HEADER TRANSLATION 04-MAY-23 8J9S TITLE LEUCINE ZIPPER COMPLEX OF AIMP1 AND AIMP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL COMPND 3 PROTEIN 1; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P43; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL COMPND 9 PROTEIN 2; COMPND 10 CHAIN: C; COMPND 11 SYNONYM: MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P38,PROTEIN JTV-1; COMPND 12 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: AIMP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: AIMP2, JTV1, PRO0992; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMINOACYL-TRNA SYNTHETASE, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR D.K.KIM,B.S.KANG REVDAT 1 08-MAY-24 8J9S 0 JRNL AUTH D.K.KIM,B.S.KANG JRNL TITL ASSEMBLY OF HUMAN MULTI-TRNA SYNTHETASE COMPLEX THROUGH JRNL TITL 2 LEUCINE ZIPPER MOTIFS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.240 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 6523 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 652 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 34.6600 - 5.1400 1.00 1387 152 0.2224 0.2483 REMARK 3 2 5.1400 - 4.0800 0.99 1291 143 0.2050 0.2490 REMARK 3 3 4.0800 - 3.5700 0.98 1247 139 0.2335 0.2504 REMARK 3 4 3.5700 - 3.2400 0.96 1220 136 0.2572 0.3329 REMARK 3 5 3.2400 - 3.0100 0.58 726 82 0.2875 0.3426 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.408 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.753 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.23 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 : 0.002 1375 REMARK 3 ANGLE : 0.473 1828 REMARK 3 CHIRALITY : 0.030 218 REMARK 3 PLANARITY : 0.002 232 REMARK 3 DIHEDRAL : 4.370 178 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8J9S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300036602. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97957 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7226 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 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 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 62% MPD, PH 8.2, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 37.19950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.72250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.72250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.59975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.72250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.72250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.79925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.72250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.72250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.59975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.72250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.72250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.79925 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 37.19950 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 300 REMARK: OTHER EXPERIMENTAL RESULTS INDICATE THAT AIMP1 INTERACTS REMARK 300 BOTH AIMP1 AND AIMP2 THROUGH ITS C-AND N-TERMINAL PARTS, REMARK 300 RESPECTIVELY. 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 APPLY THE FOLLOWING TO CHAINS: B, C REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 -47.72250 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 47.72250 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 18.59975 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASN A 3 REMARK 465 VAL A 75 REMARK 465 LYS A 76 REMARK 465 GLN A 77 REMARK 465 ILE A 78 REMARK 465 PRO A 79 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASN B 3 REMARK 465 ASN B 4 REMARK 465 GLN B 72 REMARK 465 ASN B 73 REMARK 465 GLY B 74 REMARK 465 VAL B 75 REMARK 465 LYS B 76 REMARK 465 GLN B 77 REMARK 465 ILE B 78 REMARK 465 PRO B 79 REMARK 465 MET C 50 REMARK 465 PRO C 83 REMARK 465 ASP C 84 REMARK 465 ALA C 85 REMARK 465 ASP C 86 REMARK 465 LEU C 87 REMARK 465 ASP C 88 REMARK 465 VAL C 89 REMARK 465 THR C 90 REMARK 465 LEU C 91 REMARK 465 GLU C 92 REMARK 465 HIS C 93 REMARK 465 HIS C 94 REMARK 465 HIS C 95 REMARK 465 HIS C 96 REMARK 465 HIS C 97 REMARK 465 HIS C 98 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 ASN A 4 CG OD1 ND2 DBREF 8J9S A 1 79 UNP Q12904 AIMP1_HUMAN 1 79 DBREF 8J9S B 1 79 UNP Q12904 AIMP1_HUMAN 1 79 DBREF 8J9S C 51 90 UNP Q13155 AIMP2_HUMAN 51 90 SEQADV 8J9S MET C 50 UNP Q13155 INITIATING METHIONINE SEQADV 8J9S LEU C 91 UNP Q13155 EXPRESSION TAG SEQADV 8J9S GLU C 92 UNP Q13155 EXPRESSION TAG SEQADV 8J9S HIS C 93 UNP Q13155 EXPRESSION TAG SEQADV 8J9S HIS C 94 UNP Q13155 EXPRESSION TAG SEQADV 8J9S HIS C 95 UNP Q13155 EXPRESSION TAG SEQADV 8J9S HIS C 96 UNP Q13155 EXPRESSION TAG SEQADV 8J9S HIS C 97 UNP Q13155 EXPRESSION TAG SEQADV 8J9S HIS C 98 UNP Q13155 EXPRESSION TAG SEQRES 1 A 79 MET ALA ASN ASN ASP ALA VAL LEU LYS ARG LEU GLU GLN SEQRES 2 A 79 LYS GLY ALA GLU ALA ASP GLN ILE ILE GLU TYR LEU LYS SEQRES 3 A 79 GLN GLN VAL SER LEU LEU LYS GLU LYS ALA ILE LEU GLN SEQRES 4 A 79 ALA THR LEU ARG GLU GLU LYS LYS LEU ARG VAL GLU ASN SEQRES 5 A 79 ALA LYS LEU LYS LYS GLU ILE GLU GLU LEU LYS GLN GLU SEQRES 6 A 79 LEU ILE GLN ALA GLU ILE GLN ASN GLY VAL LYS GLN ILE SEQRES 7 A 79 PRO SEQRES 1 B 79 MET ALA ASN ASN ASP ALA VAL LEU LYS ARG LEU GLU GLN SEQRES 2 B 79 LYS GLY ALA GLU ALA ASP GLN ILE ILE GLU TYR LEU LYS SEQRES 3 B 79 GLN GLN VAL SER LEU LEU LYS GLU LYS ALA ILE LEU GLN SEQRES 4 B 79 ALA THR LEU ARG GLU GLU LYS LYS LEU ARG VAL GLU ASN SEQRES 5 B 79 ALA LYS LEU LYS LYS GLU ILE GLU GLU LEU LYS GLN GLU SEQRES 6 B 79 LEU ILE GLN ALA GLU ILE GLN ASN GLY VAL LYS GLN ILE SEQRES 7 B 79 PRO SEQRES 1 C 49 MET SER LEU GLN ALA LEU GLU SER ARG GLN ASP ASP ILE SEQRES 2 C 49 LEU LYS ARG LEU TYR GLU LEU LYS ALA ALA VAL ASP GLY SEQRES 3 C 49 LEU SER LYS MET ILE GLN THR PRO ASP ALA ASP LEU ASP SEQRES 4 C 49 VAL THR LEU GLU HIS HIS HIS HIS HIS HIS HET IOD A 101 1 HET IOD A 102 1 HET IOD A 103 1 HET IOD B 101 1 HET IOD B 102 1 HETNAM IOD IODIDE ION FORMUL 4 IOD 5(I 1-) HELIX 1 AA1 ASP A 5 ASN A 73 1 69 HELIX 2 AA2 ALA B 6 ILE B 71 1 66 HELIX 3 AA3 LEU C 52 ILE C 80 1 29 CRYST1 95.445 95.445 74.399 90.00 90.00 90.00 P 41 21 2 16 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 0.010477 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013441 0.00000