HEADER RIBOSOME, RNA BINDING PROTEIN 11-DEC-05 2FC3 TITLE CRYSTAL STRUCTURE OF THE EXTREMELY THERMOSTABLE AEROPYRUM PERNIX L7AE TITLE 2 MULTIFUNCTIONAL 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: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 56636; SOURCE 4 GENE: RPL7AE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALPHA-BETA-ALPHA SANDWICH, RIBOSOME, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.A.BROWN II,J.SURYADI,Z.ZHOU,T.B.GUPTON JR.,S.L.FLOWERS REVDAT 5 30-AUG-23 2FC3 1 REMARK REVDAT 4 18-OCT-17 2FC3 1 REMARK REVDAT 3 11-SEP-13 2FC3 1 JRNL VERSN REVDAT 2 24-FEB-09 2FC3 1 VERSN REVDAT 1 28-NOV-06 2FC3 0 JRNL AUTH M.W.BHUIYA,J.SURYADI,Z.ZHOU,B.A.BROWN JRNL TITL STRUCTURE OF THE AEROPYRUM PERNIX L7AE MULTIFUNCTIONAL JRNL TITL 2 PROTEIN AND INSIGHT INTO ITS EXTREME THERMOSTABILITY. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 69 979 2013 JRNL REFN ESSN 1744-3091 JRNL PMID 23989144 JRNL DOI 10.1107/S1744309113021799 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 13737 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 + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 695 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) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 217 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 10 REMARK 3 BIN FREE R VALUE : 0.8750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.56000 REMARK 3 B33 (A**2) : 0.54000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.913 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 970 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 689 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1311 ; 1.419 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1693 ; 0.928 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 123 ; 5.482 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 37 ;27.439 ;24.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 185 ;11.016 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;15.801 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 156 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1049 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 171 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 208 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 739 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 493 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 506 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 76 ; 0.121 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.049 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.363 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.118 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 808 ; 1.542 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 249 ; 0.431 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1007 ; 1.822 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 389 ; 3.161 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 304 ; 4.634 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1947 ; 2.132 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 119 ;11.286 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1646 ; 3.042 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2FC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-04 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC CONFOCAL BLUE MAX-FLUX REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, CRYSTALCLEAR V. 1.3.6 REMARK 200 (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, CRYSTALCLEAR V. 1.3.6 REMARK 200 (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 65.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.5 REMARK 200 DATA REDUNDANCY : 2.450 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 15.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.08 REMARK 200 R MERGE FOR SHELL (I) : 0.28900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR 2.5 REMARK 200 STARTING MODEL: 1XBI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 10% ISOPROPANOL, 100 MM REMARK 280 HEPES-KOH, PH 7.5, 1 MM ZNCL2 MIXED 1:2 WITH 500 MICROMOLAR L7AE REMARK 280 PROTEIN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 17.52700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.52400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.59400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.52400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.52700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.59400 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 DBREF 2FC3 A 4 127 UNP Q9YAX7 RL7A_AERPE 4 127 SEQRES 1 A 124 PRO ILE TYR VAL ARG PHE GLU VAL PRO GLU ASP LEU ALA SEQRES 2 A 124 GLU LYS ALA TYR GLU ALA VAL LYS ARG ALA ARG GLU THR SEQRES 3 A 124 GLY ARG ILE LYS LYS GLY THR ASN GLU THR THR LYS ALA SEQRES 4 A 124 VAL GLU ARG GLY LEU ALA LYS LEU VAL VAL ILE ALA GLU SEQRES 5 A 124 ASP VAL ASP PRO PRO GLU ILE VAL MET HIS LEU PRO LEU SEQRES 6 A 124 LEU CYS ASP GLU LYS LYS ILE PRO TYR VAL TYR VAL PRO SEQRES 7 A 124 SER LYS LYS ARG LEU GLY GLU ALA ALA GLY ILE GLU VAL SEQRES 8 A 124 ALA ALA ALA SER VAL ALA ILE ILE GLU PRO GLY ASP ALA SEQRES 9 A 124 GLU THR LEU VAL ARG GLU ILE VAL GLU LYS VAL LYS GLU SEQRES 10 A 124 LEU ARG ALA LYS ALA GLY VAL FORMUL 2 HOH *119(H2 O) HELIX 1 1 PRO A 12 GLY A 30 1 19 HELIX 2 2 GLY A 35 ARG A 45 1 11 HELIX 3 3 PRO A 59 VAL A 63 5 5 HELIX 4 4 HIS A 65 LYS A 73 1 9 HELIX 5 5 SER A 82 ALA A 90 1 9 HELIX 6 6 PRO A 104 ASP A 106 5 3 HELIX 7 7 ALA A 107 GLY A 126 1 20 SHEET 1 A 4 ARG A 31 LYS A 34 0 SHEET 2 A 4 SER A 98 GLU A 103 -1 O ALA A 100 N LYS A 33 SHEET 3 A 4 LEU A 50 ALA A 54 -1 N LEU A 50 O ILE A 101 SHEET 4 A 4 TYR A 77 VAL A 80 1 O VAL A 78 N VAL A 51 CISPEP 1 ASP A 58 PRO A 59 0 1.89 CRYST1 35.054 49.188 65.048 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 0.028530 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015370 0.00000