HEADER ISOMERASE/RNA 01-NOV-06 2NRE TITLE CRYSTAL STRUCTURE OF PSEUDOUDIRINDE SYNTHASE TRUA IN TITLE 2 COMPLEX WITH LEUCYL TRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCYL TRNA; COMPND 3 CHAIN: F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRNA PSEUDOURIDINE SYNTHASE A; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: TRNA-URIDINE ISOMERASE I, TRNA PSEUDOURIDYLATE COMPND 9 SYNTHASE I, PSU-I; COMPND 10 EC: 5.4.99.12; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: OCCURS NATURALLY IN E. COLI. SYNTHESIZED BY SOURCE 4 T7 IN VITRO TRANSCRIPTION; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 7 ORGANISM_TAXID: 83333; SOURCE 8 STRAIN: K-12; SOURCE 9 GENE: TRUA; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21/DE3; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PSEUDOURIDINE SYNTHASE, ANTICODON STEM LOOP, TRNA, KEYWDS 2 MULTISITE SPECIFICITY, ISOMERASE/RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.HUR,R.M.STROUD REVDAT 2 24-FEB-09 2NRE 1 VERSN REVDAT 1 15-MAY-07 2NRE 0 JRNL AUTH S.HUR,R.M.STROUD JRNL TITL HOW U38, 39, AND 40 OF MANY TRNAS BECOME THE JRNL TITL 2 TARGETS FOR PSEUDOURIDYLATION BY TRUA. JRNL REF MOL.CELL V. 26 189 2007 JRNL REFN ISSN 1097-2765 JRNL PMID 17466622 JRNL DOI 10.1016/J.MOLCEL.2007.02.027 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 5809 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) : 0.265 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.357 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 328 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) : 4.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 343 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1961 REMARK 3 NUCLEIC ACID ATOMS : 1196 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -1.07000 REMARK 3 B12 (A**2) : 0.36000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 1.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.980 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 71.759 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.842 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.708 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3444 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4945 ; 1.327 ; 2.381 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 6.097 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;37.650 ;22.574 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 328 ;21.798 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.920 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 593 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2214 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1899 ; 0.308 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2221 ; 0.337 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 162 ; 0.340 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.206 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.262 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.325 ; 0.500 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): 1292 ; 0.762 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2081 ; 1.378 ; 3.