HEADER LIGASE 29-AUG-18 6HHY TITLE KLEBSIELLA PNEUMONIAE SERYL-TRNA SYNTHETASE IN COMPLEX WITH 5'-O-(N- TITLE 2 (L-SERYL)-SULFAMOYL)N3-METHYLURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SERYL-TRNA SYNTHETASE; COMPND 5 SYNONYM: SERYL-TRNA SYNTHETASE,SERRS,SERYL-TRNA(SER/SEC) SYNTHETASE; COMPND 6 EC: 6.1.1.11; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 ATCC: BAA 1705; SOURCE 5 GENE: SERS, AGG09_05015, B1727_25560, B4U21_07300, B4U22_08075, SOURCE 6 BB785_18280, BL124_0015080, BN49_2024, C3483_17160, C3F39_05595, SOURCE 7 C9J88_18700, CPT10_05250, CSC88_02630, CWQ24_18365, PMK1_03261, SOURCE 8 SM57_00973; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 PLYSS; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PETRUK KEYWDS COIL-COIL, BETA BARREL, TRNA SYNTHETASE, INHIBITOR, COMPLEX, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.PANG,S.DE GRAEF,S.D.WEEKS,S.V.STRELKOV REVDAT 5 17-JAN-24 6HHY 1 LINK REVDAT 4 04-MAR-20 6HHY 1 JRNL REVDAT 3 15-JAN-20 6HHY 1 JRNL REVDAT 2 08-JAN-20 6HHY 1 JRNL REVDAT 1 18-DEC-19 6HHY 0 JRNL AUTH L.PANG,M.NAUTIYAL,S.DE GRAEF,B.GADAKH,V.ZORZINI,A.ECONOMOU, JRNL AUTH 2 S.V.STRELKOV,A.VAN AERSCHOT,S.D.WEEKS JRNL TITL STRUCTURAL INSIGHTS INTO THE BINDING OF NATURAL JRNL TITL 2 PYRIMIDINE-BASED INHIBITORS OF CLASS II AMINOACYL-TRNA JRNL TITL 3 SYNTHETASES. JRNL REF ACS CHEM.BIOL. V. 15 407 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 31869198 JRNL DOI 10.1021/ACSCHEMBIO.9B00887 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38511 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1950 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 19 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.27 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2914 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2247 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2771 REMARK 3 BIN R VALUE (WORKING SET) : 0.2248 REMARK 3 BIN FREE R VALUE : 0.2231 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.91 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3298 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.94640 REMARK 3 B22 (A**2) : -8.94640 REMARK 3 B33 (A**2) : 17.89280 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.310 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.181 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.151 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.179 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.151 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3401 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4604 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1213 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 95 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 502 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3401 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 442 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3776 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.58 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.91 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|*} REMARK 3 ORIGIN FOR THE GROUP (A): -11.5872 -31.0369 -9.7036 REMARK 3 T TENSOR REMARK 3 T11: -0.0701 T22: -0.0702 REMARK 3 T33: -0.1236 T12: 0.0471 REMARK 3 T13: -0.0116 T23: 0.0442 REMARK 3 L TENSOR REMARK 3 L11: 0.4251 L22: 0.2973 REMARK 3 L33: 1.2879 L12: 0.1137 REMARK 3 L13: 0.0505 L23: 0.4012 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: -0.0427 S13: -0.0426 REMARK 3 S21: -0.0567 S22: -0.0484 S23: -0.0602 REMARK 3 S31: 0.0626 S32: 0.3265 S33: 0.0152 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-17 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972422 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57726 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 76.