HEADER CELL CYCLE 21-NOV-13 4CGC TITLE CRYSTAL STRUCTURE OF THE TRIMERIZATION DOMAIN OF HUMAN EML4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 4; COMPND 3 CHAIN: A, C, B; COMPND 4 FRAGMENT: TRIMERIZATION DOMAIN, RESIDUES 6-64; COMPND 5 SYNONYM: EMAP-4, RESTRICTEDLY OVEREXPRESSED COMPND 6 PROLIFERATION-ASSOCIATED PROTEIN, ROPP 120, ECHINODERM MICROTUBULE COMPND 7 ASSOCIATED PROTEIN-LIKE PROTEIN 4; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30TEV KEYWDS CELL CYCLE, EML4-ALK, NSCLC, COILED-COIL EXPDTA X-RAY DIFFRACTION AUTHOR M.W.RICHARDS,R.BAYLISS REVDAT 3 29-APR-15 4CGC 1 JRNL REVDAT 2 18-MAR-15 4CGC 1 JRNL REVDAT 1 10-DEC-14 4CGC 0 JRNL AUTH M.W.RICHARDS,L.O'REGAN,D.ROTH,J.M.MONTGOMERY,A.STRAUBE, JRNL AUTH 2 A.M.FRY,R.BAYLISS JRNL TITL MICROTUBULE ASSOCIATION OF EML PROTEINS AND THE EML4-ALK JRNL TITL 2 VARIANT 3 ONCOPROTEIN REQUIRE AN N-TERMINAL TRIMERIZATION JRNL TITL 3 DOMAIN. JRNL REF BIOCHEM.J. V. 467 529 2015 JRNL REFN ISSN 0264-6021 JRNL PMID 25740311 JRNL DOI 10.1042/BJ20150039 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.901 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.723 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.38 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.98 REMARK 3 NUMBER OF REFLECTIONS : 4949 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2687 REMARK 3 R VALUE (WORKING SET) : 0.2675 REMARK 3 FREE R VALUE : 0.2915 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.6 REMARK 3 FREE R VALUE TEST SET COUNT : 228 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 47.7299 - 3.6552 1.00 2355 120 0.2558 0.2613 REMARK 3 2 3.6552 - 2.9014 1.00 2366 108 0.3012 0.3861 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) : 0.41 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.35 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 : 0.006 651 REMARK 3 ANGLE : 1.020 875 REMARK 3 CHIRALITY : 0.052 106 REMARK 3 PLANARITY : 0.005 119 REMARK 3 DIHEDRAL : 23.604 259 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: REMARK 3 ONLY RESIDUES 16-44 ARE VISIBLE IN THE ELECTION DENSITY. REMARK 3 RESIDUES 6-15 AND 45-64 WERE NOT MODELLED. REMARK 4 REMARK 4 4CGC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-13. REMARK 100 THE PDBE ID CODE IS EBI-59049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2864 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.90 REMARK 200 RESOLUTION RANGE LOW (A) : 67.49 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.4 REMARK 200 R MERGE (I) : 0.13 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.30 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.4 REMARK 200 R MERGE FOR SHELL (I) : 1.25 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SCALA REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 18.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS/HCL PH 8.5, 30% PEG REMARK 280 4000, 200 MM MGCL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 25.30000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.74550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.74550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.95000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.74550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.74550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.65000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.74550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.74550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.95000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.74550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.74550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 12.65000 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 25.30000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A 6 REMARK 465 SER A 7 REMARK 465 LEU A 8 REMARK 465 ASP A 9 REMARK 465 ASP A 10 REMARK 465 SER A 11 REMARK 465 ILE A 12 REMARK 465 SER A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 SER A 16 REMARK 