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2152 ; 0.374 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2864 ; 0.632 ; 3.000 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 : 1 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 : F 5 F 69 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5580 -28.6230 25.5500 REMARK 3 T TENSOR REMARK 3 T11: 0.8532 T22: 0.2332 REMARK 3 T33: 0.2665 T12: -0.5022 REMARK 3 T13: 0.0326 T23: 0.0264 REMARK 3 L TENSOR REMARK 3 L11: 0.7861 L22: 5.1351 REMARK 3 L33: 2.1378 L12: 1.9651 REMARK 3 L13: -0.9894 L23: -2.0272 REMARK 3 S TENSOR REMARK 3 S11: -0.2476 S12: 0.5527 S13: -0.2204 REMARK 3 S21: -0.5464 S22: 0.4767 S23: 0.2514 REMARK 3 S31: 0.0983 S32: -0.1231 S33: -0.2291 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 REMARK 3 RIDING POSITIONS TLS PARAMETER WAS REFINED FOR TRNA (TREATED REMARK 3 AS A SINGLE TLS GROUP) REMARK 4 REMARK 4 2NRE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-06. REMARK 100 THE RCSB ID CODE IS RCSB040209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-04 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 : ALS REMARK 200 BEAMLINE : 8.3.1 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 : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6998 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.000 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.17200 REMARK 200 FOR THE DATA SET : 9.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53100 REMARK 200 FOR SHELL : 3.380 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: 1DJ0 AND 1EHZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M K3 CITRATE, 5 REMARK 280 MM SPERMINE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 136.91533 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 68.45767 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 68.45767 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 136.91533 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 300 REMARK: A MOLECULE OF ID A FORMS A DIMER WITH ITS REMARK 300 CRYSTALLOGRAPHIC SYMMETRY MATE (Y,X,-Z), AND F IS THE SUBSTRATE REMARK 300 TRNA BOUND TO THE ENZYME. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 68.45767 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 G F 1 REMARK 465 C F 2 REMARK 465 C F 3 REMARK 465 G F 4 REMARK 465 U F 32 REMARK 465 U F 33 REMARK 465 G F 34 REMARK 465 A F 35 REMARK 465 G F 36 REMARK 465 G F 37 REMARK 465 U F 38 REMARK 465 G F 44A REMARK 465 C F 44B REMARK 465 C F 44C REMARK 465 C F 44D REMARK 465 A F 44E REMARK 465 A F 44F REMARK 465 U F 44G REMARK 465 A F 44H REMARK 465 G F 44I REMARK 465 G F 44J REMARK 465 G F 44K REMARK 465 C F 44L REMARK 465 U F 44M REMARK 465 G F 70 REMARK 465 G F 71 REMARK 465 U F 72 REMARK 465 A F 73 REMARK 465 C F 74 REMARK 465 C F 75 REMARK 465 A F 76 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 6 REMARK 465 GLN A 168 REMARK 465 CYS A 169 REMARK 465 GLN A 170 REMARK 465 SER A 171 REMARK 465 ARG A 172 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 LYS A 11 CG CD CE NZ REMARK 470 GLU A 17 CG CD OE1 OE2 REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 GLN A 27 CG CD OE1 NE2 REMARK 470 GLN A 29 CB CG CD OE1 NE2 REMARK 470 ASN A 30 CB CG OD1 ND2 REMARK 470 GLU A 31 CD OE1 OE2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 GLN A 45 CD OE1 NE2 REMARK 470 GLU A 73 CB CG CD OE1 OE2 REMARK 470 LEU A 77 CD1 CD2 REMARK 470 VAL A 131 CB CG1 CG2 REMARK 470 LEU A 132 CG CD1 CD2 REMARK 470 ASP A 144 CG OD1 OD2 REMARK 470 GLU A 146 CB CG CD OE1 