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 2.33900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.13-2998 REMARK 200 STARTING MODEL: MODEL GENERATED FROM STRUCTURE 2DQ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HOLO PROTEIN, CONCENTRATED TO 10 MG/ML REMARK 280 IN 10 MM TRIS PH 7, 100 MM NACL, 5 MM DTT, WAS MIXED WITH AN REMARK 280 EQUAL VOLUME OF 7.5% W/V PEG 8000, 50 MM CACL2, 20% V/V ETHYLENE REMARK 280 GLYCOL, 100 MM MORPHEUS BUFFER SYSTEM 1 (MES/IMIDAZOLE) PH 6.5. REMARK 280 SUITABLE CRYSTALS WERE SOAKED WITH 2 MM COMPOUND IN A SIMILAR REMARK 280 CRYSTALLIZATION SOLUTION CONTAINING A 10% W/V PEG 8000., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 114.20950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.86050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.86050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 171.31425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.86050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.86050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.10475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.86050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.86050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 171.31425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.86050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.86050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 57.10475 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 114.20950 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: 6870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 65 REMARK 465 GLU A 66 REMARK 465 ASP A 67 REMARK 465 ALA A 271 REMARK 465 GLY A 272 REMARK 465 SER A 273 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 GLU A 10 CD OE1 OE2 REMARK 470 GLU A 16 CD OE1 OE2 REMARK 470 LYS A 24 CE NZ REMARK 470 ARG A 51 NE CZ NH1 NH2 REMARK 470 LYS A 62 CG CD CE NZ REMARK 470 ARG A 64 CD NE CZ NH1 NH2 REMARK 470 LEU A 71 CG CD1 CD2 REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 77 CD CE NZ REMARK 470 ARG A 115 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 224 CG CD OE1 OE2 REMARK 470 GLU A 225 CG CD OE1 OE2 REMARK 470 GLU A 270 CG CD OE1 OE2 REMARK 470 TYR A 274 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 276 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 283 CD NE CZ NH1 NH2 REMARK 470 ARG A 373 CZ NH1 NH2 REMARK 470 LYS A 377 CD CE NZ REMARK 470 LYS A 380 CD CE NZ 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 THR A 158 -78.17 -131.17 REMARK 500 ARG A 161 31.09 74.14 REMARK 500 THR A 237 146.88 -175.89 REMARK 500 TRP A 363 -138.27 61.78 REMARK 500 ASP A 379 129.38 -35.84 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 CA A 505 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 254 O REMARK 620 2 HOH A 616 O 88.8 REMARK 620 3 HOH A 627 O 86.2 160.8 REMARK 620 4 HOH A 630 O 73.8 79.2 81.5 REMARK 620 5 HOH A 654 O 140.2 88.7 83.5 66.7 REMARK 620 6 HOH A 655 O 81.6 76.9 120.5 145.9 135.9 REMARK 620 7 HOH A 685 O 149.9 94.1 99.6 136.2 69.9 69.