HEADER STRUCTURAL PROTEIN 31-OCT-03 1RA4 TITLE CRYSTAL STRUCTURE OF THE METHANOCOCCUS JANNASCHII L7AE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L7AE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: RPL7AE, MJ1203; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS (NOVAGEN); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALPHA-BETA-ALPHA SANDWICH FOLD, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SURYADI,E.J.TRAN,E.S.MAXWELL,B.A.BROWN REVDAT 4 23-AUG-23 1RA4 1 SEQADV REVDAT 3 24-FEB-09 1RA4 1 VERSN REVDAT 2 09-AUG-05 1RA4 1 JRNL REVDAT 1 16-NOV-04 1RA4 0 JRNL AUTH J.SURYADI,E.J.TRAN,E.S.MAXWELL,B.A.BROWN JRNL TITL THE CRYSTAL STRUCTURE OF THE METHANOCALDOCOCCUS JANNASCHII JRNL TITL 2 MULTIFUNCTIONAL L7AE RNA-BINDING PROTEIN REVEALS AN JRNL TITL 3 INDUCED-FIT INTERACTION WITH THE BOX C/D RNAS. JRNL REF BIOCHEMISTRY V. 44 9657 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16008351 JRNL DOI 10.1021/BI050568Q REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.J.TRAN,X.ZHANG,E.S.MAXWELL REMARK 1 TITL EFFICIENT RNA 2'-O-METHYLATION REQUIRES JUXAPOSED AND REMARK 1 TITL 2 SYMMETRICALLY ASSEMBLED ARCHAEAL BOX C/D AND C'/D' RNPS REMARK 1 REF EMBO J. V. 22 3930 2003 REMARK 1 REFN ISSN 0261-4189 REMARK 1 DOI 10.1093/EMBOJ/CDG368 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.F.KUHN,E.J.TRAN,E.S.MAXWELL REMARK 1 TITL ARCHAEAL RIBOSOMAL PROTEIN L7 IS A FUNCTIONAL HOMOLOG OF THE REMARK 1 TITL 2 EUKARYOTIC 15.5KD/SNU13P SNORNP CORE PROTEIN REMARK 1 REF NUCLEIC ACIDS RES. V. 30 931 2002 REMARK 1 REFN ISSN 0305-1048 REMARK 1 DOI 10.1093/NAR/30.4.931 REMARK 2 REMARK 2 RESOLUTION. 1.86 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 486425.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 9576 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) : 0.173 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 991 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1385 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 137 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 211 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : 0.75000 REMARK 3 B33 (A**2) : -1.40000 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) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.03 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.790 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 : 0.41 REMARK 3 BSOL : 54.75 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 : 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: NULL REMARK 4 REMARK 4 1RA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000020623. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 35.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 26.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15100 REMARK 200 FOR SHELL : 12.97 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: THREADED MODEL CREATED IN SWISS PROT USING A REMARK 200 COMPOSITE OF THE FOLLOWING PDB ENTRIES: 1E7K 1CK2 1JJ2 MOL_ID 8; REMARK 200 CHAIN: F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % PEG 4000, 10 % ISOPROPANOL, 100 REMARK 280 MM HEPES-NAOH, PH 7.5 , VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K 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 21.94850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.98750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.18000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.98750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.94850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.18000 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 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 54 O HOH A 286 2.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 1RA4 A 4 120 UNP P54066 RL7A_METJA 1 117 SEQADV 1RA4 GLY A 1 UNP P54066 CLONING ARTIFACT SEQADV 1RA4 SER A 2 UNP P54066 CLONING ARTIFACT SEQADV 1RA4 HIS A 3 UNP P54066 CLONING ARTIFACT SEQRES 1 A 120 GLY SER HIS MET ALA VAL TYR VAL LYS PHE LYS VAL PRO SEQRES 2 A 120 GLU GLU ILE GLN LYS GLU LEU LEU ASP ALA VAL ALA LYS SEQRES 3 A 120 ALA GLN LYS ILE LYS LYS GLY ALA ASN GLU VAL THR LYS SEQRES 4 A 120 ALA VAL GLU ARG GLY ILE ALA LYS LEU VAL ILE ILE ALA SEQRES 5 A 120 GLU ASP VAL LYS PRO GLU GLU VAL VAL ALA HIS LEU PRO SEQRES 6 A 120 TYR LEU CYS GLU GLU LYS GLY ILE PRO TYR ALA TYR VAL SEQRES 7 A 120 ALA SER LYS GLN ASP LEU GLY LYS ALA ALA GLY LEU GLU SEQRES 8 A 120 VAL ALA ALA SER SER VAL ALA ILE ILE ASN GLU GLY ASP SEQRES 9 A 120 ALA GLU GLU LEU LYS VAL LEU ILE GLU LYS VAL ASN VAL SEQRES 10 A 120 LEU LYS GLN FORMUL 2 HOH *211(H2 O) HELIX 1 1 PRO A 13 ALA A 27 1 15 HELIX 2 2 GLY A 33 ARG A 43 1 11 HELIX 3 3 PRO A 57 VAL A 61 5 5 HELIX 4 4 HIS A 63 LYS A 71 1 9 HELIX 5 5 SER A 80 ALA A 88 1 9 HELIX 6 6 ASP A 104 LYS A 119 1 16 SHEET 1 A 4 LYS A 29 LYS A 32 0 SHEET 2 A 4 SER A 96 ASN A 101 -1 O ILE A 100 N LYS A 29 SHEET 3 A 4 LEU A 48 ALA A 52 -1 N ILE A 50 O VAL A 97 SHEET 4 A 4 TYR A 75 VAL A 78 1 O ALA A 76 N ILE A 51 CISPEP 1 LYS A 56 PRO A 57 0 -2.97 CRYST1 43.897 46.360 53.975 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 0.022781 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018527 0.00000