LEU PHE PRO GLY VAL LYS ILE SEQRES 8 A 144 GLU SER ILE ASN VAL ARG GLU ARG ASN GLY VAL LYS GLN SEQRES 9 A 144 VAL VAL ILE LYS VAL SER GLU ASP ASP LYS GLY ALA ALA SEQRES 10 A 144 ILE GLY LYS GLY GLY LYS ASN VAL LYS ARG ALA ARG LEU SEQRES 11 A 144 VAL LEU SER LYS LEU PHE GLY VAL GLU LYS VAL VAL ILE SEQRES 12 A 144 ARG FORMUL 2 HOH *25(H2 O) HELIX 1 1 THR A 8 GLY A 23 1 16 HELIX 2 2 GLU A 33 ASN A 35 5 3 HELIX 3 3 GLU A 46 GLY A 52 1 7 HELIX 4 4 GLY A 55 GLY A 66 1 12 HELIX 5 5 ASP A 77 PHE A 86 1 10 HELIX 6 6 ASP A 113 GLY A 119 1 7 HELIX 7 7 GLY A 122 GLY A 137 1 16 SHEET 1 A 3 ALA A 26 ASP A 32 0 SHEET 2 A 3 ARG A 37 VAL A 42 -1 O LEU A 41 N ARG A 28 SHEET 3 A 3 ASN A 68 GLU A 73 1 O GLU A 70 N PHE A 40 SHEET 1 B 3 SER A 93 ARG A 99 0 SHEET 2 B 3 VAL A 102 LYS A 108 -1 O LYS A 108 N SER A 93 SHEET 3 B 3 VAL A 138 ILE A 143 1 O VAL A 142 N ILE A 107 CRYST1 99.770 99.770 45.812 90.00 90.00 90.00 I 41 8 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 0.010023 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021828 0.00000