10 20 30 40 50 60 70 80 1DUH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER RNA 17-JAN-00 1DUH
TITLE CRYSTAL STRUCTURE OF THE CONSERVED DOMAIN IV OF E. COLI TITLE 2 4.5S RNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4.5S RNA DOMAIN IV; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN IV; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA SEQUENCE TAKEN FROM ESCHERICHIA COLI SOURCE 4 4.5S RNA. THE RNA WAS PRODUCED BY T7 RNA POLYMERASE IN SOURCE 5 VITRO TRANSCRIPTION USING RIBOZYME TECHNOLOGY
KEYWDS 4.5S RNA, DOMAIN IV, HELIX 8, SIGNAL RECOGNITION PARTICLE, KEYWDS 2 SRP, FFH, SRP54, ELONGATION FACTOR G, EF-G, 23S RNA, NON- KEYWDS 3 CANONICAL BASE PAIRS, MISMATCH
EXPDTA X-RAY DIFFRACTION
AUTHOR L.JOVINE,T.HAINZL,C.OUBRIDGE,W.G.SCOTT,J.LI,T.K.SIXMA, AUTHOR 2 A.WONACOTT,T.SKARZYNSKI,K.NAGAI
REVDAT 3 24-FEB-09 1DUH 1 VERSN REVDAT 2 14-AUG-00 1DUH 1 REMARK REVDAT 1 08-MAY-00 1DUH 0
JRNL AUTH L.JOVINE,T.HAINZL,C.OUBRIDGE,W.G.SCOTT,J.LI, JRNL AUTH 2 T.K.SIXMA,A.WONACOTT,T.SKARZYNSKI,K.NAGAI JRNL TITL CRYSTAL STRUCTURE OF THE FFH AND EF-G BINDING JRNL TITL 2 SITES IN THE CONSERVED DOMAIN IV OF ESCHERICHIA JRNL TITL 3 COLI 4.5S RNA. JRNL REF STRUCTURE FOLD.DES. V. 8 527 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10801497 JRNL DOI 10.1016/S0969-2126(00)00137-4
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.JOVINE,T.HAINZL,C.OUBRIDGE,K.NAGAI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF REMARK 1 TITL 2 THE CONSERVED DOMAIN IV OF E. COLI 4.5S RNA REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 1033 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444900006910
REMARK 2 REMARK 2 RESOLUTION. 2.70 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 : PARKINSON ET AL. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1101782.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.9 REMARK 3 NUMBER OF REFLECTIONS : 10539 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) : 0.230 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 909 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 858 REMARK 3 BIN R VALUE (WORKING SET) : 0.5310 REMARK 3 BIN FREE R VALUE : 0.5310 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 86 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.057 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 970 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 100.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 26.51000 REMARK 3 B22 (A**2) : 26.51000 REMARK 3 B33 (A**2) : -53.03000 REMARK 3 B12 (A**2) : 21.46000 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) : 0.50 REMARK 3 ESD FROM SIGMAA (A) : 0.92 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) : 0.53 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.90 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 15.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.24 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 : 0.27 REMARK 3 BSOL : 36.81 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 : DNA_RNA_REP+.PARAM REMARK 3 PARAMETER FILE 2 : ION_REP+.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARA REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA_RNA+.TOP REMARK 3 TOPOLOGY FILE 2 : ION+.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A LOW RESOLUTION LIMIT OF 8.0 A WAS REMARK 3 USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. REMARK 3 NUCLEOTIDE A39 WAS REFINED WITH OCCUPANCY OF 0.5 TO ACCOUNT REMARK 3 FOR ITS ALTERNATIVELY ORDERED AND DISORDERED CONFORMATION IN REMARK 3 ADJACENT MOLECULES WITHIN THE CRYSTAL. THE APPARENT REMARK 3 DISCREPANCY BETWEEN DATA COMPLETENESS IN SCALING AND REMARK 3 REFINEMENT IS DUE TO THE VERY HIGH ANISOTROPY OF THE CRYSTAL REMARK 3 DIFFRACTION, SO THAT, ALTHOUGH DATA COVERAGE WAS COMPLETE UP REMARK 3 TO 2.70 A RESOLUTION, A SIGNIFICANT PROPORTION OF REFLECTIONS REMARK 3 AT HIGH RESOLUTION WERE EXTINCT. THIS RESULTS IN THE HIGH R REMARK 3 SYM IN THE OUTER SHELL, AND THE LOWER EFFECTIVE DATA REMARK 3 COMPLETENESS DURING REFINEMENT (EXTINCT REFLECTIONS WERE REMARK 3 OMITTED BY CNS).
REMARK 4 REMARK 4 1DUH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-00. REMARK 100 THE RCSB ID CODE IS RCSB010379.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0302, 1.3366, 1.3369, REMARK 200 0.9968, 1.3359 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12371 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 22.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZED FROM 1.60-1.90 M (NH4) REMARK 280 2SO4, 0.09 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH REMARK 280 6.0, AT 303 K. CRYSTALS WERE STABILISED AT 292 K IN A SOLUTION REMARK 280 OF 2.20 M (NH4)2SO4, 0.01 M MGCL2, 0.05 M BIS-TRIS-HCL PH 6.0. REMARK 280 SOAK CONDITIONS: CRYSTALS WERE SOAKED IN STABILISATION REMARK 280 SOLUTION CONTAINING 0.002 M LUTETIUM CHLORIDE HEXAHYDRATE. REMARK 280 CRYOPROTECTION CONDITIONS: AFTER ADDITION OF 20% GLYCEROL (W/ REMARK 280 V) TO THE SOAK SOLUTION, CRYSTALS WERE FLASH-FROZEN IN LIQUID REMARK 280 NITROGEN., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 303.15K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 56.06800 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 28.03400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.03400 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 56.06800 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: DIMERIC 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
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 MG A 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 60 OP1 REMARK 620 2 A A 59 O3' 62.1 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LU A 1 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 4
DBREF 1DUH A 31 74 EMBL X01074 ECRNA45 192 235
SEQRES 1 A 45 C U C U G U U U A C C A G SEQRES 2 A 45 G U C A G G U C C G G A A SEQRES 3 A 45 G G A A G C A G C C A A G SEQRES 4 A 45 G C A G A PGP
MODRES 1DUH PGP A 75 G GUANOSINE-3',5'-DIPHOSPHATE
HET PGP A 75 27 HET LU A 1 1 HET MG A 2 1 HET SO4 A 3 5 HET SO4 A 4 5
HETNAM PGP GUANOSINE-3',5'-DIPHOSPHATE HETNAM LU LUTETIUM (III) ION HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION
HETSYN LU LU
FORMUL 1 PGP C10 H15 N5 O11 P2 FORMUL 2 LU LU 3+ FORMUL 3 MG MG 2+ FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *6(H2 O)
LINK MG MG A 2 OP1 A A 60 1555 1555 2.74 LINK MG MG A 2 O3' A A 59 1555 1555 1.92 LINK O3' A A 74 P PGP A 75 1555 1555 1.61
SITE 1 AC1 1 PGP A 75 SITE 1 AC2 2 A A 59 A A 60 SITE 1 AC3 1 C A 31 SITE 1 AC4 3 G A 48 G A 49 C A 62
CRYST1 69.697 69.697 84.102 90.00 90.00 120.00 P 32 2 1 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 0.014348 0.008284 0.000000 0.00000
SCALE2 0.000000 0.016567 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011890 0.00000