HEADER TRANSLATION 01-MAR-08 2VPL TITLE THE STRUCTURE OF THE COMPLEX BETWEEN THE FIRST DOMAIN OF L1 PROTEIN TITLE 2 FROM THERMUS THERMOPHILUS AND MRNA FROM METHANOCOCCUS JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L1; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: FIRST DOMAIN, RESIDUES 2-68,160-229; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1- COMPND 8 BINDING SITE; COMPND 9 CHAIN: B, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 8 ORGANISM_TAXID: 2190; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBOSOMAL PROTEIN, RNA-PROTEIN COMPLEX, TRANSLATION REGULATION, KEYWDS 2 TRANSLATION, REPRESSOR, RNA-BINDING, TRNA-BINDING, RRNA-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR V.KLJASHTORNY,S.TISHCHENKO,N.NEVSKAYA,S.NIKONOV,M.GARBER REVDAT 6 13-DEC-23 2VPL 1 REMARK LINK REVDAT 5 24-JUL-19 2VPL 1 REMARK REVDAT 4 09-AUG-17 2VPL 1 JRNL REVDAT 3 23-DEC-08 2VPL 1 COMPND REVDAT 2 16-DEC-08 2VPL 1 VERSN JRNL REVDAT 1 23-SEP-08 2VPL 0 JRNL AUTH S.TISHCHENKO,V.KLJASHTORNY,O.KOSTAREVA,N.NEVSKAYA,A.NIKULIN, JRNL AUTH 2 P.GULAK,W.PIENDL,M.GARBER,S.NIKONOV JRNL TITL DOMAIN II OF THERMUS THERMOPHILUS RIBOSOMAL PROTEIN L1 JRNL TITL 2 HINDERS RECOGNITION OF ITS MRNA. JRNL REF J. MOL. BIOL. V. 383 301 2008 JRNL REFN ESSN 1089-8638 JRNL PMID 18778715 JRNL DOI 10.1016/J.JMB.2008.08.058 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 26514 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1401 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1905 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2140 REMARK 3 NUCLEIC ACID ATOMS : 2020 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 318 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : -3.42000 REMARK 3 B33 (A**2) : 4.05000 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): 0.358 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.265 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4480 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6524 ; 1.415 ; 2.525 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 280 ; 3.021 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;24.883 ;22.292 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;11.865 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ; 8.459 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2654 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1528 ; 0.161 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2780 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 247 ; 0.210 ; 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): 29 ; 0.068 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.248 ; 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): 1383 ; 7.146 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2240 ; 8.929 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3097 ; 9.361 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4279 ;11.494 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2VPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1290035515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8423 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2HW8 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 38.05000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.17500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C2074 LIES ON A SPECIAL POSITION. 