HEADER LIGASE 16-FEB-14 4OUD TITLE ENGINEERED TYROSYL-TRNA SYNTHETASE WITH THE NONSTANDARD AMINO ACID L- TITLE 2 4,4-BIPHENYLALANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 EC: 6.1.1.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TYROSYL-TRNA SYNTHETASE; COMPND 9 CHAIN: B; COMPND 10 EC: 6.1.1.1; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 1403831; SOURCE 4 STRAIN: K-12 SUBSTR. MC4100; SOURCE 5 GENE: TYRS, BN896_1452; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 1403831; SOURCE 11 STRAIN: K-12 SUBSTR. MC4100; SOURCE 12 GENE: TYRS, BN896_1452; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX WITH L-TYROSINE, ROSSMANN FOLD, LIGASE, TRNA EXPDTA X-RAY DIFFRACTION AUTHOR R.TAKEUCHI,D.J.MANDELL,M.J.LAJOIE,G.M.CHURCH,B.L.STODDARD REVDAT 3 20-SEP-23 4OUD 1 REMARK SEQADV LINK REVDAT 2 18-FEB-15 4OUD 1 JRNL REVDAT 1 28-JAN-15 4OUD 0 JRNL AUTH D.J.MANDELL,M.J.LAJOIE,M.T.MEE,R.TAKEUCHI,G.KUZNETSOV, JRNL AUTH 2 J.E.NORVILLE,C.J.GREGG,B.L.STODDARD,G.M.CHURCH JRNL TITL BIOCONTAINMENT OF GENETICALLY MODIFIED ORGANISMS BY JRNL TITL 2 SYNTHETIC PROTEIN DESIGN. JRNL REF NATURE V. 518 55 2015 JRNL REFN ISSN 0028-0836 JRNL PMID 25607366 JRNL DOI 10.1038/NATURE14121 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 26407 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1899 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6038 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.61000 REMARK 3 B22 (A**2) : 2.41000 REMARK 3 B33 (A**2) : 0.99000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.054 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.398 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.294 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.510 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6168 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5868 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8331 ; 1.530 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13451 ; 3.616 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 762 ; 8.728 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 301 ;38.786 ;24.784 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1045 ;18.931 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;19.721 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 905 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7115 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1480 ; 0.008 ; 0.020 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): 3075 ; 2.544 ; 5.082 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3074 ; 2.541 ; 5.082 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3828 ; 4.263 ; 7.606 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3829 ; 3.962 ; 5.411 