HEADER RIBOSOMAL PROTEIN 01-APR-08 3CPQ TITLE CRYSTAL STRUCTURE OF L30E A RIBOSOMAL PROTEIN FROM METHANOCALDOCOCCUS TITLE 2 JANNASCHII DSM2661 (MJ1044) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L30E; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII; SOURCE 4 ORGANISM_TAXID: 2190; SOURCE 5 STRAIN: DSM2661; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS RIBOSOMAL, RNA-PROTEIN, ELONGATION FACTOR, RIBONUCLEOPROTEIN, KEYWDS 2 RIBOSOMAL PROTEIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 3 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR J.JEYAKANTHAN,R.SARANI,P.MRIDULA,K.SEKAR,S.KURAMITSU,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 2 01-NOV-23 3CPQ 1 REMARK REVDAT 1 07-APR-09 3CPQ 0 JRNL AUTH J.JEYAKANTHAN,R.SARANI,P.MRIDULA,K.SEKAR,S.KURAMITSU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF L30E A RIBOSOMAL PROTEIN FROM JRNL TITL 2 METHANOCALDOCOCCUS JANNASCHII DSM2661 (MJ1044) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 984491.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 15776 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) : 0.202 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 765 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1755 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 84 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1532 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.49000 REMARK 3 B22 (A**2) : 2.35000 REMARK 3 B33 (A**2) : -4.84000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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 : 0.38 REMARK 3 BSOL : 64.07 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 3 : ION.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : WATER_PROTIN.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CPQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 1 1 1 DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : RH COATED BENT-CYRINDRICAL REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16282 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : 0.54100 REMARK 200 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1W41 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG400, 0.1 MES, 5% PEG3000, PH REMARK 280 6.0, MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.25450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.88175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.62725 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 GLU A 5 REMARK 465 ASN A 6 REMARK 465 LYS A 106 REMARK 465 GLU A 107 REMARK 465 GLY A 108 REMARK 465 GLY A 109 REMARK 465 GLU A 110 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 3 REMARK 465 ARG B 4 REMARK 465 GLU B 5 REMARK 465 ASN B 6 REMARK 465 GLY B 108 REMARK 465 GLY B 109 REMARK 465 GLU B 110 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 LYS B 105 40.44 -107.64 REMARK 500 REMARK 500 REMARK: NULL DBREF 3CPQ A 1 110 UNP P54061 RL30E_METJA 1 110 DBREF 3CPQ B 1 110 UNP P54061 RL30E_METJA 1 110 SEQRES 1 A 110 MET ARG ARG ARG GLU ASN MET ASP VAL ASN LYS ALA ILE SEQRES 2 A 110 ARG THR ALA VAL ASP THR GLY LYS VAL ILE LEU GLY SER SEQRES 3 A 110 LYS ARG THR ILE LYS PHE VAL LYS HIS GLY GLU GLY LYS SEQRES 4 A 110 LEU VAL VAL LEU ALA GLY ASN ILE PRO LYS ASP LEU GLU SEQRES 5 A 110 GLU ASP VAL LYS TYR TYR ALA LYS LEU SER ASN ILE PRO SEQRES 6 A 110 VAL TYR GLN HIS LYS ILE THR SER LEU GLU LEU GLY ALA SEQRES 7 A 110 VAL CYS GLY LYS PRO PHE PRO VAL ALA ALA LEU LEU VAL SEQRES 8 A 110 LEU ASP GLU GLY LEU SER ASN ILE MET GLU LEU VAL GLU SEQRES 9 A 110 LYS LYS GLU GLY GLY GLU SEQRES 1 B 110 MET ARG ARG ARG GLU ASN MET ASP VAL ASN LYS ALA ILE SEQRES 2 B 110 ARG THR ALA VAL ASP THR GLY LYS VAL ILE LEU GLY SER SEQRES 3 B 110 LYS ARG THR ILE LYS PHE VAL LYS HIS GLY GLU GLY LYS SEQRES 4 B 110 LEU VAL VAL LEU ALA GLY ASN ILE PRO LYS ASP LEU GLU SEQRES 5 B 110 GLU ASP VAL LYS TYR TYR ALA LYS LEU SER ASN ILE PRO SEQRES 6 B 110 VAL TYR GLN HIS LYS ILE THR SER LEU GLU LEU GLY ALA SEQRES 7 B 110 VAL CYS GLY LYS PRO PHE PRO VAL ALA ALA LEU LEU VAL SEQRES 8 B 110 LEU ASP GLU GLY LEU SER ASN ILE MET GLU LEU VAL GLU SEQRES 9 B 110 LYS LYS GLU GLY GLY GLU FORMUL 3 HOH *127(H2 O) HELIX 1 1 MET A 7 GLY A 20 1 14 HELIX 2 2 GLY A 25 HIS A 35 1 11 HELIX 3 3 PRO A 48 SER A 62 1 15 HELIX 4 4 THR A 72 CYS A 80 1 9 HELIX 5 5 ASN A 98 LYS A 105 1 8 HELIX 6 6 MET B 7 GLY B 20 1 14 HELIX 7 7 GLY B 25 HIS B 35 1 11 HELIX 8 8 PRO B 48 SER B 62 1 15 HELIX 9 9 THR B 72 CYS B 80 1 9 HELIX 10 10 ASN B 98 LYS B 105 1 8 SHEET 1 A 4 LYS A 21 LEU A 24 0 SHEET 2 A 4 ALA A 88 ASP A 93 -1 O LEU A 90 N ILE A 23 SHEET 3 A 4 LEU A 40 LEU A 43 -1 N LEU A 40 O VAL A 91 SHEET 4 A 4 VAL A 66 GLN A 68 1 O TYR A 67 N VAL A 41 SHEET 1 B 4 LYS B 21 LEU B 24 0 SHEET 2 B 4 ALA B 88 ASP B 93 -1 O LEU B 90 N ILE B 23 SHEET 3 B 4 LEU B 40 LEU B 43 -1 N LEU B 40 O VAL B 91 SHEET 4 B 4 VAL B 66 GLN B 68 1 O TYR B 67 N VAL B 41 CRYST1 46.115 46.115 98.509 90.00 90.00 90.00 P 43 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 0.021685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010151 0.00000