HEADER NUCLEOTIDE BINDING PROTEIN/RNA 23-JUL-09 3IEV TITLE CRYSTAL STRUCTURE OF ERA IN COMPLEX WITH MGGNP AND THE 3' END OF 16S TITLE 2 RRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN ERA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(P*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3'; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 STRAIN: GENOMIC DNA; SOURCE 5 GENE: AQ_1994, ERA, ERA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PDONR201; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBA1971; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THE RNA HAS BEEN COMMERCIALLY SYNTHESIZED. KEYWDS ERA, GTPASE, KH DOMAIN, ANTI-SD, 16S RRNA, 30S RIBOSOME ASSEMBLY, KEYWDS 2 GTP-BINDING, NUCLEOTIDE-BINDING, RNA-BINDING, NUCLEOTIDE BINDING KEYWDS 3 PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.TU,X.JI REVDAT 5 06-SEP-23 3IEV 1 REMARK REVDAT 4 30-AUG-23 3IEV 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 13-JUL-11 3IEV 1 VERSN REVDAT 2 13-OCT-09 3IEV 1 JRNL REVDAT 1 25-AUG-09 3IEV 0 JRNL AUTH C.TU,X.ZHOU,J.E.TROPEA,B.P.AUSTIN,D.S.WAUGH,D.L.COURT,X.JI JRNL TITL STRUCTURE OF ERA IN COMPLEX WITH THE 3' END OF 16S RRNA: JRNL TITL 2 IMPLICATIONS FOR RIBOSOME BIOGENESIS JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 14843 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19706445 JRNL DOI 10.1073/PNAS.0904032106 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0057 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 26655 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1428 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1787 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2395 REMARK 3 NUCLEIC ACID ATOMS : 224 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.17000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.555 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2869 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3974 ; 1.111 ; 2.130 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 4.797 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;37.843 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 519 ;14.792 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.248 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 477 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1985 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1569 ; 0.381 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2599 ; 0.727 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1300 ; 1.122 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1357 ; 1.861 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 185 REMARK 3 ORIGIN FOR THE GROUP (A): -18.8230 31.1090 -4.3580 REMARK 3 T TENSOR REMARK 3 T11: 0.0099 T22: -0.2265 REMARK 3 T33: -0.0596 T12: -0.0280 REMARK 3 T13: -0.0807 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 1.2279 L22: 1.2667 REMARK 3 L33: 3.1195 L12: 0.3793 REMARK 3 L13: 0.0558 L23: 0.0260 REMARK 3 S TENSOR REMARK 3 S11: 0.0119 S12: -0.1148 S13: -0.0299 REMARK 3 S21: 0.1244 S22: -0.0192 S23: 0.0367 REMARK 3 S31: 0.2268 S32: -0.1545 S33: 0.0073 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 186 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2760 52.1210 -21.1320 REMARK 3 T TENSOR REMARK 3 T11: 0.0338 T22: -0.2542 REMARK 3 T33: -0.0499 T12: -0.0021 REMARK 3 T13: -0.1054 T23: 0.0251 REMARK 3 L TENSOR REMARK 3 L11: 3.1411 L22: 1.5920 REMARK 3 L33: 1.0603 L12: 0.1078 REMARK 3 L13: 0.0871 L23: -0.0598 REMARK 3 S TENSOR REMARK 3 S11: 0.0029 S12: 0.0501 S13: 0.0685 REMARK 3 S21: 0.0561 S22: -0.0451 S23: -0.0678 REMARK 3 S31: -0.1554 S32: -0.0122 S33: 0.0422 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 30 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2720 63.1590 -24.2550 REMARK 3 T TENSOR REMARK 3 T11: 0.0149 T22: -0.1329 REMARK 3 T33: 0.0947 T12: -0.0554 REMARK 3 T13: -0.0425 T23: 0.0980 REMARK 3 L TENSOR REMARK 3 L11: 7.3093 L22: 4.4960 REMARK 3 L33: 0.8625 L12: -3.0623 REMARK 3 L13: 0.3210 L23: 0.7329 REMARK 3 S TENSOR REMARK 3 S11: -0.0869 S12: -0.1112 S13: 1.0472 REMARK 3 S21: -0.0610 S22: 0.2641 S23: -0.3627 REMARK 3 S31: -0.2502 S32: 0.1915 S33: -0.1772 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 1000 REMARK 3 ORIGIN FOR THE GROUP (A): -14.3330 41.9640 -2.2080 REMARK 3 T TENSOR REMARK 3 T11: 0.0360 T22: -0.1279 REMARK 3 T33: -0.0239 T12: -0.0193 REMARK 3 T13: -0.0349 T23: -0.0280 REMARK 3 L TENSOR REMARK 3 L11: 12.5710 L22: 6.8295 REMARK 3 L33: 30.7568 L12: 3.5109 REMARK 3 L13: 17.9416 L23: 5.4026 REMARK 3 S TENSOR REMARK 3 S11: -0.0404 S12: -0.1020 S13: 0.1216 REMARK 3 S21: 0.1035 S22: 0.1245 S23: 0.1183 REMARK 3 S31: -0.5182 S32: -0.2613 S33: -0.0841 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3IEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27880 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.50100 REMARK 200 R SYM FOR SHELL (I) : 0.50100 REMARK 200 FOR SHELL : 1.900 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 1WF3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M (NH4)2SO4, 0.1 M CACODYLATE AND REMARK 280 30% PEG 8000, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 59.80000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.80000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.80000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 A 477 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 GLY A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 A D 1542 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 ASN A 13 7.37 81.01 REMARK 500 GLU A 51 -53.01 -134.08 REMARK 500 GLU A 208 -123.03 63.39 REMARK 500 REMARK 500 REMARK: NULL 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 400 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 THR A 38 OG1 82.8 REMARK 620 3 HOH A 306 O 87.2 83.5 REMARK 620 4 HOH A 310 O 84.4 94.0 171.5 REMARK 620 5 GNP A 501 O2G 170.4 87.6 92.2 95.9 REMARK 620 6 GNP A 501 O2B 91.0 170.6 89.2 92.4 98.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EGA RELATED DB: PDB REMARK 900 LIGAND-FREE E. COLI ERA REMARK 900 RELATED ID: 1WF3 RELATED DB: PDB REMARK 900 T. THERMOPHILUS ERA IN COMPLEX WITH MGGNP REMARK 900 RELATED ID: 1X1L RELATED DB: PDB REMARK 900 CRYO-EM MODEL OF ERA IN COMPLEX WITH THE 3' MINOR DOMAIN OF 16S REMARK 900 RRNA WITHIN THE MATURE 30S RIBOSOME REMARK 900 RELATED ID: 3IEU RELATED DB: PDB REMARK 900 E. COLI ERA IN COMPLEX WITH GDP. DBREF 3IEV A 1 301 UNP O67800 ERA_AQUAE 1 301 DBREF 3IEV D 1531 1542 PDB 3IEV 3IEV 1531 1542 SEQADV 3IEV GLY A -6 UNP O67800 EXPRESSION TAG SEQADV 3IEV HIS A -5 UNP O67800 EXPRESSION TAG SEQADV 3IEV HIS A -4 UNP O67800 EXPRESSION TAG SEQADV 3IEV HIS A -3 UNP O67800 EXPRESSION TAG SEQADV 3IEV HIS A -2 UNP O67800 EXPRESSION TAG SEQADV 3IEV HIS A -1 UNP O67800 EXPRESSION TAG SEQADV 3IEV HIS A 0 UNP O67800 EXPRESSION TAG SEQRES 1 A 308 GLY HIS HIS HIS HIS HIS HIS MET LYS VAL GLY TYR VAL SEQRES 2 A 308 ALA ILE VAL GLY LYS PRO ASN VAL GLY LYS SER THR LEU SEQRES 3 A 308 LEU ASN ASN LEU LEU GLY THR LYS VAL SER ILE ILE SER SEQRES 4 A 308 PRO LYS ALA GLY THR THR ARG MET ARG VAL LEU GLY VAL SEQRES 5 A 308 LYS ASN ILE PRO ASN GLU ALA