OE2 REMARK 470 ASP A 160 CB CG OD1 OD2 REMARK 470 TRP A 175 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 175 CZ3 CH2 REMARK 470 ARG A 176 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 195 CB CG CD CE NZ REMARK 470 LYS A 231 CD CE NZ REMARK 470 ARG A 255 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 270 O 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 G F 26 OP1 - P - OP2 ANGL. DEV. = -12.8 DEGREES REMARK 500 G F 26 P - O5' - C5' ANGL. DEV. = -13.3 DEGREES REMARK 500 C F 25 C3' - O3' - P ANGL. DEV. = -17.7 DEGREES REMARK 500 G F 26 O3' - P - O5' ANGL. DEV. = 14.3 DEGREES REMARK 500 G F 39 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 G F 39 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 U F 48 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 A F 58 C3' - O3' - P ANGL. DEV. = 10.5 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 SER A 21 -39.89 78.76 REMARK 500 ARG A 28 -131.04 -70.91 REMARK 500 GLN A 29 79.00 103.50 REMARK 500 ASN A 30 106.22 -0.13 REMARK 500 GLU A 31 -73.43 157.41 REMARK 500 VAL A 32 -113.25 -103.39 REMARK 500 VAL A 35 -75.44 -57.18 REMARK 500 LYS A 41 -79.45 -49.44 REMARK 500 VAL A 46 37.34 -90.97 REMARK 500 ALA A 47 0.48 -172.29 REMARK 500 ASN A 48 -3.91 48.04 REMARK 500 PRO A 50 113.58 -28.86 REMARK 500 ARG A 58 65.39 -61.03 REMARK 500 ASP A 60 -150.60 -88.92 REMARK 500 THR A 66 10.93 -143.90 REMARK 500 ALA A 81 -54.14 -162.29 REMARK 500 THR A 84 -88.43 -88.21 REMARK 500 VAL A 87 -82.57 -25.57 REMARK 500 ASN A 88 -3.39 -57.91 REMARK 500 THR A 102 97.06 -65.75 REMARK 500 ASP A 105 -29.50 -37.39 REMARK 500 ALA A 115 148.54 -171.07 REMARK 500 ASN A 124 1.60 -159.83 REMARK 500 ARG A 126 -5.12 82.18 REMARK 500 ARG A 128 131.03 -12.49 REMARK 500 VAL A 131 67.49 -67.20 REMARK 500 LEU A 132 115.04 55.09 REMARK 500 SER A 133 -114.44 -55.81 REMARK 500 LYS A 134 101.39 -18.77 REMARK 500 VAL A 136 -41.31 -165.12 REMARK 500 THR A 137 125.82 56.98 REMARK 500 TYR A 140 -101.65 -82.18 REMARK 500 ARG A 147 -72.15 -73.98 REMARK 500 MET A 148 -71.83 -16.94 REMARK 500 GLN A 153 67.59 -48.86 REMARK 500 CYS A 154 -5.75 -174.44 REMARK 500 GLU A 158 -5.98 156.21 REMARK 500 ASN A 159 -178.56 -41.19 REMARK 500 ASN A 182 114.31 168.99 REMARK 500 ARG A 185 74.41 -116.30 REMARK 500 HIS A 201 127.53 -32.99 REMARK 500 HIS A 202 -74.94 49.35 REMARK 500 MET A 203 -103.86 55.09 REMARK 500 VAL A 204 -71.15 2.94 REMARK 500 SER A 210 10.18 -68.22 REMARK 500 HIS A 217 -130.64 77.10 REMARK 500 ASN A 218 -24.05 65.68 REMARK 500 TRP A 223 -23.73 -39.54 REMARK 500 THR A 234 26.52 -53.03 REMARK 500 LEU A 235 -51.93 -121.36 REMARK 500 ALA A 236 -177.49 -69.60 REMARK 500 LYS A 241 -120.14 0.09 REMARK 500 ALA A 242 -53.65 -171.93 REMARK 500 GLU A 243 42.39 -64.13 REMARK 500 ALA A 249 145.81 170.17 REMARK 500 ASP A 257 84.58 55.59 REMARK 500 PRO A 261 -167.88 -101.17 REMARK 500 LEU A 266 -135.44 -137.22 REMARK 500 LEU A 268 98.73 -23.81 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 K F 77 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C F 30 OP1 REMARK 620 2 C F 30 OP2 56.1 REMARK 620 3 C F 30 O5' 48.1 49.