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3093 ; 2.460 ; 5.295 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3093 ; 2.303 ; 3.854 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4504 ; 3.849 ; 5.667 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7311 ; 6.309 ;28.784 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7308 ; 6.301 ;28.779 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 424 REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 RESIDUE RANGE : A 601 A 636 REMARK 3 ORIGIN FOR THE GROUP (A): 92.8513 7.0709 95.4924 REMARK 3 T TENSOR REMARK 3 T11: 0.0418 T22: 0.0441 REMARK 3 T33: 0.0545 T12: -0.0076 REMARK 3 T13: 0.0111 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 0.7307 L22: 0.0984 REMARK 3 L33: 0.1766 L12: 0.1282 REMARK 3 L13: 0.3055 L23: 0.0205 REMARK 3 S TENSOR REMARK 3 S11: 0.0223 S12: -0.1251 S13: -0.0281 REMARK 3 S21: -0.0517 S22: -0.0081 S23: -0.0143 REMARK 3 S31: 0.0368 S32: -0.0325 S33: -0.0142 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 5 B 424 REMARK 3 RESIDUE RANGE : A 637 A 637 REMARK 3 RESIDUE RANGE : B 501 B 520 REMARK 3 ORIGIN FOR THE GROUP (A): 56.9021 6.7326 47.6903 REMARK 3 T TENSOR REMARK 3 T11: 0.0776 T22: 0.0384 REMARK 3 T33: 0.0428 T12: 0.0001 REMARK 3 T13: 0.0236 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.4940 L22: 0.0439 REMARK 3 L33: 0.6626 L12: -0.0096 REMARK 3 L13: 0.5124 L23: -0.0101 REMARK 3 S TENSOR REMARK 3 S11: 0.0340 S12: 0.0667 S13: -0.0379 REMARK 3 S21: 0.0550 S22: -0.0031 S23: 0.0289 REMARK 3 S31: 0.0372 S32: 0.0103 S33: -0.0309 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 4OUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084959. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : SI 220 ASYMMETRIC CUT SINGLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26929 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.650 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 2YXN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM MALONATE, 18 % PEG 3350, REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 33.60250 REMARK 290 SMTRY3 2 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: 3090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 0 REMARK 465 PRO A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 ASP A 232 REMARK 465 GLY A 233 REMARK 465 THR A 234 REMARK 465 LYS A 235 REMARK 465 ALA A 236 REMARK 465 GLY A 237 REMARK 465 LYS A 238 REMARK 465 THR A 239 REMARK 465 GLU A 240 REMARK 465 GLY A 241 REMARK 465 GLY B 0 REMARK 465 PRO B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 PRO B 82 REMARK 465 SER B 83 REMARK 465 PHE B 84 REMARK 465 LYS B 85 REMARK 465 ALA B 86 REMARK 465 ALA B 87 REMARK 465 GLU B 88 REMARK 465 ARG B 89 REMARK 465 LYS B 90 REMARK 465 LEU B 91 REMARK 465 