PDB Short entry for 1FL0 HEADER RNA BINDING PROTEIN 11-AUG-00 1FL0 TITLE CRYSTAL STRUCTURE OF THE EMAP2/RNA-BINDING DOMAIN OF THE P43 PROTEIN TITLE 2 FROM HUMAN AMINOACYL-TRNA SYNTHETASE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN/RNA-BINDING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-28B KEYWDS RNA-BINDING DOMAIN, OB-FOLD, TRNA SYNTHETASE COMPLEX, RNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.RENAULT,P.KERJAN,S.PASQUALATO,J.MENETREY,J.-C.ROBINSON,S.KAWAGUCHI, AUTHOR 2 D.G.VASSYLYEV,S.YOKOYAMA,M.MIRANDE,J.CHERFILS REVDAT 6 07-FEB-24 1FL0 1 SEQADV REVDAT 5 08-FEB-17 1FL0 1 AUTHOR VERSN REVDAT 4 24-FEB-09 1FL0 1 VERSN REVDAT 3 01-APR-03 1FL0 1 JRNL REVDAT 2 07-FEB-01 1FL0 1 JRNL REVDAT 1 06-DEC-00 1FL0 0 JRNL AUTH L.RENAULT,P.KERJAN,S.PASQUALATO,J.MENETREY,J.C.ROBINSON, JRNL AUTH 2 S.KAWAGUCHI,D.G.VASSYLYEV,S.YOKOYAMA,M.MIRANDE,J.CHERFILS JRNL TITL STRUCTURE OF THE EMAPII DOMAIN OF HUMAN AMINOACYL-TRNA JRNL TITL 2 SYNTHETASE COMPLEX REVEALS EVOLUTIONARY DIMER MIMICRY. JRNL REF EMBO J. V. 20 570 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11157763 JRNL DOI 10.1093/EMBOJ/20.3.570 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.100 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 85632626.060 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23301 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) : 0.221 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3676 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 193 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : 1.65000 REMARK 3 B33 (A**2) : -1.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.94000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 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) : 1.580 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.600 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.900 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.600 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 30.05 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1000011676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 6.20000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 15.7000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 3000 OR 6000, 100MM TRIS REMARK 280 PH7.5, 100-300 MM NACL, 2MM DTE WITH A PROTEIN CONCENTRATION OF REMARK 280 11 MG/ML, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 29.84150 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 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 GLU A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 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 ALA A 171 81.92 -166.06 REMARK 500 ASP A 172 -8.34 -59.63 REMARK 500 ARG A 219 54.63 91.11 REMARK 500 LYS A 235 150.86 179.88 REMARK 500 LYS A 268 -41.60 104.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 1FL0 A 150 312 UNP Q12904 MCA1_HUMAN 150 312 SEQADV 1FL0 LEU A 313 UNP Q12904 EXPRESSION TAG SEQADV 1FL0 GLU A 314 UNP Q12904 EXPRESSION TAG SEQADV 1FL0 HIS A 315 UNP Q12904 EXPRESSION TAG SEQADV 1FL0 HIS A 316 UNP Q12904 EXPRESSION TAG SEQADV 1FL0 HIS A 317 UNP Q12904 EXPRESSION TAG SEQADV 1FL0 HIS A 318 UNP Q12904 EXPRESSION TAG SEQADV 1FL0 HIS A 319 UNP Q12904 EXPRESSION TAG SEQADV 1FL0 HIS A 320 UNP Q12904 EXPRESSION TAG SEQRES 1 A 171 ILE ASP VAL SER ARG LEU ASP LEU ARG ILE GLY CYS ILE SEQRES 2 A 171 ILE THR ALA ARG LYS HIS PRO ASP ALA ASP SER LEU TYR SEQRES 3 A 171 VAL GLU GLU VAL ASP VAL GLY GLU ILE ALA PRO ARG THR SEQRES 4 A 171 VAL VAL SER GLY LEU VAL ASN HIS VAL PRO LEU GLU GLN SEQRES 5 A 171 MET GLN ASN ARG MET VAL ILE LEU LEU CYS ASN LEU LYS SEQRES 6 A 171 PRO ALA LYS MET ARG GLY VAL LEU SER GLN ALA MET VAL SEQRES 7 A 171 MET CYS ALA SER SER PRO GLU LYS ILE GLU ILE LEU ALA SEQRES 8 A 171 PRO PRO ASN GLY SER VAL PRO GLY ASP ARG ILE THR PHE SEQRES 9 A 171 ASP ALA PHE PRO GLY GLU PRO ASP LYS GLU LEU ASN PRO SEQRES 10 A 171 LYS LYS LYS ILE TRP GLU GLN ILE GLN PRO ASP LEU HIS SEQRES 11 A 171 THR ASN ASP GLU CYS VAL ALA THR TYR LYS GLY VAL PRO SEQRES 12 A 171 PHE GLU VAL LYS GLY LYS GLY VAL CYS ARG ALA GLN THR SEQRES 13 A 171 MET SER ASN SER GLY ILE LYS LEU GLU HIS HIS HIS HIS SEQRES 14 A 171 HIS HIS FORMUL 2 HOH *247(H2 O) HELIX 1 1 ASP A 151 LEU A 155 5 5 HELIX 2 2 PRO A 198 GLN A 203 5 6 HELIX 3 3 ILE A 270 GLN A 275 1 6 SHEET 1 A 5 ARG A 187 SER A 191 0 SHEET 2 A 5 ALA A 171 ASP A 180 -1 N TYR A 175 O SER A 191 SHEET 3 A 5 LEU A 157 HIS A 168 -1 O CYS A 161 N ASP A 180 SHEET 4 A 5 ARG A 205 LEU A 210 -1 O ARG A 205 N ILE A 162 SHEET 5 A 5 MET A 226 VAL A 227 -1 O MET A 226 N LEU A 210 SHEET 1 B 2 ALA A 216 LYS A 217 0 SHEET 2 B 2 LEU A 222 SER A 223 -1 N SER A 223 O ALA A 216 SHEET 1 C 3 LYS A 235 ILE A 238 0 SHEET 2 C 3 CYS A 229 SER A 232 -1 N ALA A 230 O GLU A 237 SHEET 3 C 3 GLY A 310 ILE A 311 -1 O GLY A 310 N SER A 231 SHEET 1 D 3 LEU A 278 THR A 280 0 SHEET 2 D 3 ALA A 286 TYR A 288 -1 O THR A 287 N HIS A 279 SHEET 3 D 3 VAL A 291 PRO A 292 -1 N VAL A 291 O TYR A 288 SHEET 1 E 2 GLU A 294 VAL A 295 0 SHEET 2 E 2 GLY A 299 VAL A 300 -1 O GLY A 299 N VAL A 295 CRYST1 35.954 59.683 37.850 90.00 114.83 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 0.027813 0.000000 0.012867 0.00000 SCALE2 0.000000 0.016755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029110 0.00000