GLN ILE ILE PHE LEU ASP SEQRES 6 A 308 THR PRO GLY ILE TYR GLU PRO LYS LYS SER ASP VAL LEU SEQRES 7 A 308 GLY HIS SER MET VAL GLU ILE ALA LYS GLN SER LEU GLU SEQRES 8 A 308 GLU ALA ASP VAL ILE LEU PHE MET ILE ASP ALA THR GLU SEQRES 9 A 308 GLY TRP ARG PRO ARG ASP GLU GLU ILE TYR GLN ASN PHE SEQRES 10 A 308 ILE LYS PRO LEU ASN LYS PRO VAL ILE VAL VAL ILE ASN SEQRES 11 A 308 LYS ILE ASP LYS ILE GLY PRO ALA LYS ASN VAL LEU PRO SEQRES 12 A 308 LEU ILE ASP GLU ILE HIS LYS LYS HIS PRO GLU LEU THR SEQRES 13 A 308 GLU ILE VAL PRO ILE SER ALA LEU LYS GLY ALA ASN LEU SEQRES 14 A 308 ASP GLU LEU VAL LYS THR ILE LEU LYS TYR LEU PRO GLU SEQRES 15 A 308 GLY GLU PRO LEU PHE PRO GLU ASP MET ILE THR ASP LEU SEQRES 16 A 308 PRO LEU ARG LEU LEU ALA ALA GLU ILE VAL ARG GLU LYS SEQRES 17 A 308 ALA MET MET LEU THR ARG GLU GLU VAL PRO THR SER ILE SEQRES 18 A 308 ALA VAL LYS ILE ASN GLU ILE LYS PRO GLY ASP ALA ASN SEQRES 19 A 308 PRO ASN MET LEU VAL ILE LYS GLY GLU ILE ILE VAL ASP SEQRES 20 A 308 ARG GLU ASN LEU LYS PRO ILE ILE ILE GLY LYS LYS GLY SEQRES 21 A 308 GLN ARG LEU LYS GLU ILE GLY LYS ARG ALA ARG GLN GLU SEQRES 22 A 308 LEU GLU LEU ILE LEU GLY ARG PRO VAL TYR LEU GLU LEU SEQRES 23 A 308 TRP VAL LYS VAL VAL PRO ASP TRP ARG ARG ARG PRO GLU SEQRES 24 A 308 TYR VAL ARG LEU PHE GLY TYR ALA LEU SEQRES 1 D 12 A U C A C C U C C U U A HET MG A 400 1 HET GNP A 501 32 HET SO4 A 601 5 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM SO4 SULFATE ION FORMUL 3 MG MG 2+ FORMUL 4 GNP C10 H17 N6 O13 P3 FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *245(H2 O) HELIX 1 1 GLY A 15 GLY A 25 1 11 HELIX 2 2 ASP A 69 ALA A 86 1 18 HELIX 3 3 ARG A 100 ILE A 111 1 12 HELIX 4 4 LYS A 112 ASN A 115 5 4 HELIX 5 5 LYS A 124 ILE A 128 5 5 HELIX 6 6 PRO A 130 ASN A 133 5 4 HELIX 7 7 VAL A 134 HIS A 145 1 12 HELIX 8 8 ASN A 161 LEU A 173 1 13 HELIX 9 9 PRO A 189 LEU A 205 1 17 HELIX 10 10 GLU A 209 ILE A 214 1 6 HELIX 11 11 ARG A 241 ASN A 243 5 3 HELIX 12 12 LEU A 244 GLY A 250 1 7 HELIX 13 13 GLY A 253 GLY A 272 1 20 HELIX 14 14 ASP A 286 ARG A 289 5 4 HELIX 15 15 ARG A 290 PHE A 297 1 8 SHEET 1 A 6 VAL A 42 ILE A 48 0 SHEET 2 A 6 ALA A 52 ASP A 58 -1 O ILE A 54 N LYS A 46 SHEET 3 A 6 LYS A 2 VAL A 9 1 N VAL A 6 O ILE A 55 SHEET 4 A 6 VAL A 88 ASP A 94 1 O LEU A 90 N ALA A 7 SHEET 5 A 6 VAL A 118 ASN A 123 1 O ILE A 119 N ILE A 89 SHEET 6 A 6 ILE A 151 PRO A 153 1 O VAL A 152 N VAL A 120 SHEET 1 B 3 ALA A 215 PRO A 223 0 SHEET 2 B 3 LEU A 231 VAL A 239 -1 O VAL A 232 N LYS A 222 SHEET 3 B 3 VAL A 275 VAL A 283 1 O TYR A 276 N ILE A 233 LINK OG SER A 17 MG MG A 400 1555 1555 2.14 LINK OG1 THR A 38 MG MG A 400 1555 1555 2.14 LINK O HOH A 306 MG MG A 400 1555 1555 2.28 LINK O HOH A 310 MG MG A 400 1555 1555 2.07 LINK MG MG A 400 O2G GNP A 501 1555 1555 1.91 LINK MG MG A 400 O2B GNP A 501 1555 1555 1.97 SITE 1 AC1 5 SER A 17 THR A 38 HOH A 306 HOH A 310 SITE 2 AC1 5 GNP A 501 SITE 1 AC2 30 PRO A 12 ASN A 13 VAL A 14 GLY A 15 SITE 2 AC2 30 LYS A 16 SER A 17 THR A 18 ILE A 31 SITE 3 AC2 30 SER A 32 PRO A 33 GLY A 36 THR A 37 SITE 4 AC2 30 THR A 38 GLY A 61 ASN A 123 LYS A 124 SITE 5 AC2 30 ASP A 126 SER A 155 ALA A 156 LEU A 157 SITE 6 AC2 30 HOH A 303 HOH A 306 HOH A 308 HOH A 310 SITE 7 AC2 30 HOH A 321 HOH A 341 HOH A 348 HOH A 368 SITE 8 AC2 30 MG A 400 HOH A 413 SITE 1 AC3 3 ARG A 241 GLU A 242 HOH A 497 CRYST1 119.600 71.600 43.600 90.00 101.50 90.00 C 1 2 1 4 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 0.008361 0.000000 0.001701 0.00000 SCALE2 0.000000 0.013966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023406 0.00000