PDB Short entry for 2NRE HEADER ISOMERASE/RNA 01-NOV-06 2NRE TITLE CRYSTAL STRUCTURE OF PSEUDOUDIRINDE SYNTHASE TRUA IN COMPLEX WITH TITLE 2 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 SYNTHASE I, COMPND 9 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 T7 IN SOURCE 4 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, MULTISITE KEYWDS 2 SPECIFICITY, ISOMERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.HUR,R.M.STROUD REVDAT 3 30-AUG-23 2NRE 1 REMARK LINK 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 TARGETS FOR JRNL TITL 2 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 2 REMARK 2 RESOLUTION. 4.00 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) : 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2152 ; 0.374 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2864 ; 0.632 ; 3.000 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 : 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 TLS PARAMETER WAS REFINED FOR TRNA (TREATED AS A SINGLE TLS GROUP) REMARK 4 REMARK 4 2NRE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040209. 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 MM REMARK 280 SPERMINE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, 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 CRYSTALLOGRAPHIC REMARK 300 SYMMETRY MATE (Y,X,-Z), AND F IS THE SUBSTRATE TRNA BOUND TO THE REMARK 300 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 C F 25 C3' - O3' - P ANGL. DEV. = -17.7 DEGREES REMARK 500 G F 26 O3' - P - O5' ANGL. DEV. = 14.2 DEGREES 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 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 PRO A 142 C - N - CA ANGL. DEV. = 9.8 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 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. 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 78 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U F 17 O3' REMARK 620 2 G F 18 OP1 46.5 REMARK 620 N 1 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 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 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 O3' U F 17 K K F 78 1555 1555 3.21 LINK OP1 G F 18 K K F 78 1555 1555 3.06 LINK OP1 C F 30 K K F 77 1555 1555 2.84 LINK OP2 C F 30 K K F 77 1555 1555 2.58 LINK O5' C F 30 K K F 77 1555 1555 3.25 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