HEADER LIGASE 10-MAY-00 1E1T TITLE LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE TITLE 2 LYSYL_ADENYLATE INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSYL-TRNA SYNTHETASE, LYSINE--TRNA LIGASE, LYSRS; COMPND 5 EC: 6.1.1.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: LYSU; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: TG2; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PXLYS5; SOURCE 11 EXPRESSION_SYSTEM_GENE: LYSU KEYWDS LIGASE, AMINOACYL-TRNA SYNTHETASE, PROTEIN BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR G.DESOGUS,F.TODONE,P.BRICK,S.ONESTI REVDAT 6 06-DEC-23 1E1T 1 LINK REVDAT 5 24-JUL-19 1E1T 1 REMARK REVDAT 4 12-JUL-17 1E1T 1 REVDAT 3 24-AUG-11 1E1T 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 HETSYN FORMUL VERSN REVDAT 2 24-FEB-09 1E1T 1 VERSN REVDAT 1 28-JUL-00 1E1T 0 JRNL AUTH G.DESOGUS,F.TODONE,P.BRICK,S.ONESTI JRNL TITL ACTIVE SITE OF LYSYL-TRNA SYNTHETASE: STRUCTURAL STUDIES OF JRNL TITL 2 THE ADENYLATION REACTION JRNL REF BIOCHEMISTRY V. 39 8418 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10913247 JRNL DOI 10.1021/BI0006722 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 40860 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 SET) : 0.186 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1639 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4675 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 209 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3834 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.660 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.400 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.200 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.300 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WHEN CRYSTALS GROWN IN THE PRESENCE OF REMARK 3 LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND REMARK 3 MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED REMARK 3 THAT THE FIRST STEP OF THE REACTION HAD OCCURRED WITHIN THE REMARK 3 CRYSTAL WITH THE FORMATION OF THE LYSYL-ADENYLATE INTERMEDIATE. REMARK 3 AN ADDITIONAL ELECTRON DENSITY PEAK COULD BE MODELLED AS A REMARK 3 PARTIALLY OCCUPIED PYROPHOSPHATE MOLECULE. THE ASSIGNMENT OF THE REMARK 3 ELECTRON DENSITY PEAKS AS MG2+ IONS IS BASED ON THE POSITIONS REMARK 3 OBSERVED FOR METAL IONS WHEN THE ELECTRON- DENSE MN2+ IONS WERE REMARK 3 USED. REMARK 4 REMARK 4 1E1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1290004927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-95 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41908 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20400 REMARK 200 R SYM FOR SHELL (I) : 0.20400 REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1E1O REMARK 200 REMARK 200 REMARK: STRUCTURE WAS SOLVED BY DIFFERENCE FOURIER METHODS USING REMARK 200 PHASES FROM 1E1O REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN WAS CONCENTRATED TO 12 REMARK 280 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM REMARK 280 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, REMARK 280 A SMALL AMOUNT OF A SOLUTION CONTAINING ATP AND MGCL2 WAS ADDED REMARK 280 TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM., PH 6.80 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 58.70000 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 117.40000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.05000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 