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 A D 22 REMARK 465 C D 23 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 B 2094 O HOH B 2095 2.16 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 A B 9 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 U B 24 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 G B 28 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 C B 40 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 A D 9 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G D 36 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 C D 47 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 12 41.75 -94.39 REMARK 500 LYS A 13 -10.16 -154.75 REMARK 500 ASN A 17 47.17 -106.65 REMARK 500 LYS A 36 41.80 -76.02 REMARK 500 HIS A 227 47.11 -102.44 REMARK 500 ALA C 33 79.74 -111.51 REMARK 500 LYS C 36 34.66 -73.42 REMARK 500 GLN C 56 40.05 -106.16 REMARK 500 GLU C 202 46.48 -91.17 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 A2046 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH C2047 DISTANCE = 6.05 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1229 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 42 OE1 REMARK 620 2 GLU A 42 OE2 43.5 REMARK 620 3 THR A 216 O 93.2 70.7 REMARK 620 4 THR A 217 O 129.8 86.4 67.5 REMARK 620 5 U B 41 O2' 157.9 143.5 77.3 65.0 REMARK 620 6 U B 41 O2 112.5 112.7 146.1 78.8 84.9 REMARK 620 7 U B 42 O4' 96.3 139.4 114.6 133.9 70.6 85.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C1229 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 42 OE1 REMARK 620 2 GLU C 42 OE2 42.2 REMARK 620 3 THR C 216 O 98.3 74.0 REMARK 620 4 THR C 217 O 131.1 89.7 68.4 REMARK 620 5 U D 41 O2' 164.7 147.2 79.5 62.4 REMARK 620 6 U D 41 O2 108.0 109.0 143.0 74.7 81.4 REMARK 620 7 U D 42 O4' 99.8 141.4 114.6 128.9 68.0 86.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1229 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C 1229 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZHO RELATED DB: PDB REMARK 900 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1 IN COMPLEX WITH MRNA REMARK 900 RELATED ID: 1AD2 RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L1 MUTANT WITH SERINE 179 REPLACEDBY CYSTEINE REMARK 900 RELATED ID: 2J01 RELATED DB: PDB REMARK 900 STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH REMARK 900 MRNA, TRNA AND PAROMOMYCIN REMARK 900 RELATED ID: 1EG0 RELATED DB: PDB REMARK 900 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM REMARK 900 MAP OF THE E.COLI 70S RIBOSOME REMARK 900 RELATED ID: 487D RELATED DB: PDB REMARK 900 SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO- ELECTRONMICROSCOPIC MAP REMARK 900 OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMSRESOLUTION REMARK 900 RELATED ID: 1U63 RELATED DB: PDB REMARK 900 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1- MRNA COMPLEX DBREF 2VPL A 1 67 UNP P27150 RL1_THETH 2 68 DBREF 2VPL A 159 228 UNP P27150 RL1_THETH 160 229 DBREF 2VPL B 2 48 PDB 2VPL 2VPL 2 48 DBREF 2VPL C 1 67 UNP P27150 RL1_THETH 2 68 DBREF 2VPL C 159 228 UNP P27150 RL1_THETH 160 229 DBREF 2VPL D 2 48 PDB 2VPL 2VPL 2 48 SEQRES 1 A 137 PRO LYS HIS GLY LYS ARG TYR ARG ALA LEU LEU GLU LYS SEQRES 2 A 137 VAL ASP PRO ASN LYS ILE TYR THR ILE ASP GLU ALA ALA SEQRES 3 A 137 HIS LEU VAL LYS GLU LEU ALA THR ALA LYS PHE ASP GLU SEQRES 4 A 137 THR VAL