ASN B 92 REMARK 465 ARG B 160 REMARK 465 LEU B 161 REMARK 465 ASN B 162 REMARK 465 ARG B 163 REMARK 465 GLU B 164 REMARK 465 ASP B 165 REMARK 465 GLN B 166 REMARK 465 LYS B 230 REMARK 465 ALA B 231 REMARK 465 ASP B 232 REMARK 465 GLY B 233 REMARK 465 THR B 234 REMARK 465 LYS B 235 REMARK 465 ALA B 236 REMARK 465 GLY B 237 REMARK 465 LYS B 238 REMARK 465 THR B 239 REMARK 465 GLU B 240 REMARK 465 GLY B 241 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 CYS A 116 O HOH A 603 2.14 REMARK 500 NZ LYS B 250 O HOH B 514 2.15 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 ARG A 413 NE - CZ - NH1 ANGL. DEV. = 3.5 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 ILE A 79 -50.96 -125.28 REMARK 500 ASP A 115 47.70 -149.80 REMARK 500 HIS A 145 0.32 -67.45 REMARK 500 GLU A 164 25.25 -152.07 REMARK 500 THR A 229 68.97 -64.05 REMARK 500 SER A 293 64.54 -58.11 REMARK 500 ASP A 346 -4.39 -153.23 REMARK 500 GLU A 367 -4.02 81.01 REMARK 500 LYS A 416 -2.60 -142.60 REMARK 500 PRO B 42 37.40 -93.81 REMARK 500 GLU B 95 40.19 -105.39 REMARK 500 VAL B 97 98.72 -68.93 REMARK 500 GLU B 99 -79.48 -65.42 REMARK 500 ALA B 156 81.40 -28.08 REMARK 500 LYS B 295 47.37 83.38 REMARK 500 UNK B 364 -29.95 -32.87 REMARK 500 UNK B 371 15.50 85.04 REMARK 500 PHE B 408 -178.90 -172.54 REMARK 500 LYS B 416 -49.16 -140.98 REMARK 500 TRP B 423 106.14 -50.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 162 ARG A 163 -101.13 REMARK 500 GLU B 155 ALA B 156 -119.26 REMARK 500 SER B 329 GLY B 330 148.90 REMARK 500 ARG B 403 LEU B 404 -142.37 REMARK 500 PHE B 405 GLY B 406 145.91 REMARK 500 GLY B 406 ARG B 407 94.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYR A 501 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 355 THROUGH 402 ARE MISSING IN THE COORDINATES OF CHAIN B. REMARK 999 HOWEVER THE AUTHORS SEE THE BACKBONE OF A 17-RESIDUE STRETCH IN REMARK 999 THIS REGION. SINCE THEY DO NOT KNOW THE CORRESPONDENCE OF THE REMARK 999 SEQUENCE WITH THE COORDINATES IN THIS REGION. THIS 17-RESIDUE REMARK 999 STRETCH HAS BEEN LABELED AS UNK DBREF 4OUD A 2 424 UNP U6N9P2 U6N9P2_ECOLI 2 424 DBREF 4OUD B 2 424 UNP U6N9P2 U6N9P2_ECOLI 2 424 SEQADV 4OUD GLY A 0 UNP U6N9P2 EXPRESSION TAG SEQADV 4OUD PRO A 1 UNP U6N9P2 EXPRESSION TAG SEQADV 4OUD ALA A 49 UNP U6N9P2 LEU 49 ENGINEERED MUTATION SEQADV 4OUD ALA A 236 UNP U6N9P2 PHE 236 ENGINEERED MUTATION SEQADV 4OUD ALA A 260 UNP U6N9P2 TRP 260 ENGINEERED MUTATION SEQADV 4OUD ALA A 263 UNP U6N9P2 THR 263 ENGINEERED MUTATION SEQADV 4OUD TRP A 271 UNP U6N9P2 PHE 271 ENGINEERED MUTATION SEQADV 4OUD GLY A 275 UNP U6N9P2 PHE 275 ENGINEERED MUTATION SEQADV 4OUD BIF A 303 UNP U6N9P2 LEU 303 ENGINEERED MUTATION SEQADV 4OUD GLY B 0 UNP U6N9P2 EXPRESSION TAG SEQADV 4OUD PRO B 1 UNP U6N9P2 EXPRESSION