146.75000 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 29.35000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.70000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 117.40000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 146.75000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 88.05000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 29.35000 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: 15280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.7 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.70000 REMARK 400 REMARK 400 COMPOUND REMARK 400 WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED REMARK 400 OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE REMARK 400 ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE REMARK 400 FIRST STEP OF THE REACTION HAD OCCURRED WITHIN THE CRYSTAL REMARK 400 WITH THE FORMATION OF THE LYSYL-ADENYLATE INTERMEDIATE. AN REMARK 400 ADDITIONAL ELECTRON DENSITY PEAK COULD BE MODELLED AS A REMARK 400 PARTIALLY OCCUPIED PYROPHOSPHATE MOLECULE. 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 SER A 1 REMARK 465 GLU A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 ARG A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 ASN A 9 REMARK 465 GLU A 10 REMARK 465 ASP A 154 REMARK 465 LYS A 155 REMARK 465 PHE A 156 REMARK 465 HIS A 157 REMARK 465 GLY A 158 REMARK 465 LEU A 159 REMARK 465 GLN A 160 REMARK 465 GLN A 503 REMARK 465 LYS A 504 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 ILE A 12 CG1 CG2 CD1 REMARK 470 ASP A 13 CG OD1 OD2 REMARK 470 ASP A 16 CG OD1 OD2 REMARK 470 GLU A 50 CG CD OE1 OE2 REMARK 470 GLN A 58 CG CD OE1 NE2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 GLN A 131 CG CD OE1 NE2 REMARK 470 THR A 132 OG1 CG2 REMARK 470 ASP A 161 CG OD1 OD2 REMARK 470 GLN A 162 CG CD OE1 NE2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 ASP A 177 CG OD1 OD2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 GLN A 181 CG CD OE1 NE2 REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 LYS A 363 CG CD CE NZ REMARK 470 ASP A 451 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 37 84.81 -157.80 REMARK 500 ASP A 38 -37.35 -146.73 REMARK 500 ASN A 64 60.01 36.96 REMARK 500 MET A 79 50.21 -109.82 REMARK 500 GLN A 111 -69.50 -124.52 REMARK 500 ALA A 238 144.85 -173.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 414 OE2 REMARK 620 2 GLU A 421 OE2 64.6 REMARK 620 3 LAD A 601 O1A 100.1 62.5 REMARK 620 4 POP A 602 O4 131.9 79.8 89.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 POP A 602 O1 REMARK 620 2 POP A 602 O 69.4 REMARK 620 3 POP A 602 O5 125.3 61.4 REMARK 620 4 HOH A 732 O 136.9 86.1 62.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LAD B 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 521 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 522 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 524 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 525 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 526 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LYL RELATED DB: PDB REMARK 900 LYSYL-TRNA SYNTHETASE (LYSU) (E.C.6.1.1.6) COMPLEXED WITH LYSINE REMARK 900 RELATED ID: 1E1O RELATED DB: PDB REMARK 900 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM, COMPLEXED WITH LYSINE REMARK 900 RELATED ID: 1E22 RELATED DB: PDB REMARK 900 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE REMARK 900 AND THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP REMARK 900 RELATED ID: 1E24 RELATED DB: PDB REMARK 900 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE REMARK 900 AND ATP AND MN2+ DBREF 1E1T A 1 504 UNP P0A8N6 SYK2_ECO57 2 505 SEQRES 1 A 504 SER GLU GLN GLU THR ARG GLY ALA ASN GLU ALA ILE ASP SEQRES 2 A 504 PHE ASN ASP GLU LEU ARG ASN ARG ARG GLU LYS LEU ALA SEQRES 3 A 504 ALA LEU ARG GLN GLN GLY VAL ALA PHE PRO ASN ASP PHE SEQRES 4 A 504 ARG ARG ASP HIS THR SER ASP GLN LEU HIS GLU GLU PHE SEQRES 5 A 504 ASP ALA LYS ASP ASN GLN GLU LEU GLU SER LEU ASN ILE SEQRES 6 A 504 GLU VAL SER VAL ALA GLY ARG MET MET THR ARG ARG ILE SEQRES 7 A 504 MET GLY LYS ALA SER PHE VAL THR LEU GLN ASP VAL GLY SEQRES 8 A 504 GLY ARG ILE GLN LEU TYR VAL ALA ARG ASP SER LEU PRO SEQRES 9 A 504 GLU GLY VAL TYR ASN ASP GLN PHE LYS LYS TRP ASP LEU SEQRES 10 A 504 GLY ASP ILE ILE GLY ALA ARG GLY THR LEU PHE LYS THR SEQRES 11 A 504 GLN THR GLY GLU LEU SER ILE HIS CYS THR GLU LEU ARG SEQRES 12 A 504 LEU LEU THR LYS ALA LEU ARG PRO LEU PRO ASP LYS PHE SEQRES 13 A 504 HIS GLY LEU GLN ASP GLN GLU VAL ARG TYR ARG GLN ARG SEQRES 14 A 504 TYR LEU ASP LEU ILE ALA ASN ASP LYS SER ARG GLN THR SEQRES 15 A 504 PHE VAL VAL ARG SER LYS ILE LEU ALA ALA ILE ARG GLN SEQRES 16 A 504 PHE MET VAL ALA ARG GLY PHE MET GLU VAL GLU THR PRO SEQRES 17 A 504 MET MET GLN VAL ILE PRO GLY GLY ALA SER ALA ARG PRO SEQRES 18 A 504 PHE ILE THR HIS HIS ASN ALA LEU ASP LEU ASP MET TYR SEQRES 19 A 504 LEU ARG ILE ALA PRO GLU LEU TYR LEU LYS ARG LEU VAL SEQRES 20 A 504 VAL GLY GLY PHE GLU ARG VAL PHE GLU ILE ASN ARG ASN SEQRES 21 A 504 PHE ARG ASN GLU GLY ILE SER VAL ARG HIS ASN PRO GLU SEQRES 22 A 504 PHE THR MET MET GLU LEU TYR MET ALA TYR ALA ASP TYR SEQRES 23 A 504 HIS ASP LEU ILE GLU LEU THR GLU SER LEU PHE ARG THR SEQRES 24 A 504 LEU ALA GLN GLU VAL LEU GLY THR THR LYS VAL THR TYR SEQRES 25 A 504 GLY GLU HIS VAL PHE ASP PHE GLY LYS PRO PHE GLU LYS SEQRES 26 A 504 LEU THR MET ARG GLU ALA ILE LYS LYS TYR ARG PRO GLU SEQRES 27 A 504 THR ASP MET ALA ASP LEU ASP ASN PHE ASP ALA ALA LYS SEQRES 28 A 504 ALA LEU ALA GLU SER ILE GLY ILE THR VAL GLU LYS SER SEQRES 29 A 504 TRP GLY LEU GLY ARG ILE VAL THR GLU ILE PHE ASP GLU SEQRES 30 A 504 VAL ALA GLU ALA HIS LEU ILE GLN PRO THR PHE ILE THR SEQRES 31 A 504 GLU TYR PRO ALA GLU VAL SER PRO LEU ALA ARG ARG ASN SEQRES 32 A 504 ASP VAL ASN PRO GLU ILE THR ASP ARG PHE GLU PHE PHE SEQRES 33 A 504 ILE GLY GLY ARG GLU ILE GLY ASN GLY PHE SER GLU LEU SEQRES 34 A 504 ASN ASP ALA GLU ASP GLN ALA GLU ARG PHE GLN GLU GLN SEQRES 35 A 504 VAL ASN ALA LYS ALA ALA GLY ASP ASP GLU ALA MET PHE SEQRES 36 A 504 TYR ASP GLU ASP TYR VAL THR ALA LEU GLU TYR GLY LEU SEQRES 37 A 504 PRO PRO THR ALA GLY LEU GLY ILE GLY ILE ASP ARG MET SEQRES 38 A 504 ILE MET LEU PHE THR ASN SER HIS THR ILE ARG ASP VAL SEQRES 39 A 504 ILE LEU PHE PRO ALA MET ARG PRO GLN LYS HET LAD A 601 32 HET POP A 602 9 HET MG A 603 1 HET MG A 604 1 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET GOL A 608 6 HET GOL A 609 6 HET GOL A 610 6 HET GOL A 611 6 HETNAM LAD ADENOSINE-5'-[LYSYL-PHOSPHATE] HETNAM POP PYROPHOSPHATE 2- HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 LAD C16 H26 N7 O8 P FORMUL 3 POP H2 O7 P2 2- FORMUL 4 MG 2(MG 2+) FORMUL 6 GOL 7(C3 H8 O3) FORMUL 13 HOH *337(H2 O) HELIX 1 1 ILE A 12 GLY A 32 1 21 HELIX 2 2 THR A 44 ASP A 53 1 10 HELIX 3 3 ASP A 56 ASN A 64 1 9 HELIX 4 4 GLY A 106 GLN A 111 1 6 HELIX 5 5 PHE A 112 TRP A 115 5 4 HELIX 6 6 