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FZT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HHV RELATED DB: PDB REMARK 900 STRUCTURE OF T. THERMOPHILUS ASPRS IN COMPLEX WITH 5'-O-(N-(L- REMARK 900 ASPARTYL)-SULFAMOYL)N3-METHYLURIDINE REMARK 900 RELATED ID: 6HHX RELATED DB: PDB REMARK 900 STRUCTURE OF T. THERMOPHILUS ASPRS IN COMPLEX WITH 5'-O-(N-(L- REMARK 900 ASPARTYL)-SULFAMOYL)CYTIDINE REMARK 900 RELATED ID: 6HHW RELATED DB: PDB REMARK 900 STRUCTURE OF T. THERMOPHILUS ASPRS IN COMPLEX WITH 5'-O-(N-(L- REMARK 900 ASPARTYL)-SULFAMOYL)URIDINE REMARK 900 RELATED ID: 6HE3 RELATED DB: PDB REMARK 900 PSEUDOMONAS AERUGINOSA SERYL-TRNA SYNTHETASE IN COMPLEX WITH 5'-O- REMARK 900 (N-(L-SERYL)-SULFAMOYL)CYTIDINE REMARK 900 RELATED ID: 6HDZ RELATED DB: PDB REMARK 900 PSEUDOMONAS AERUGINOSA SERYL-TRNA SYNTHETASE IN COMPLEX WITH 5'-O- REMARK 900 (N-(L-SERYL)-SULFAMOYL)URIDINE REMARK 900 RELATED ID: 6HE1 RELATED DB: PDB REMARK 900 PSEUDOMONAS AERUGINOSA SERYL-TRNA SYNTHETASE IN COMPLEX WITH 5'-O- REMARK 900 (N-(L-SERYL)-SULFAMOYL)N3-METHYLURIDINE REMARK 900 RELATED ID: 6HHZ RELATED DB: PDB REMARK 900 RELATED ID: 6HI0 RELATED DB: PDB DBREF 6HHY A 1 430 UNP W9BNU9 W9BNU9_KLEPN 1 430 SEQRES 1 A 430 MET LEU ASP PRO ASN LEU LEU ARG THR GLU PRO ASP ALA SEQRES 2 A 430 VAL ALA GLU LYS LEU ALA ARG ARG GLY PHE LYS LEU ASP SEQRES 3 A 430 VAL ASP LYS LEU ARG ALA LEU GLU GLU ARG ARG LYS VAL SEQRES 4 A 430 LEU GLN VAL GLN THR GLU ASN LEU GLN ALA GLU ARG ASN SEQRES 5 A 430 SER ARG SER LYS SER ILE GLY GLN ALA LYS ALA ARG GLY SEQRES 6 A 430 GLU ASP ILE GLU PRO LEU ARG LEU GLU VAL ASN LYS LEU SEQRES 7 A 430 GLY GLU GLN LEU ASP ALA ALA LYS SER GLU LEU GLU THR SEQRES 8 A 430 LEU LEU ALA GLU ILE ARG ASP ILE ALA LEU ALA ILE PRO SEQRES 9 A 430 ASN ILE PRO HIS ASP ASP VAL PRO VAL GLY ARG ASP GLU SEQRES 10 A 430 ASN ASP ASN VAL GLU VAL SER ARG TRP GLY THR PRO ARG SEQRES 11 A 430 GLN PHE ASP PHE GLU VAL ARG ASP HIS VAL THR LEU GLY SEQRES 12 A 430 GLU MET HIS GLY GLY LEU ASP PHE ALA ALA ALA VAL LYS SEQRES 13 A 430 LEU THR GLY SER ARG PHE VAL VAL MET LYS GLY GLN LEU SEQRES 14 A 430 ALA ARG LEU HIS ARG ALA LEU ALA GLN PHE MET LEU ASP SEQRES 15 A 430 LEU HIS THR GLU GLN HIS GLY TYR SER GLU ASN TYR VAL SEQRES 16 A 430 PRO TYR LEU VAL ASN GLN ASP THR LEU TYR GLY THR GLY SEQRES 17 A 430 GLN LEU PRO LYS PHE ALA GLY ASP LEU PHE HIS THR ARG SEQRES 18 A 430 PRO LEU GLU GLU GLU ALA ASP SER SER ASN TYR ALA LEU SEQRES 19 A 430 ILE PRO THR ALA GLU VAL PRO LEU THR ASN LEU VAL ARG SEQRES 20 A 430 ASP GLU ILE ILE ASP GLU ASP ASP LEU PRO ILE LYS MET SEQRES 21 A 430 THR ALA HIS THR PRO CYS PHE ARG SER GLU ALA GLY SER SEQRES 22 A 430 TYR GLY ARG ASP THR ARG GLY LEU ILE ARG MET HIS GLN SEQRES 23 A 430 PHE ASP LYS VAL GLU MET VAL GLN ILE VAL ARG PRO GLU SEQRES 24 A 430 ASP SER MET ALA ALA LEU GLU GLU MET THR GLY HIS ALA SEQRES 25 A 430 GLU LYS VAL LEU GLN LEU LEU GLY LEU PRO TYR ARG LYS SEQRES 26 A 430 VAL ALA LEU CYS THR GLY ASP MET GLY PHE SER ALA CYS SEQRES 27 A 430 LYS THR TYR ASP LEU GLU VAL TRP VAL PRO ALA GLN ASN SEQRES 28 A 430 THR TYR ARG GLU ILE SER SER CYS SER ASN VAL TRP ASP SEQRES 29 A 430 PHE GLN ALA ARG ARG MET GLN ALA ARG CYS ARG SER LYS SEQRES 30 A 430 SER ASP LYS LYS THR ARG LEU VAL HIS THR LEU ASN GLY SEQRES 31 A 430 SER GLY LEU ALA VAL GLY ARG THR LEU VAL ALA LEU MET SEQRES 32 A 430 GLU ASN TYR GLN GLN ALA ASP GLY ARG ILE GLU ILE PRO SEQRES 33 A 430 GLU VAL LEU ARG PRO TYR MET