HEADER RNA BINDING DOMAIN 13-SEP-00 1E7Z 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 RESIDUES 147-312; 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 KEYWDS RNA BINDING DOMAIN, OB-FOLD, TRNA SYNTHETASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.PASQUALATO,P.KERJAN,L.RENAULT,J.MENETREY,M.MIRANDE,J.CHERFILS REVDAT 4 13-DEC-23 1E7Z 1 REMARK LINK REVDAT 3 24-FEB-09 1E7Z 1 VERSN REVDAT 2 06-FEB-01 1E7Z 1 JRNL REVDAT 1 27-NOV-00 1E7Z 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 DIMERIC 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. 2.05 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 : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 7632586.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 9020 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 : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 947 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1331 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 173 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1337 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 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) : 1.540 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.500 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.930 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.870 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 62.12 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1E7Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1290005338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 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, TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11716 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18300 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: CNS 1.0 REMARK 200 STARTING MODEL: PDB ENTRY 1FL0 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: PH 7.50 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 26.96900 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: PQS 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 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 ILE A 150 69.69 -107.52 REMARK 500 GLU A 234 -77.94 -80.16 REMARK 500 LYS A 269 55.82 33.38 REMARK 500 LEU A 313 16.98 -143.97 REMARK 500 GLU A 314 -65.92 -158.75 REMARK 500 HIS A 315 -20.08 -38.73 REMARK 500 HIS A 316 -27.92 -18.82 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 HG A 500 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 161 SG REMARK 620 2 ASN A 204 O 102.5 REMARK 620 3 ASN A 204 OD1 82.3 63.1 REMARK 620 4 MET A 206 SD 95.9 119.5 177.2 REMARK 620 5 HOH A2043 O 81.4 159.1 97.6 80.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 501 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 283 O REMARK 620 2 CYS A 284 SG 84.8 REMARK 620 3 HOH A2112 O 105.4 131.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FL0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EMAP2/RNA-BINDING DOMAIN OF THE P43 REMARK 900 PROTEIN FROM HUMAN AMINOACYL-TRNA SYNTHETASE COMPLEX DBREF 1E7Z A 147 312 UNP Q12904 Q12904 147 312 DBREF 1E7Z A 313 320 PDB 1E7Z 1E7Z 313 320 SEQADV 1E7Z ALA A 147 UNP Q12904 SER 147 CLONING ARTIFACT SEQRES 1 A 174 ALA LYS PRO ILE ASP VAL SER ARG LEU ASP LEU ARG ILE SEQRES 2 A 174 GLY CYS ILE ILE THR ALA ARG LYS HIS PRO ASP ALA ASP SEQRES 3 A 174 SER LEU TYR VAL GLU GLU VAL ASP VAL GLY GLU ILE ALA SEQRES 4 A 174 PRO ARG THR VAL VAL SER GLY LEU VAL ASN HIS VAL PRO SEQRES 5 A 174 LEU GLU GLN MET GLN ASN ARG MET VAL ILE LEU LEU CYS SEQRES 6 A 174 ASN LEU LYS PRO ALA LYS MET ARG GLY VAL LEU SER GLN SEQRES 7 A 174 ALA MET VAL MET CYS ALA SER SER PRO GLU LYS ILE GLU SEQRES 8 A 174 ILE LEU ALA PRO PRO ASN GLY SER VAL PRO GLY ASP ARG SEQRES 9 A 174 ILE THR PHE ASP ALA PHE PRO GLY GLU PRO ASP LYS GLU SEQRES 10 A 174 LEU ASN PRO LYS LYS LYS ILE TRP GLU GLN ILE GLN PRO SEQRES 11 A 174 ASP LEU HIS THR ASN ASP GLU CYS VAL ALA THR TYR LYS SEQRES 12 A 174 GLY VAL PRO PHE GLU VAL LYS GLY LYS GLY VAL CYS ARG SEQRES 13 A 174 ALA GLN THR MET SER ASN SER GLY ILE LYS LEU GLU HIS SEQRES 14 A 174 HIS HIS HIS HIS HIS HET HG A 500 1 HET HG A 501 1 HETNAM HG MERCURY (II) ION FORMUL 2 HG 2(HG 2+) FORMUL 4 HOH *142(H2 O) HELIX 1 1 ASP A 151 LEU A 155 5 5 HELIX 2 2 PRO A 198 GLN A 203 1 6 HELIX 3 3 ASN A 265 LYS A 268 5 4 HELIX 4 4 LYS A 269 GLN A 275 1 7 SHEET 1 A 4 MET A 206 LEU A 210 0 SHEET 2 A 4 LEU A 157 LYS A 167 -1 N GLY A 160 O VAL A 207 SHEET 3 A 4 TYR A 175 ASP A 180 -1 N ASP A 180 O CYS A 161 SHEET 4 A 4 ARG A 187 SER A 191 -1 N SER A 191 O TYR A 175 SHEET 1 B 2 ALA A 216 MET A 218 0 SHEET 2 B 2 VAL A 221 SER A 223 -1 N SER A 223 O ALA A 216 SHEET 1 C 3 ILE A 236 ILE A 238 0 SHEET 2 C 3 CYS A 229 SER A 231 -1 N ALA A 230 O GLU A 237 SHEET 3 C 3 GLY A 310 LYS A 312 -1 N LYS A 312 O CYS A 229 SHEET 1 D 2 LEU A 278 THR A 280 0 SHEET 2 D 2 ALA A 286 TYR A 288 -1 N THR A 287 O HIS A 279 LINK SG CYS A 161 HG HG A 500 1555 1555 2.41 LINK O ASN A 204 HG HG A 500 1555 1555 3.27 LINK OD1 ASN A 204 HG HG A 500 1555 1555 2.98 LINK SD MET A 206 HG HG A 500 1555 1555 3.18 LINK O GLU A 283 HG HG A 501 1555 1555 3.02 LINK SG CYS A 284 HG HG A 501 1555 1555 2.74 LINK HG HG A 500 O HOH A2043 1555 1555 3.20 LINK HG HG A 501 O HOH A2112 1555 1555 3.51 SITE 1 AC1 3 CYS A 161 ASN A 204 MET A 206 SITE 1 AC2 3 GLU A 283 CYS A 284 ARG A 302 CRYST1 36.141 53.938 41.371 90.00 111.92 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 0.027669 0.000000 0.011134 0.00000 SCALE2 0.000000 0.018540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026055 0.00000