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K F 78 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G F 18 OP1 REMARK 620 2 U F 17 O3' 46.5 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 K F 77 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K F 78 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DJ0 RELATED DB: PDB REMARK 900 APO TRUA REMARK 900 RELATED ID: 2NQP RELATED DB: PDB REMARK 900 RELATED ID: 2NR0 RELATED DB: PDB DBREF 2NRE A 7 270 UNP P07649 TRUA_ECOLI 7 270 DBREF 2NRE F 1 76 PDB 2NRE 2NRE 1 76 SEQRES 1 F 87 G C C G A G G U G G U G G SEQRES 2 F 87 A A U U G G U A G A C A C SEQRES 3 F 87 G C U A C C U U G A G G U SEQRES 4 F 87 G G U A G U G C C C A A U SEQRES 5 F 87 A G G G C U U A C G G G U SEQRES 6 F 87 U C A A G U C C C G U C C SEQRES 7 F 87 U C G G U A C C A SEQRES 1 A 270 MET SER ASP GLN GLN GLN PRO PRO VAL TYR LYS ILE ALA SEQRES 2 A 270 LEU GLY ILE GLU TYR ASP GLY SER LYS TYR TYR GLY TRP SEQRES 3 A 270 GLN ARG GLN ASN GLU VAL ARG SER VAL GLN GLU LYS LEU SEQRES 4 A 270 GLU LYS ALA LEU SER GLN VAL ALA ASN GLU PRO ILE THR SEQRES 5 A 270 VAL PHE CYS ALA GLY ARG THR ASP ALA GLY VAL HIS GLY SEQRES 6 A 270 THR GLY GLN VAL VAL HIS PHE GLU THR THR ALA LEU ARG SEQRES 7 A 270 LYS ASP ALA ALA TRP THR LEU GLY VAL ASN ALA ASN LEU SEQRES 8 A 270 PRO GLY ASP ILE ALA VAL ARG TRP VAL LYS THR VAL PRO SEQRES 9 A 270 ASP ASP PHE HIS ALA ARG PHE SER ALA THR ALA ARG ARG SEQRES 10 A 270 TYR ARG TYR ILE ILE TYR ASN HIS ARG LEU ARG PRO ALA SEQRES 11 A 270 VAL LEU SER LYS GLY VAL THR HIS PHE TYR GLU PRO LEU SEQRES 12 A 270 ASP ALA GLU ARG MET HIS ARG ALA ALA GLN CYS LEU LEU SEQRES 13 A 270 GLY GLU ASN ASP PHE THR SER PHE ARG ALA VAL GLN CYS SEQRES 14 A 270 GLN SER ARG THR PRO TRP ARG ASN VAL MET HIS ILE ASN SEQRES 15 A 270 VAL THR ARG HIS GLY PRO TYR VAL VAL VAL ASP ILE LYS SEQRES 16 A 270 ALA ASN ALA PHE VAL HIS HIS MET VAL ARG ASN ILE VAL SEQRES 17 A 270 GLY SER LEU MET GLU VAL GLY ALA HIS ASN GLN PRO GLU SEQRES 18 A 270 SER TRP ILE ALA GLU LEU LEU ALA ALA LYS ASP ARG THR SEQRES 19 A 270 LEU ALA ALA ALA THR ALA LYS ALA GLU GLY LEU TYR LEU SEQRES 20 A 270 VAL ALA VAL ASP TYR PRO ASP ARG TYR ASP LEU PRO LYS SEQRES 21 A 270 PRO PRO MET GLY PRO LEU PHE LEU ALA ASP HET K F 77 1 HET K F 78 1 HETNAM K POTASSIUM ION FORMUL 3 K 2(K 1+) HELIX 1 1 SER A 34 VAL A 46 1 13 HELIX 2 2 GLY A 86 ASN A 90 5 5 HELIX 3 3 HIS A 108 ALA A 113 1 6 HELIX 4 4 ASP A 144 GLN A 153 1 10 HELIX 5 5 ASP A 160 PHE A 164 5 5 HELIX 6 6 MET A 203 HIS A 217 1 15 HELIX 7 7 SER A 222 LYS A 231 1 10 SHEET 1 A 4 PHE A 54 CYS A 55 0 SHEET 2 A 4 VAL A 69 THR A 74 -1 O HIS A 71 N PHE A 54 SHEET 3 A 4 TYR A 10 TYR A 18 -1 N TYR A 10 O THR A 74 SHEET 4 A 4 ILE A 95 THR A 102 -1 O ALA A 96 N GLU A 17 SHEET 1 B 2 HIS A 64 GLY A 65 0 SHEET 2 B 2 TYR A 246 LEU A 247 1 O LEU A 247 N HIS A 64 SHEET 1 C 4 VAL A 183 THR A 184 0 SHEET 2 C 4 VAL A 190 ILE A 194 -1 O VAL A 191 N THR A 184 SHEET 3 C 4 ALA A 115 ILE A 122 -1 N TYR A 120 O VAL A 192 SHEET 4 C 4 ALA A 249 ASP A 251 -1 O ASP A 251 N ALA A 115 LINK K K F 77 OP1 C F 30 1555 1555 2.84 LINK K K F 77 OP2 C F 30 1555 1555 2.58 LINK K K F 77 O5' C F 30 1555 1555 3.25 LINK K K F 78 OP1 G F 18 1555 1555 3.06 LINK K K F 78 O3' U F 17 1555 1555 3.21 CISPEP 1 GLY A 264 PRO A 265 0 4.92 SITE 1 AC1 1 C F 30 SITE 1 AC2 2 U F 17 G F 18 CRYST1 80.355 80.355 205.373 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 0.012445 0.007185 0.000000 0.00000 SCALE2 0.000000 0.014370 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004869 0.00000 MASTER 477 0 2 7 10 0 2 6 0 0 0 28 END