PDB Short entry for 1PXW HEADER RIBOSOME 07-JUL-03 1PXW TITLE CRYSTAL STRUCTURE OF L7AE SRNP CORE PROTEIN FROM PYROCOCCUS ABYSSII COMPND MOL_ID: 1; COMPND 2 MOLECULE: LSU RIBOSOMAL PROTEIN L7AE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 29292; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBOSOME EXPDTA X-RAY DIFFRACTION AUTHOR C.CHARRON,X.MANIVAL,B.CHARPENTIER,C.BRANLANT,A.AUBRY REVDAT 4 14-FEB-24 1PXW 1 REMARK REVDAT 3 11-OCT-17 1PXW 1 REMARK REVDAT 2 24-FEB-09 1PXW 1 VERSN REVDAT 1 27-JAN-04 1PXW 0 JRNL AUTH C.CHARRON,X.MANIVAL,B.CHARPENTIER,C.BRANLANT,A.AUBRY JRNL TITL PURIFICATION, CRYSTALLIZATION AND PRELIMINARY X-RAY JRNL TITL 2 DIFFRACTION DATA OF L7AE SRNP CORE PROTEIN FROM PYROCOCCUS JRNL TITL 3 ABYSSII. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 122 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 14684904 JRNL DOI 10.1107/S090744490302239X REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 932 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 72 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1903 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.233 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME 2000, MAGNESIUM CHLORIDE, REMARK 280 SODIUM ACETATE, PH 4.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 33.59500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.27500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 3 REMARK 465 TRP B 4 REMARK 465 MET B 5 REMARK 465 MET B 6 REMARK 465 ALA B 7 REMARK 465 LYS B 8 DBREF 1PXW A 1 128 UNP P62008 RL7A_PYRAB 1 128 DBREF 1PXW B 1 128 UNP P62008 RL7A_PYRAB 1 128 SEQRES 1 A 128 MET GLU GLY TRP MET MET ALA LYS PRO SER TYR VAL LYS SEQRES 2 A 128 PHE GLU VAL PRO LYS GLU LEU ALA GLU LYS ALA LEU GLN SEQRES 3 A 128 ALA VAL GLU ILE ALA ARG ASP THR GLY LYS ILE ARG LYS SEQRES 4 A 128 GLY THR ASN GLU THR THR LYS ALA VAL GLU ARG GLY GLN SEQRES 5 A 128 ALA LYS LEU VAL ILE ILE ALA GLU ASP VAL ASP PRO GLU SEQRES 6 A 128 GLU ILE VAL ALA HIS LEU PRO PRO LEU CYS GLU GLU LYS SEQRES 7 A 128 GLU ILE PRO TYR ILE TYR VAL PRO SER LYS LYS GLU LEU SEQRES 8 A 128 GLY ALA ALA ALA GLY ILE GLU VAL ALA ALA ALA SER VAL SEQRES 9 A 128 ALA ILE ILE GLU PRO GLY LYS ALA ARG ASP LEU VAL GLU SEQRES 10 A 128 GLU ILE ALA MET LYS VAL ARG GLU LEU MET LYS SEQRES 1 B 128 MET GLU GLY TRP MET MET ALA LYS PRO SER TYR VAL LYS SEQRES 2 B 128 PHE GLU VAL PRO LYS GLU LEU ALA GLU LYS ALA LEU GLN SEQRES 3 B 128 ALA VAL GLU ILE ALA ARG ASP THR GLY LYS ILE ARG LYS SEQRES 4 B 128 GLY THR ASN GLU THR THR LYS ALA VAL GLU ARG GLY GLN SEQRES 5 B 128 ALA LYS LEU VAL ILE ILE ALA GLU ASP VAL ASP PRO GLU SEQRES 6 B 128 GLU ILE VAL ALA HIS LEU PRO PRO LEU CYS GLU GLU LYS SEQRES 7 B 128 GLU ILE PRO TYR ILE TYR VAL PRO SER LYS LYS GLU LEU SEQRES 8 B 128 GLY ALA ALA ALA GLY ILE GLU VAL ALA ALA ALA SER VAL SEQRES 9 B 128 ALA ILE ILE GLU PRO GLY LYS ALA ARG ASP LEU VAL GLU SEQRES 10 B 128 GLU ILE ALA MET LYS VAL ARG GLU LEU MET LYS FORMUL 3 HOH *133(H2 O) HELIX 1 1 GLY A 3 ALA A 7 5 5 HELIX 2 2 PRO A 17 GLY A 35 1 19 HELIX 3 3 GLY A 40 ARG A 50 1 11 HELIX 4 4 PRO A 64 VAL A 68 5 5 HELIX 5 5 HIS A 70 LYS A 78 1 9 HELIX 6 6 SER A 87 ALA A 95 1 9 HELIX 7 7 PRO A 109 LYS A 111 5 3 HELIX 8 8 ALA A 112 MET A 127 1 16 HELIX 9 9 PRO B 17 GLY B 35 1 19 HELIX 10 10 GLY B 40 ARG B 50 1 11 HELIX 11 11 PRO B 64 VAL B 68 5 5 HELIX 12 12 HIS B 70 LYS B 78 1 9 HELIX 13 13 SER B 87 ALA B 95 1 9 HELIX 14 14 PRO B 109 LYS B 111 5 3 HELIX 15 15 ALA B 112 MET B 127 1 16 SHEET 1 A 4 LYS A 36 LYS A 39 0 SHEET 2 A 4 SER A 103 GLU A 108 -1 O ILE A 107 N LYS A 36 SHEET 3 A 4 LEU A 55 ALA A 59 -1 N ILE A 57 O VAL A 104 SHEET 4 A 4 TYR A 82 VAL A 85 1 O ILE A 83 N VAL A 56 SHEET 1 B 4 LYS B 36 LYS B 39 0 SHEET 2 B 4 SER B 103 GLU B 108 -1 O ALA B 105 N ARG B 38 SHEET 3 B 4 LEU B 55 ALA B 59 -1 N ILE B 57 O VAL B 104 SHEET 4 B 4 TYR B 82 VAL B 85 1 O ILE B 83 N ILE B 58 CISPEP 1 ASP A 63 PRO A 64 0 -0.25 CISPEP 2 ASP B 63 PRO B 64 0 -0.07 CRYST1 67.190 112.550 34.510 90.00 90.00 90.00 P 21 21 2 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 0.014883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028977 0.00000