HEADER TRANSLATION 31-AUG-16 5T5S 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 4 16-OCT-24 5T5S 1 REMARK REVDAT 3 04-OCT-23 5T5S 1 REMARK REVDAT 2 04-JAN-17 5T5S 1 JRNL REVDAT 1 30-NOV-16 5T5S 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. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2306: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 16634 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 841 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.4938 - 3.9993 0.96 2996 175 0.1690 0.2116 REMARK 3 2 3.9993 - 3.1756 0.94 2860 130 0.2091 0.2822 REMARK 3 3 3.1756 - 2.7745 1.00 2961 167 0.2356 0.2914 REMARK 3 4 2.7745 - 2.5210 0.98 2877 147 0.2321 0.2844 REMARK 3 5 2.5210 - 2.3404 0.80 2369 131 0.2406 0.2829 REMARK 3 6 2.3404 - 2.2024 0.59 1730 91 0.2875 0.3012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.160 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1593 REMARK 3 ANGLE : 1.023 2142 REMARK 3 CHIRALITY : 0.047 250 REMARK 3 PLANARITY : 0.006 279 REMARK 3 DIHEDRAL : 17.709 1016 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 32.1008 -2.1386 14.8135 REMARK 3 T TENSOR REMARK 3 T11: 0.1601 T22: 0.3697 REMARK 3 T33: 0.2885 T12: -0.0464 REMARK 3 T13: -0.0055 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 0.1792 L22: 2.1629 REMARK 3 L33: 2.5112 L12: -0.3799 REMARK 3 L13: -0.2022 L23: 0.3296 REMARK 3 S TENSOR REMARK 3 S11: -0.0629 S12: 0.0547 S13: -0.0160 REMARK 3 S21: 0.0997 S22: 0.0011 S23: 0.2228 REMARK 3 S31: 0.1439 S32: -0.6710 S33: 0.1095 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5T5S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-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 : 16637 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.202 REMARK 200 RESOLUTION RANGE LOW (A) : 75.557 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10900 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 5T76 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M TRIS, PH REMARK 280 8.5, 25% W/V PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.53850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.53850 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.41450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.07050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.41450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.07050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.53850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.41450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.07050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 29.53850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.41450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.07050 REMARK 290 SMTRY3 8 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 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 APPLY THE FOLLOWING TO CHAINS: A 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 59.07700 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 465 ASP A 209 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 183 CD 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 OD1 ASP A 72 NH1 ARG A 75 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 GLU A 3 -86.21 -56.17 REMARK 500 ASN A 188 99.50 -68.95 REMARK 500 CYS A 191 52.88 -100.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI DBREF 5T5S A 1 209 UNP P49588 SYAC_HUMAN 757 965 SEQADV 5T5S HIS A -5 UNP P49588 EXPRESSION TAG SEQADV 5T5S HIS A -4 UNP P49588 EXPRESSION TAG SEQADV 5T5S HIS A -3 UNP P49588 EXPRESSION TAG SEQADV 5T5S HIS A -2 UNP P49588 EXPRESSION TAG SEQADV 5T5S HIS A -1 UNP P49588 EXPRESSION TAG SEQADV 5T5S HIS A 0 UNP P49588 EXPRESSION TAG SEQADV 5T5S 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 MET 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 MET 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 MET GLU SER GLY ALA THR SEQRES 10 A 215 ALA LYS ALA LEU ASN GLU ALA LEU LYS LEU PHE LYS MET SEQRES 11 A 215 HIS SER PRO GLN THR SER ALA MET 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 MET 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 FORMUL 2 HOH *133(H2 O) HELIX 1 AA1 ALA A 2 GLN A 28 1 27 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 ARG A 156 1 7 HELIX 6 AA6 LYS A 159 MET A 171 1 13 HELIX 7 AA7 CYS A 191 GLY A 208 1 18 SHEET 1 AA1 4 LEU A 101 GLU A 105 0 SHEET 2 AA1 4 SER A 130 ASP A 137 1 O MET A 132 N VAL A 102 SHEET 3 AA1 4 LYS A 142 GLN A 148 -1 O LEU A 146 N LEU A 133 SHEET 4 AA1 4 SER A 181 LYS A 187 -1 O GLY A 186 N ILE A 143 SSBOND 1 CYS A 17 CYS A 191 1555 4556 2.04 CRYST1 90.829 136.141 59.077 90.00 90.00 90.00 C 2 2 21 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 0.011010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016927 0.00000