GLU VAL HIS ALA LYS LEU GLY ILE ASP PRO ARG SEQRES 5 A 137 ARG SER ASP GLN ASN VAL ARG GLY THR VAL SER LEU PRO SEQRES 6 A 137 HIS GLY GLY ARG ILE GLU PHE ARG ASN ASP LYS THR GLY SEQRES 7 A 137 ALA ILE HIS ALA PRO VAL GLY LYS ALA SER PHE PRO PRO SEQRES 8 A 137 GLU LYS LEU ALA ASP ASN ILE ARG ALA PHE ILE ARG ALA SEQRES 9 A 137 LEU GLU ALA HIS LYS PRO GLU GLY ALA LYS GLY THR PHE SEQRES 10 A 137 LEU ARG SER VAL TYR VAL THR THR THR MET GLY PRO SER SEQRES 11 A 137 VAL ARG ILE ASN PRO HIS SER SEQRES 1 B 48 G G A G U G A A G G A G G SEQRES 2 B 48 C U C G C G A A C U C G C SEQRES 3 B 48 G A A G C C G A G A A A C SEQRES 4 B 48 U U C A C U C C C SEQRES 1 C 137 PRO LYS HIS GLY LYS ARG TYR ARG ALA LEU LEU GLU LYS SEQRES 2 C 137 VAL ASP PRO ASN LYS ILE TYR THR ILE ASP GLU ALA ALA SEQRES 3 C 137 HIS LEU VAL LYS GLU LEU ALA THR ALA LYS PHE ASP GLU SEQRES 4 C 137 THR VAL GLU VAL HIS ALA LYS LEU GLY ILE ASP PRO ARG SEQRES 5 C 137 ARG SER ASP GLN ASN VAL ARG GLY THR VAL SER LEU PRO SEQRES 6 C 137 HIS GLY GLY ARG ILE GLU PHE ARG ASN ASP LYS THR GLY SEQRES 7 C 137 ALA ILE HIS ALA PRO VAL GLY LYS ALA SER PHE PRO PRO SEQRES 8 C 137 GLU LYS LEU ALA ASP ASN ILE ARG ALA PHE ILE ARG ALA SEQRES 9 C 137 LEU GLU ALA HIS LYS PRO GLU GLY ALA LYS GLY THR PHE SEQRES 10 C 137 LEU ARG SER VAL TYR VAL THR THR THR MET GLY PRO SER SEQRES 11 C 137 VAL ARG ILE ASN PRO HIS SER SEQRES 1 D 48 G G A G U G A A G G A G G SEQRES 2 D 48 C U C G C G A A C U C G C SEQRES 3 D 48 G A A G C C G A G A A A C SEQRES 4 D 48 U U C A C U C C C HET K A1229 1 HET K C1229 1 HETNAM K POTASSIUM ION FORMUL 5 K 2(K 1+) FORMUL 7 HOH *318(H2 O) HELIX 1 1 GLY A 4 LEU A 11 1 8 HELIX 2 2 GLU A 12 VAL A 14 5 3 HELIX 3 3 THR A 21 VAL A 29 1 9 HELIX 4 4 ARG A 53 ASN A 57 5 5 HELIX 5 5 PRO A 181 ALA A 198 1 18 HELIX 6 6 GLY C 4 LEU C 11 1 8 HELIX 7 7 THR C 21 VAL C 29 1 9 HELIX 8 8 PRO C 181 HIS C 199 1 19 SHEET 1 AA 4 ALA A 170 LYS A 177 0 SHEET 2 AA 4 THR A 40 LEU A 47 -1 O VAL A 41 N VAL A 175 SHEET 3 AA 4 LEU A 209 THR A 216 -1 N ARG A 210 O LYS A 46 SHEET 4 AA 4 SER A 221 ARG A 223 -1 O VAL A 222 N VAL A 214 SHEET 1 AB 2 ARG A 59 SER A 63 0 SHEET 2 AB 2 ARG A 160 ARG A 164 -1 O ILE A 161 N VAL A 62 SHEET 1 CA 4 ALA C 170 LYS C 177 0 SHEET 2 CA 4 THR C 40 LEU C 47 -1 O VAL C 41 N VAL C 175 SHEET 3 CA 4 LEU C 209 THR C 216 -1 N ARG C 210 O LYS C 46 SHEET 4 CA 4 VAL C 222 ILE C 224 -1 O VAL C 222 N VAL C 214 SHEET 1 CB 2 ARG C 59 SER C 63 0 SHEET 2 CB 2 ARG C 160 ARG C 164 -1 O ILE C 161 N VAL C 62 LINK OE1 GLU A 42 K K A1229 1555 1555 2.92 LINK OE2 GLU A 42 K K A1229 1555 1555 2.96 LINK O THR A 216 K K A1229 1555 1555 2.83 LINK O THR A 217 K K A1229 1555 1555 3.14 LINK K K A1229 O2' U B 41 1555 1555 3.03 LINK K K A1229 O2 U B 41 1555 1555 2.48 LINK K K A1229 O4' U B 42 1555 1555 3.28 LINK OE1 GLU C 42 K K C1229 1555 1555 3.15 LINK OE2 GLU C 42 K K C1229 1555 1555 2.86 LINK O THR C 216 K K C1229 1555 1555 2.78 LINK O THR C 217 K K C1229 1555 1555 3.31 LINK K K C1229 O2' U D 41 1555 1555 2.91 LINK K K C1229 O2 U D 41 1555 1555 2.83 LINK K K C1229 O4' U D 42 1555 1555 3.32 SITE 1 AC1 5 GLU A 42 THR A 216 THR A 217 U B 41 SITE 2 AC1 5 U B 42 SITE 1 AC2 5 GLU C 42 THR C 216 THR C 217 U D 41 SITE 2 AC2 5 U D 42 CRYST1 76.100 144.350 56.160 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 0.013141 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017806 0.00000