465 LEU A 45 REMARK 465 ALA A 46 REMARK 465 ASP A 47 REMARK 465 VAL A 48 REMARK 465 LEU A 49 REMARK 465 ARG A 50 REMARK 465 ARG A 51 REMARK 465 LEU A 52 REMARK 465 ALA A 53 REMARK 465 ILE A 54 REMARK 465 SER A 55 REMARK 465 GLU A 56 REMARK 465 ASP A 57 REMARK 465 HIS A 58 REMARK 465 VAL A 59 REMARK 465 ALA A 60 REMARK 465 SER A 61 REMARK 465 VAL A 62 REMARK 465 LYS A 63 REMARK 465 LYS A 64 REMARK 465 GLY B 6 REMARK 465 SER B 7 REMARK 465 LEU B 8 REMARK 465 ASP B 9 REMARK 465 ASP B 10 REMARK 465 SER B 11 REMARK 465 ILE B 12 REMARK 465 SER B 13 REMARK 465 ALA B 14 REMARK 465 ALA B 15 REMARK 465 SER B 16 REMARK 465 THR B 17 REMARK 465 SER B 18 REMARK 465 LEU B 45 REMARK 465 ALA B 46 REMARK 465 ASP B 47 REMARK 465 VAL B 48 REMARK 465 LEU B 49 REMARK 465 ARG B 50 REMARK 465 ARG B 51 REMARK 465 LEU B 52 REMARK 465 ALA B 53 REMARK 465 ILE B 54 REMARK 465 SER B 55 REMARK 465 GLU B 56 REMARK 465 ASP B 57 REMARK 465 HIS B 58 REMARK 465 VAL B 59 REMARK 465 ALA B 60 REMARK 465 SER B 61 REMARK 465 VAL B 62 REMARK 465 LYS B 63 REMARK 465 LYS B 64 REMARK 465 GLY C 6 REMARK 465 SER C 7 REMARK 465 LEU C 8 REMARK 465 ASP C 9 REMARK 465 ASP C 10 REMARK 465 SER C 11 REMARK 465 ILE C 12 REMARK 465 SER C 13 REMARK 465 ALA C 14 REMARK 465 ALA C 15 REMARK 465 LEU C 45 REMARK 465 ALA C 46 REMARK 465 ASP C 47 REMARK 465 VAL C 48 REMARK 465 LEU C 49 REMARK 465 ARG C 50 REMARK 465 ARG C 51 REMARK 465 LEU C 52 REMARK 465 ALA C 53 REMARK 465 ILE C 54 REMARK 465 SER C 55 REMARK 465 GLU C 56 REMARK 465 ASP C 57 REMARK 465 HIS C 58 REMARK 465 VAL C 59 REMARK 465 ALA C 60 REMARK 465 SER C 61 REMARK 465 VAL C 62 REMARK 465 LYS C 63 REMARK 465 LYS C 64 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 THR A 17 OG1 CG2 REMARK 470 SER C 16 OG REMARK 470 THR C 17 OG1 CG2 REMARK 470 SER C 18 OG 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 OE1 GLU A 28 NH2 ARG C 23 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CGB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TRIMERIZATION DOMAIN OF EML2 DBREF 4CGC A 6 64 UNP Q9HC35 EMAL4_HUMAN 6 64 DBREF 4CGC B 6 64 UNP Q9HC35 EMAL4_HUMAN 6 64 DBREF 4CGC C 6 64 UNP Q9HC35 EMAL4_HUMAN 6 64 SEQADV 4CGC MSE A 38 UNP Q9HC35 ILE 38 ENGINEERED SEQADV 4CGC MSE B 38 UNP Q9HC35 ILE 38 ENGINEERED SEQADV 4CGC MSE C 38 UNP Q9HC35 ILE 38 ENGINEERED SEQRES 1 A 59 GLY SER LEU ASP ASP SER ILE SER ALA ALA SER THR SER SEQRES 2 A 59 ASP VAL GLN ASP ARG LEU SER ALA LEU GLU SER ARG VAL SEQRES 3 A 59 GLN GLN GLN GLU ASP GLU MSE THR VAL LEU LYS ALA ALA SEQRES 4 A 59 LEU ALA ASP VAL LEU ARG ARG LEU ALA ILE SER GLU ASP SEQRES 5 A 59 HIS VAL ALA SER VAL LYS LYS SEQRES 1 B 59 GLY SER LEU ASP ASP SER ILE SER ALA ALA SER THR SER SEQRES 2 B 59 ASP VAL GLN ASP ARG LEU SER ALA LEU GLU SER ARG VAL SEQRES 3 B 59 GLN GLN GLN GLU ASP GLU MSE THR VAL LEU LYS ALA ALA SEQRES 4 B 59 LEU ALA ASP VAL LEU ARG ARG LEU ALA ILE SER GLU ASP SEQRES 5 B 59 HIS VAL ALA SER VAL LYS LYS SEQRES 1 C 59 GLY SER LEU ASP ASP SER ILE SER ALA ALA SER THR SER SEQRES 2 C 59 ASP VAL GLN ASP ARG LEU SER ALA LEU GLU SER ARG VAL SEQRES 3 C 59 GLN GLN GLN GLU ASP GLU MSE THR VAL LEU LYS ALA ALA SEQRES 4 C 59 LEU ALA ASP VAL LEU ARG ARG LEU ALA ILE SER GLU ASP SEQRES 5 C 59 HIS VAL ALA SER VAL LYS LYS MODRES 4CGC MSE A 38 MET SELENOMETHIONINE MODRES 4CGC MSE B 38 MET SELENOMETHIONINE MODRES 4CGC MSE C 38 MET SELENOMETHIONINE HET MSE A 38 13 HET MSE B 38 8 HET MSE C 38 8 HETNAM MSE SELENOMETHIONINE FORMUL 4 MSE 3(C5 H11 N O2 SE) HELIX 1 1 THR A 17 ALA A 44 1 28 HELIX 2 2 ASP B 19 ALA B 44 1 26 HELIX 3 3 SER C 16 ALA C 44 1 29 LINK C GLU A 37 N MSE A 38 1555 1555 1.33 LINK C MSE A 38 N THR A 39 1555 1555 1.36 LINK C GLU B 37 N MSE B 38 1555 1555 1.33 LINK C MSE B 38 N THR B 39 1555 1555 1.33 LINK C GLU C 37 N MSE C 38 1555 1555 1.33 LINK C MSE C 38 N THR C 39 1555 1555 1.33 CRYST1 67.491 67.491 50.600 90.00 90.00 90.00 P 43 21 2 24 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 0.014817 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019763 0.00000