PDB Short entry for 1H7M HEADER RIBOSOMAL PROTEIN 09-JUL-01 1H7M TITLE RIBOSOMAL PROTEIN L30E FROM THERMOCOCCUS CELER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L30E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RPL30E, RPL30; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS CELER; SOURCE 3 ORGANISM_TAXID: 2264; SOURCE 4 ATCC: 35543; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSET-A KEYWDS RIBOSOMAL PROTEIN, RNA-BINDING, RIBOSOME, THERMOPHILIC EXPDTA X-RAY DIFFRACTION AUTHOR Y.W.CHEN,K.B.WONG REVDAT 3 24-JAN-18 1H7M 1 SOURCE REVDAT 2 24-FEB-09 1H7M 1 VERSN REVDAT 1 04-APR-03 1H7M 0 JRNL AUTH Y.W.CHEN,M.BYCROFT,K.B.WONG JRNL TITL CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L30E FROM THE EXTREME JRNL TITL 2 THERMOPHILE THERMOCCCUS CELER: THERMAL STABILITY AND RNA JRNL TITL 3 BINDING JRNL REF BIOCHEMISTRY V. 42 2857 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12627951 JRNL DOI 10.1021/BI027131S REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.B.WONG,W.K.WANG,M.R.PROCTOR,M.BYCROFT,Y.W.CHEN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC STUDIES OF REMARK 1 TITL 2 A RIBOSOMAL PROTEIN L30E FROM THE HYPERTHERMOPHILIC ARCHAEON REMARK 1 TITL 3 THERMOCOCCUS CELER REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. D57 865 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11375510 REMARK 1 DOI 10.1107/S0907444901004607 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.MAO,J.R.WILLAMSON REMARK 1 TITL LOCAL FOLDING COUPLED TO RNA BINDING IN THE YEAST RIBOSOMAL REMARK 1 TITL 2 PROTEIN L30 REMARK 1 REF J.MOL.BIOL. V. 292 345 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10493880 REMARK 1 DOI 10.1006/JMBI.1999.3044 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.MAO,S.A.WHITE,J.R.WILLAMSON REMARK 1 TITL A NOVEL LOOP-LOOP RECOGNITION MOTIF IN THE YEAST RIBOSOMAL REMARK 1 TITL 2 PROTEIN L30 AUTOREGULATORY RNA COMPLEX REMARK 1 REF NAT.STRUCT.BIOL. V. 6 1139 1999 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 10581556 REMARK 1 DOI 10.1038/70081 REMARK 1 REFERENCE 4 REMARK 1 AUTH N.BAN,P.NISSEN,J.HANSEN,P.B.MOORE,T.A.STEITZ REMARK 1 TITL THE COMPLETE ATOMIC STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT REMARK 1 TITL 2 AT 2.4 A RESOLUTION REMARK 1 REF SCIENCE V. 289 905 2000 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 10937989 REMARK 1 DOI 10.1126/SCIENCE.289.5481.905 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 7608 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 618 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 729 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.55000 REMARK 3 B12 (A**2) : 0.52000 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): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.612 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: GLY-97 - GLU-100 ARE NOT SEEN IN THE REMARK 3 DENISTY MAPS SIDECHAINS OF MET-18, SER-67 AND SER-80 HAVE REMARK 3 MULTIPLE CONFORMATIONS REMARK 4 REMARK 4 1H7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1290008280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 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 : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8226 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 24.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.34300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: UNPUBLISHED NMR STRUCTURE OF THE SAME L30E PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM KH2PO4, 20%(W/V) PEG8000, PH 5.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.80667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.61333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.21000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.01667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.40333 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 BELONGS TO THE L30E FAMILY OF RIBOSOMAL PROTEINS. 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 98 REMARK 465 LYS A 99 REMARK 465 GLU A 100 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLY A -2 N CA O REMARK 470 ARG A 21 CD NE CZ NH1 NH2 REMARK 470 ARG A 39 CD NE CZ NH1 NH2 REMARK 470 ARG A 76 CD NE CZ NH1 NH2 REMARK 470 GLY A 97 CA C O 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 O HOH A 2026 O HOH A 2027 1.94 REMARK 500 O HOH A 2083 O HOH A 2120 2.04 REMARK 500 O HOH A 2059 O HOH A 2060 2.10 REMARK 500 O HOH A 2026 O HOH A 2103 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 48 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2012 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2041 DISTANCE = 6.33 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GO0 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF RIBOSOMAL PROTEIN L30E FROM THERMOCOCCUS CELER. REMARK 900 RELATED ID: 1GO1 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF RIBOSOMAL PROTEIN L30E FROM THERMOCOCCUS CELER. DBREF 1H7M A -2 -1 PDB 1H7M 1H7M -2 -1 DBREF 1H7M A 1 100 UNP P29160 RL3E_THECE 2 101 SEQRES 1 A 102 GLY SER VAL ASP PHE ALA PHE GLU LEU ARG LYS ALA GLN SEQRES 2 A 102 ASP THR GLY LYS ILE VAL MET GLY ALA ARG LYS SER ILE SEQRES 3 A 102 GLN TYR ALA LYS MET GLY GLY ALA LYS LEU ILE ILE VAL SEQRES 4 A 102 ALA ARG ASN ALA ARG PRO ASP ILE LYS GLU ASP ILE GLU SEQRES 5 A 102 TYR TYR ALA ARG LEU SER GLY ILE PRO VAL TYR GLU PHE SEQRES 6 A 102 GLU GLY THR SER VAL GLU LEU GLY THR LEU LEU GLY ARG SEQRES 7 A 102 PRO HIS THR VAL SER ALA LEU ALA VAL VAL ASP PRO GLY SEQRES 8 A 102 GLU SER ARG ILE LEU ALA LEU GLY GLY LYS GLU FORMUL 2 HOH *120(H2 O) HELIX 1 1 ASP A 2 GLY A 14 1 13 HELIX 2 2 GLY A 19 MET A 29 1 11 HELIX 3 3 ARG A 42 GLY A 57 1 16 HELIX 4 4 THR A 66 LEU A 74 1 9 HELIX 5 5 ARG A 92 LEU A 96 5 5 SHEET 1 AA 4 LYS A 15 MET A 18 0 SHEET 2 AA 4 ALA A 82 ASP A 87 -1 O ALA A 84 N VAL A 17 SHEET 3 AA 4 LEU A 34 ALA A 38 -1 O LEU A 34 N VAL A 85 SHEET 4 AA 4 VAL A 60 PHE A 63 1 O TYR A 61 N VAL A 37 CRYST1 48.320 48.320 86.420 90.00 90.00 120.00 P 61 6 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 0.020695 0.011948 0.000000 0.00000 SCALE2 0.000000 0.023897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011571 0.00000