TAG SEQADV 4OUD ALA B 49 UNP U6N9P2 LEU 49 ENGINEERED MUTATION SEQADV 4OUD ALA B 236 UNP U6N9P2 PHE 236 ENGINEERED MUTATION SEQADV 4OUD ALA B 260 UNP U6N9P2 TRP 260 ENGINEERED MUTATION SEQADV 4OUD ALA B 263 UNP U6N9P2 THR 263 ENGINEERED MUTATION SEQADV 4OUD TRP B 271 UNP U6N9P2 PHE 271 ENGINEERED MUTATION SEQADV 4OUD GLY B 275 UNP U6N9P2 PHE 275 ENGINEERED MUTATION SEQADV 4OUD BIF B 303 UNP U6N9P2 LEU 303 ENGINEERED MUTATION SEQRES 1 A 425 GLY PRO ALA SER SER ASN LEU ILE LYS GLN LEU GLN GLU SEQRES 2 A 425 ARG GLY LEU VAL ALA GLN VAL THR ASP GLU GLU ALA LEU SEQRES 3 A 425 ALA GLU ARG LEU ALA GLN GLY PRO ILE ALA LEU TYR CYS SEQRES 4 A 425 GLY PHE ASP PRO THR ALA ASP SER LEU HIS ALA GLY HIS SEQRES 5 A 425 LEU VAL PRO LEU LEU CYS LEU LYS ARG PHE GLN GLN ALA SEQRES 6 A 425 GLY HIS LYS PRO VAL ALA LEU VAL GLY GLY ALA THR GLY SEQRES 7 A 425 LEU ILE GLY ASP PRO SER PHE LYS ALA ALA GLU ARG LYS SEQRES 8 A 425 LEU ASN THR GLU GLU THR VAL GLN GLU TRP VAL ASP LYS SEQRES 9 A 425 ILE ARG LYS GLN VAL ALA PRO PHE LEU ASP PHE ASP CYS SEQRES 10 A 425 GLY GLU ASN SER ALA ILE ALA ALA ASN ASN TYR ASP TRP SEQRES 11 A 425 PHE GLY ASN MET ASN VAL LEU THR PHE LEU ARG ASP ILE SEQRES 12 A 425 GLY LYS HIS PHE SER VAL ASN GLN MET ILE ASN LYS GLU SEQRES 13 A 425 ALA VAL LYS GLN ARG LEU ASN ARG GLU ASP GLN GLY ILE SEQRES 14 A 425 SER PHE THR GLU PHE SER TYR ASN LEU LEU GLN GLY TYR SEQRES 15 A 425 ASP PHE ALA CYS LEU ASN LYS GLN TYR GLY VAL VAL LEU SEQRES 16 A 425 GLN ILE GLY GLY SER ASP GLN TRP GLY ASN ILE THR SER SEQRES 17 A 425 GLY ILE ASP LEU THR ARG ARG LEU HIS GLN ASN GLN VAL SEQRES 18 A 425 PHE GLY LEU THR VAL PRO LEU ILE THR LYS ALA ASP GLY SEQRES 19 A 425 THR LYS ALA GLY LYS THR GLU GLY GLY ALA VAL TRP LEU SEQRES 20 A 425 ASP PRO LYS LYS THR SER PRO TYR LYS PHE TYR GLN PHE SEQRES 21 A 425 ALA ILE ASN ALA ALA ASP ALA ASP VAL TYR ARG TRP LEU SEQRES 22 A 425 LYS PHE GLY THR PHE MET SER ILE GLU GLU ILE ASN ALA SEQRES 23 A 425 LEU GLU GLU GLU ASP LYS ASN SER GLY LYS ALA PRO ARG SEQRES 24 A 425 ALA GLN TYR VAL BIF ALA GLU GLN VAL THR ARG LEU VAL SEQRES 25 A 425 HIS GLY GLU GLU GLY LEU GLN ALA ALA LYS ARG ILE THR SEQRES 26 A 425 GLU CYS LEU PHE SER GLY SER LEU SER ALA LEU SER GLU SEQRES 27 A 425 ALA ASP PHE GLU GLN LEU ALA GLN ASP GLY VAL PRO MET SEQRES 28 A 425 VAL GLU MET GLU LYS GLY ALA ASP LEU MET GLN ALA LEU SEQRES 29 A 425 VAL ASP SER GLU LEU GLN PRO SER ARG GLY GLN ALA ARG SEQRES 30 A 425 LYS THR ILE ALA SER ASN ALA ILE THR ILE ASN GLY GLU SEQRES 31 A 425 LYS GLN SER ASP PRO GLU TYR PHE PHE LYS GLU GLU ASP SEQRES 32 A 425 ARG LEU PHE GLY ARG PHE THR LEU LEU ARG ARG GLY LYS SEQRES 33 A 425 LYS ASN TYR CYS LEU ILE CYS TRP LYS SEQRES 1 B 394 GLY PRO ALA SER SER ASN LEU ILE LYS GLN LEU GLN GLU SEQRES 2 B 394 ARG GLY LEU VAL ALA GLN