PDB Short entry for 5T76 HEADER TRANSLATION 02-SEP-16 5T76 TITLE A FRAGMENT OF A HUMAN TRNA SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANINE--TRNA LIGASE, CYTOPLASMIC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 757-965; COMPND 5 SYNONYM: ALANYL-TRNA SYNTHETASE, ALARS, RENAL CARCINOMA ANTIGEN NY- COMPND 6 REN-42; COMPND 7 EC: 6.1.1.7; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AARS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 7 PPPARG4; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS TRNA SYNTHETASE, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR L.SUN,P.SCHIMMEL REVDAT 2 04-JAN-17 5T76 1 JRNL REVDAT 1 30-NOV-16 5T76 0 JRNL AUTH L.SUN,Y.SONG,D.BLOCQUEL,X.L.YANG,P.SCHIMMEL JRNL TITL TWO CRYSTAL STRUCTURES REVEAL DESIGN FOR REPURPOSING THE JRNL TITL 2 C-ALA DOMAIN OF HUMAN ALARS. JRNL REF PROC. NATL. ACAD. SCI. V. 113 14300 2016 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 27911835 JRNL DOI 10.1073/PNAS.1617316113 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12323 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 649 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1574 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 157 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5T76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13269 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.5, 25% W/V PEG3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 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 19.22450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 GLY A 1 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 HOH A 412 O HOH A 413 2.14 REMARK 500 NH1 ARG A 156 O HOH A 301 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 13 OD2 ASP A 57 2547 2.13 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 LYS A 178 -166.76 -120.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 5T76 A 1 209 UNP P49588 SYAC_HUMAN 757 965 SEQADV 5T76 HIS A -5 UNP P49588 EXPRESSION TAG SEQADV 5T76 HIS A -4 UNP P49588 EXPRESSION TAG SEQADV 5T76 HIS A -3 UNP P49588 EXPRESSION TAG SEQADV 5T76 HIS A -2 UNP P49588 EXPRESSION TAG SEQADV 5T76 HIS A -1 UNP P49588 EXPRESSION TAG SEQADV 5T76 HIS A 0 UNP P49588 EXPRESSION TAG SEQADV 5T76 THR A 111 UNP P49588 SER 867 CONFLICT SEQRES 1 A 215 HIS HIS HIS HIS HIS HIS GLY ALA GLU ALA GLN LYS ALA SEQRES 2 A 215 LEU ARG LYS ALA GLU SER LEU LYS LYS CYS LEU SER VAL SEQRES 3 A 215 MSE GLU ALA LYS VAL LYS ALA GLN THR ALA PRO ASN LYS SEQRES 4 A 215 ASP VAL GLN ARG GLU ILE ALA ASP LEU GLY GLU ALA LEU SEQRES 5 A 215 ALA THR ALA VAL ILE PRO GLN TRP GLN LYS ASP GLU LEU SEQRES 6 A 215 ARG GLU THR LEU LYS SER LEU LYS LYS VAL MSE ASP ASP SEQRES 7 A 215 LEU ASP ARG ALA SER LYS ALA ASP VAL GLN LYS ARG VAL SEQRES 8 A 215 LEU GLU LYS THR LYS GLN PHE ILE ASP SER ASN PRO ASN SEQRES 9 A 215 GLN PRO LEU VAL ILE LEU GLU MSE GLU SER GLY ALA THR SEQRES 10 A 215 ALA LYS ALA LEU ASN GLU ALA LEU LYS LEU PHE LYS MSE SEQRES 11 A 215 HIS SER PRO GLN THR SER ALA MSE LEU PHE THR VAL ASP SEQRES 12 A 215 ASN GLU ALA GLY LYS ILE THR CYS LEU CYS GLN VAL PRO SEQRES 13 A 215 GLN ASN ALA ALA ASN ARG GLY LEU LYS ALA SER GLU TRP SEQRES 14 A 215 VAL GLN GLN VAL SER GLY LEU MSE ASP GLY LYS GLY GLY SEQRES 15 A 215 GLY LYS ASP VAL SER ALA GLN ALA THR GLY LYS ASN VAL SEQRES 16 A 215 GLY CYS LEU GLN GLU ALA LEU GLN LEU ALA THR SER PHE SEQRES 17 A 215 ALA GLN LEU ARG LEU GLY ASP MODRES 5T76 MSE A 21 MET MODIFIED RESIDUE MODRES 5T76 MSE A 70 MET MODIFIED RESIDUE MODRES 5T76 MSE A 106 MET MODIFIED RESIDUE MODRES 5T76 MSE A 124 MET MODIFIED RESIDUE MODRES 5T76 MSE A 132 MET MODIFIED RESIDUE MODRES 5T76 MSE A 171 MET MODIFIED RESIDUE HET MSE A 21 8 HET MSE A 70 8 HET MSE A 106 8 HET MSE A 124 8 HET MSE A 132 8 HET MSE A 171 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 HOH *157(H2 O) HELIX 1 AA1 ALA A 2 ALA A 27 1 26 HELIX 2 AA2 ASN A 32 ALA A 49 1 18 HELIX 3 AA3 PRO A 52 ASN A 96 1 45 HELIX 4 AA4 THR A 111 SER A 126 1 16 HELIX 5 AA5 PRO A 150 GLY A 157 1 8 HELIX 6 AA6 LYS A 159 GLY A 169 1 11 HELIX 7 AA7 ASN A 188 GLY A 190 5 3 HELIX 8 AA8 CYS A 191 LEU A 205 1 15 SHEET 1 AA1 5 LEU A 101 GLU A 105 0 SHEET 2 AA1 5 SER A 130 ASP A 137 1 O PHE A 134 N LEU A 104 SHEET 3 AA1 5 LYS A 142 GLN A 148 -1 O LEU A 146 N LEU A 133 SHEET 4 AA1 5 SER A 181 GLY A 186 -1 O ALA A 184 N CYS A 145 SHEET 5 AA1 5 GLY A 173 GLY A 177 -1 N GLY A 176 O GLN A 183 LINK C VAL A 20 N MSE A 21 1555 1555 1.34 LINK C MSE A 21 N GLU A 22 1555 1555 1.33 LINK C VAL A 69 N MSE A 70 1555 1555 1.32 LINK C MSE A 70 N ASP A 71 1555 1555 1.33 LINK C GLU A 105 N MSE A 106 1555 1555 1.34 LINK C MSE A 106 N GLU A 107 1555 1555 1.34 LINK C LYS A 123 N MSE A 124 1555 1555 1.34 LINK C MSE A 124 N HIS A 125 1555 1555 1.32 LINK C ALA A 131 N MSE A 132 1555 1555 1.33 LINK C MSE A 132 N LEU A 133 1555 1555 1.33 LINK C LEU A 170 N MSE A 171 1555 1555 1.33 LINK C MSE A 171 N ASP A 172 1555 1555 1.33 CRYST1 41.645 38.449 62.471 90.00 90.50 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 0.024012 0.000000 0.000210 0.00000 SCALE2 0.000000 0.026008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016008 0.00000