GLU A 163 GLN A 168 1 6 HELIX 7 7 GLN A 168 ASN A 176 1 9 HELIX 8 8 ASN A 176 ALA A 199 1 24 HELIX 9 9 PRO A 239 GLY A 249 1 11 HELIX 10 10 ASP A 285 GLY A 306 1 22 HELIX 11 11 MET A 328 ARG A 336 1 9 HELIX 12 12 ASP A 340 ASP A 345 5 6 HELIX 13 13 ASN A 346 ILE A 357 1 12 HELIX 14 14 GLY A 366 ALA A 379 1 14 HELIX 15 15 GLU A 380 LEU A 383 5 4 HELIX 16 16 GLU A 395 SER A 397 5 3 HELIX 17 17 ASP A 431 ALA A 448 1 18 HELIX 18 18 ASP A 457 TYR A 466 1 10 HELIX 19 19 ILE A 478 THR A 486 1 9 HELIX 20 20 THR A 490 VAL A 494 5 5 SHEET 1 A 6 GLU A 66 ARG A 72 0 SHEET 2 A 6 ILE A 120 LYS A 129 -1 N GLY A 125 O VAL A 67 SHEET 3 A 6 LEU A 135 CYS A 139 -1 N HIS A 138 O THR A 126 SHEET 4 A 6 GLY A 92 ALA A 99 1 N GLN A 95 O ILE A 137 SHEET 5 A 6 ALA A 82 ASP A 89 -1 N ASP A 89 O GLY A 92 SHEET 6 A 6 ARG A 72 ILE A 78 -1 N ARG A 77 O PHE A 84 SHEET 1 B 2 ILE A 223 HIS A 226 0 SHEET 2 B 2 LEU A 231 TYR A 234 -1 N MET A 233 O THR A 224 SHEET 1 C 7 ARG A 253 PHE A 261 0 SHEET 2 C 7 GLU A 273 ALA A 282 -1 N TYR A 280 O VAL A 254 SHEET 3 C 7 THR A 471 GLY A 477 -1 N ILE A 476 O MET A 277 SHEET 4 C 7 ARG A 420 SER A 427 -1 N PHE A 426 O GLY A 473 SHEET 5 C 7 ARG A 412 ILE A 417 -1 N ILE A 417 O ARG A 420 SHEET 6 C 7 THR A 387 THR A 390 -1 N ILE A 389 O GLU A 414 SHEET 7 C 7 GLU A 324 THR A 327 1 N GLU A 324 O PHE A 388 SHEET 1 D 2 LYS A 309 TYR A 312 0 SHEET 2 D 2 HIS A 315 ASP A 318 -1 N PHE A 317 O VAL A 310 SHEET 1 E 2 ILE A 120 ARG A 124 0 SHEET 2 E 2 GLU A 141 THR A 146 -1 N THR A 146 O ILE A 120 LINK OE2 GLU A 414 MG MG A 603 1555 1555 2.55 LINK OE2 GLU A 421 MG MG A 603 1555 1555 2.86 LINK O1A LAD A 601 MG MG A 603 1555 1555 2.94 LINK O4 POP A 602 MG MG A 603 1555 1555 2.37 LINK O1 POP A 602 MG MG A 604 1555 1555 2.07 LINK O POP A 602 MG MG A 604 1555 1555 2.24 LINK O5 POP A 602 MG MG A 604 1555 1555 2.57 LINK MG MG A 604 O HOH A 732 1555 1555 2.93 SITE 1 AC1 4 GLU A 414 GLU A 421 LAD A 601 POP A 602 SITE 1 AC2 3 HIS A 270 HOH A 732 POP A 602 SITE 1 AC3 29 GLY A 216 ALA A 217 ALA A 238 GLU A 240 SITE 2 AC3 29 ARG A 262 GLU A 264 ARG A 269 HIS A 270 SITE 3 AC3 29 ASN A 271 PHE A 274 MET A 276 GLU A 278 SITE 4 AC3 29 TYR A 280 GLU A 421 ILE A 422 ASN A 424 SITE 5 AC3 29 PHE A 426 GLU A 428 GLY A 473 GLY A 475 SITE 6 AC3 29 GLY A 477 ARG A 480 ILE A 491 HOH A 705 SITE 7 AC3 29 HOH A 732 HOH A 854 POP A 602 MG A 603 SITE 8 AC3 29 HOH A 761 SITE 1 AC4 9 ARG A 262 HIS A 270 GLU A 421 ARG A 480 SITE 2 AC4 9 HOH A 732 HOH A 805 LAD A 601 MG A 603 SITE 3 AC4 9 MG A 604 SITE 1 AC5 6 TYR A 312 HIS A 315 ILE A 384 GLY A 418 SITE 2 AC5 6 ARG A 420 HIS A 489 SITE 1 AC6 8 LEU A 190 ARG A 194 GLU A 204 GLU A 206 SITE 2 AC6 8 ILE A 257 ASN A 258 HOH A 822 HOH A 703 SITE 1 AC7 7 TYR A 286 THR A 390 GLU A 391 ASN A 403 SITE 2 AC7 7 THR A 410 ASP A 411 ARG A 412 SITE 1 AC8 9 SER A 218 VAL A 396 SER A 397 PRO A 398 SITE 2 AC8 9 LEU A 399 ASN A 424 PHE A 426 HOH A 705 SITE 3 AC8 9 HOH A 761 SITE 1 AC9 3 ILE A 384 GLN A 385 HOH A 916 SITE 1 BC1 12 PRO A 214 GLY A 215 ALA A 217 SER A 218 SITE 2 BC1 12 ALA A 219 PRO A 221 ILE A 237 LYS A 446 SITE 3 BC1 12 GLU A 452 ALA A 453 MET A 454 PHE A 455 SITE 1 BC2 7 GLY A 32 VAL A 33 LYS A 333 ASN A 403 SITE 2 BC2 7 ASP A 404 HOH A 811 HOH A 729 CRYST1 143.100 143.100 176.100 90.00 90.00 120.00 P 61 2 2 12 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 0.006988 0.004034 0.000000 0.00000 SCALE2 0.000000 0.008069 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005678 0.00000