VAL THR ASP GLU GLU ALA LEU SEQRES 3 B 394 ALA GLU ARG LEU ALA GLN GLY PRO ILE ALA LEU TYR CYS SEQRES 4 B 394 GLY PHE ASP PRO THR ALA ASP SER LEU HIS ALA GLY HIS SEQRES 5 B 394 LEU VAL PRO LEU LEU CYS LEU LYS ARG PHE GLN GLN ALA SEQRES 6 B 394 GLY HIS LYS PRO VAL ALA LEU VAL GLY GLY ALA THR GLY SEQRES 7 B 394 LEU ILE GLY ASP PRO SER PHE LYS ALA ALA GLU ARG LYS SEQRES 8 B 394 LEU ASN THR GLU GLU THR VAL GLN GLU TRP VAL ASP LYS SEQRES 9 B 394 ILE ARG LYS GLN VAL ALA PRO PHE LEU ASP PHE ASP CYS SEQRES 10 B 394 GLY GLU ASN SER ALA ILE ALA ALA ASN ASN TYR ASP TRP SEQRES 11 B 394 PHE GLY ASN MET ASN VAL LEU THR PHE LEU ARG ASP ILE SEQRES 12 B 394 GLY LYS HIS PHE SER VAL ASN GLN MET ILE ASN LYS GLU SEQRES 13 B 394 ALA VAL LYS GLN ARG LEU ASN ARG GLU ASP GLN GLY ILE SEQRES 14 B 394 SER PHE THR GLU PHE SER TYR ASN LEU LEU GLN GLY TYR SEQRES 15 B 394 ASP PHE ALA CYS LEU ASN LYS GLN TYR GLY VAL VAL LEU SEQRES 16 B 394 GLN ILE GLY GLY SER ASP GLN TRP GLY ASN ILE THR SER SEQRES 17 B 394 GLY ILE ASP LEU THR ARG ARG LEU HIS GLN ASN GLN VAL SEQRES 18 B 394 PHE GLY LEU THR VAL PRO LEU ILE THR LYS ALA ASP GLY SEQRES 19 B 394 THR LYS ALA GLY LYS THR GLU GLY GLY ALA VAL TRP LEU SEQRES 20 B 394 ASP PRO LYS LYS THR SER PRO TYR LYS PHE TYR GLN PHE SEQRES 21 B 394 ALA ILE ASN ALA ALA ASP ALA ASP VAL TYR ARG TRP LEU SEQRES 22 B 394 LYS PHE GLY THR PHE MET SER ILE GLU GLU ILE ASN ALA SEQRES 23 B 394 LEU GLU GLU GLU ASP LYS ASN SER GLY LYS ALA PRO ARG SEQRES 24 B 394 ALA GLN TYR VAL BIF ALA GLU GLN VAL THR ARG LEU VAL SEQRES 25 B 394 HIS GLY GLU GLU GLY LEU GLN ALA ALA LYS ARG ILE THR SEQRES 26 B 394 GLU CYS LEU PHE SER GLY SER LEU SER ALA LEU SER GLU SEQRES 27 B 394 ALA ASP PHE GLU GLN LEU ALA GLN ASP GLY VAL PRO MET SEQRES 28 B 394 VAL GLU MET GLU UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 29 B 394 UNK UNK UNK UNK UNK UNK UNK UNK ARG LEU PHE GLY ARG SEQRES 30 B 394 PHE THR LEU LEU ARG ARG GLY LYS LYS ASN TYR CYS LEU SEQRES 31 B 394 ILE CYS TRP LYS MODRES 4OUD BIF A 303 PHE MODRES 4OUD BIF B 303 PHE HET BIF A 303 17 HET BIF B 303 17 HET TYR A 501 13 HETNAM BIF (R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC ACID HETNAM TYR TYROSINE HETSYN BIF BIPHENYLALANINE FORMUL 1 BIF 2(C15 H15 N O2) FORMUL 3 TYR C9 H11 N O3 FORMUL 4 HOH *57(H2 O) HELIX 1 1 ASN A 5 ARG A 13 1 9 HELIX 2 2 ASP A 21 GLN A 31 1 11 HELIX 3 3 HIS A 51 ALA A 64 1 14 HELIX 4 4 ALA A 75 ILE A 79 5 5 HELIX 5 5 THR A 93 ALA A 109 1 17 HELIX 6 6 PRO A 110 LEU A 112 5 3 HELIX 7 7 CYS A 116 SER A 120 5 5 HELIX 8 8 ASN A 126 GLY A 131 1 6 HELIX 9 9 ASN A 134 ILE A 142 1 9 HELIX 10 10 GLY A 143 PHE A 146 5 4 HELIX 11 11 SER A 147 LYS A 154 1 8 HELIX 12 12 LYS A 154 ASN A 162 1 9 HELIX 13 13 SER A 169 GLY A 191 1 23 HELIX 14 14 GLN A 201 GLN A 217 1 17 HELIX 