ARG GLY LEU GLU TYR ILE SEQRES 34 A 430 GLY HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HET FZT A 504 28 HET CA A 505 1 HET CA A 506 1 HET CA A 507 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM FZT 5'-O-(N-(L-SERYL)-SULFAMOYL)N3-METHYLURIDINE HETNAM CA CALCIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 3(C2 H6 O2) FORMUL 5 FZT C13 H20 N4 O10 S FORMUL 6 CA 3(CA 2+) FORMUL 9 HOH *85(H2 O) HELIX 1 AA1 ASP A 3 GLU A 10 1 8 HELIX 2 AA2 GLU A 10 ARG A 20 1 11 HELIX 3 AA3 ASP A 26 LYS A 62 1 37 HELIX 4 AA4 GLU A 69 LEU A 101 1 33 HELIX 5 AA5 ASP A 116 ASN A 120 5 5 HELIX 6 AA6 ASP A 138 HIS A 146 1 9 HELIX 7 AA7 PHE A 151 THR A 158 1 8 HELIX 8 AA8 GLY A 167 GLN A 187 1 21 HELIX 9 AA9 ASN A 200 THR A 207 1 8 HELIX 10 AB1 PHE A 213 LEU A 217 5 5 HELIX 11 AB2 LEU A 223 ALA A 227 5 5 HELIX 12 AB3 ALA A 238 ASN A 244 1 7 HELIX 13 AB4 LEU A 245 ARG A 247 5 3 HELIX 14 AB5 ASP A 254 LEU A 256 5 3 HELIX 15 AB6 ARG A 297 GLU A 299 5 3 HELIX 16 AB7 ASP A 300 LEU A 319 1 20 HELIX 17 AB8 PRO A 348 ASN A 351 5 4 HELIX 18 AB9 ASP A 364 GLN A 371 1 8 HELIX 19 AC1 VAL A 395 TYR A 406 1 12 HELIX 20 AC2 PRO A 416 ARG A 424 5 9 SHEET 1 AA1 8 VAL A 121 TRP A 126 0 SHEET 2 AA1 8 TYR A 323 ALA A 327 -1 O ALA A 327 N VAL A 121 SHEET 3 AA1 8 LYS A 339 VAL A 347 -1 O ASP A 342 N VAL A 326 SHEET 4 AA1 8 THR A 352 TRP A 363 -1 O CYS A 359 N TYR A 341 SHEET 5 AA1 8 HIS A 386 ALA A 394 -1 O THR A 387 N VAL A 362 SHEET 6 AA1 8 GLN A 286 VAL A 296 -1 N VAL A 290 O GLY A 392 SHEET 7 AA1 8 ILE A 258 PHE A 267 -1 N MET A 260 O VAL A 293 SHEET 8 AA1 8 SER A 191 GLU A 192 1 N SER A 191 O THR A 261 SHEET 1 AA2 2 LEU A 149 ASP A 150 0 SHEET 2 AA2 2 VAL A 164 MET A 165 -1 O VAL A 164 N ASP A 150 SHEET 1 AA3 3 LEU A 198 VAL A 199 0 SHEET 2 AA3 3 TYR A 232 LEU A 234 -1 O ALA A 233 N VAL A 199 SHEET 3 AA3 3 HIS A 219 THR A 220 -1 N THR A 220 O TYR A 232 SHEET 1 AA4 3 ILE A 250 ASP A 252 0 SHEET 2 AA4 3 ARG A 373 ARG A 375 1 O ARG A 373 N ILE A 251 SHEET 3 AA4 3 ARG A 383 LEU A 384 -1 O ARG A 383 N CYS A 374 SHEET 1 AA5 2 ILE A 413 GLU A 414 0 SHEET 2 AA5 2 TYR A 428 ILE A 429 -1 O ILE A 429 N ILE A 413 LINK O ASP A 254 CA CA A 505 1555 1555 2.22 LINK CA CA A 505 O HOH A 616 1555 5454 2.60 LINK CA CA A 505 O HOH A 627 1555 5454 2.88 LINK CA CA A 505 O HOH A 630 1555 5454 2.54 LINK CA CA A 505 O HOH A 654 1555 5454 2.43 LINK CA CA A 505 O HOH A 655 1555 1555 2.63 LINK CA CA A 505 O HOH A 685 1555 1555 2.41 LINK CA CA A 507 O HOH A 678 1555 1555 2.63 CISPEP 1 LEU A 210 PRO A 211 0 6.99 CISPEP 2 LEU A 256 PRO A 257 0 -2.01 CISPEP 3 GLY A 392 LEU A 393 0 3.99 SITE 1 AC1 8 MET A 165 HIS A 173 TYR A 194 GLN A 286 SITE 2 AC1 8 PHE A 287 ASP A 288 GLY A 396 HOH A 608 SITE 1 AC2 5 ASN A 200 GLN A 201 SER A 229 SER A 230 SITE 2 AC2 5 ASN A 231 SITE 1 AC3 4 PRO A 236 GLU A 239 ARG A 268 FZT A 504 SITE 1 AC4 19 THR A 237 GLU A 239 ARG A 268 LEU A 281 SITE 2 AC4 19 ILE A 282 ARG A 283 MET A 284 PHE A 287 SITE 3 AC4 19 GLU A 291 GLU A 355 ILE A 356 SER A 357 SITE 4 AC4 19 SER A 358 ASN A 389 SER A 391 ALA A 394 SITE 5 AC4 19 ARG A 397 EDO A 503 HOH A 618 SITE 1 AC5 7 ASP A 254 HOH A 616 HOH A 627 HOH A 630 SITE 2 AC5 7 HOH A 654 HOH A 655 HOH A 685 SITE 1 AC6 1 ASP A 342 SITE 1 AC7 3 GLU A 239 ASN A 389 HOH A 678 CRYST1 83.721 83.721 228.419 90.00 90.00 90.00 P 43 21 2 8 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 0.011944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004378 0.00000