15 15 SER A 252 ASN A 262 1 11 HELIX 16 16 ALA A 264 THR A 276 1 13 HELIX 17 17 SER A 279 SER A 293 1 15 HELIX 18 18 ARG A 298 GLY A 330 1 33 HELIX 19 19 SER A 336 ASP A 346 1 11 HELIX 20 20 ASP A 358 SER A 366 1 9 HELIX 21 21 SER A 371 SER A 381 1 11 HELIX 22 22 LYS A 399 GLY A 406 5 8 HELIX 23 23 LEU B 6 ARG B 13 1 8 HELIX 24 24 ASP B 21 GLY B 32 1 12 HELIX 25 25 HIS B 48 GLY B 50 5 3 HELIX 26 26 HIS B 51 ALA B 64 1 14 HELIX 27 27 GLY B 73 GLY B 80 1 8 HELIX 28 28 VAL B 97 ALA B 109 1 13 HELIX 29 29 PRO B 110 LEU B 112 5 3 HELIX 30 30 CYS B 116 SER B 120 5 5 HELIX 31 31 ASN B 126 GLY B 131 1 6 HELIX 32 32 ASN B 134 ILE B 142 1 9 HELIX 33 33 GLY B 143 PHE B 146 5 4 HELIX 34 34 SER B 147 ILE B 152 1 6 HELIX 35 35 SER B 169 SER B 174 1 6 HELIX 36 36 SER B 174 TYR B 190 1 17 HELIX 37 37 GLN B 201 GLN B 217 1 17 HELIX 38 38 SER B 252 ASN B 262 1 11 HELIX 39 39 ALA B 264 THR B 276 1 13 HELIX 40 40 SER B 279 SER B 293 1 15 HELIX 41 41 ARG B 298 SER B 329 1 32 HELIX 42 42 SER B 336 ASP B 346 1 11 HELIX 43 43 UNK B 361 UNK B 363 5 3 HELIX 44 44 UNK B 364 UNK B 371 1 8 SHEET 1 A 6 GLN A 18 VAL A 19 0 SHEET 2 A 6 PHE A 221 VAL A 225 -1 O THR A 224 N GLN A 18 SHEET 3 A 6 VAL A 192 GLY A 198 1 N VAL A 193 O PHE A 221 SHEET 4 A 6 ALA A 35 PHE A 40 1 N TYR A 37 O ILE A 196 SHEET 5 A 6 LYS A 67 VAL A 72 1 O LEU A 71 N PHE A 40 SHEET 6 A 6 ILE A 122 ASN A 125 1 O ALA A 124 N VAL A 72 SHEET 1 B 5 MET A 350 MET A 353 0 SHEET 2 B 5 ASN A 417 TRP A 423 1 O CYS A 422 N VAL A 351 SHEET 3 B 5 PHE A 408 ARG A 413 -1 N THR A 409 O ILE A 421 SHEET 4 B 5 ILE A 384 ILE A 386 -1 N THR A 385 O ARG A 412 SHEET 5 B 5 GLU A 389 LYS A 390 -1 O GLU A 389 N ILE A 386 SHEET 1 C 6 GLN B 18 VAL B 19 0 SHEET 2 C 6 PHE B 221 VAL B 225 -1 O THR B 224 N GLN B 18 SHEET 3 C 6 LEU B 194 GLY B 198 1 N GLY B 197 O VAL B 225 SHEET 4 C 6 ALA B 35 PHE B 40 1 N TYR B 37 O ILE B 196 SHEET 5 C 6 LYS B 67 VAL B 72 1 O VAL B 69 N LEU B 36 SHEET 6 C 6 ILE B 122 ASN B 125 1 O ALA B 124 N VAL B 72 SHEET 1 D 4 MET B 350 VAL B 351 0 SHEET 2 D 4 ASN B 417 ILE B 421 1 O LEU B 420 N VAL B 351 SHEET 3 D 4 THR B 409 ARG B 413 -1 N THR B 409 O ILE B 421 SHEET 4 D 4 UNK B 373 UNK B 374 -1 N UNK B 374 O ARG B 412 LINK C VAL A 302 N BIF A 303 1555 1555 1.32 LINK C BIF A 303 N ALA A 304 1555 1555 1.32 LINK C VAL B 302 N BIF B 303 1555 1555 1.32 LINK C BIF B 303 N ALA B 304 1555 1555 1.33 SITE 1 AC1 12 TYR A 37 GLY A 39 ASP A 41 LEU A 71 SITE 2 AC1 12 THR A 76 ASP A 81 TYR A 175 GLN A 179 SITE 3 AC1 12 ASP A 182 GLN A 195 GLN A 201 HOH A 619 CRYST1 81.340 67.205 90.682 90.00 102.65 90.00 P 1 21 1 2 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 0.012294 0.000000 0.002759 0.00000 SCALE2 0.000000 0.014880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011302 0.00000