PDB Short entry for 4ET7 HEADER TRANSFERASE 24-APR-12 4ET7 TITLE CRYSTAL STRUCTURE OF EPH RECEPTOR 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-A RECEPTOR 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 59-235; COMPND 5 SYNONYM: BRAIN-SPECIFIC KINASE, EPH HOMOLOGY KINASE 1, EHK-1, EPH- COMPND 6 LIKE KINASE 7, EK7, HEK7; COMPND 7 EC: 2.7.10.1; 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 GENE: BSK, EHK1, EPHA5, HEK7, TYRO4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS EPH RECEPTOR, ATP-BINDING, GLYCOPROTEIN, NUCLEOTIDE-BINDING, KEYWDS 2 PHOSPHOPROTEIN, TRANSFERASE, TRANSMEMBRANE, TYROSINE-PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.SHI,W.L.ZHU,J.X.SONG REVDAT 2 08-NOV-23 4ET7 1 SEQADV REVDAT 1 22-MAY-13 4ET7 0 JRNL AUTH J.H.SHI,W.L.ZHU,J.X.SONG JRNL TITL CRYSTAL STRUCTURE OF EPH RECEPTOR 5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 5385 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 538 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 20.6810 - 4.1190 0.97 1343 149 0.1870 0.2330 REMARK 3 2 4.1190 - 3.2740 0.94 1248 137 0.2000 0.2760 REMARK 3 3 3.2740 - 2.8610 0.88 1171 128 0.2220 0.3340 REMARK 3 4 2.8610 - 2.6000 0.83 1085 124 0.2210 0.3240 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 28.61 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.19100 REMARK 3 B22 (A**2) : 15.26600 REMARK 3 B33 (A**2) : -10.07500 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 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 : 0.007 1429 REMARK 3 ANGLE : 1.141 1931 REMARK 3 CHIRALITY : 0.081 208 REMARK 3 PLANARITY : 0.003 252 REMARK 3 DIHEDRAL : 19.319 515 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: THE STRUCTURE FACTOR FILE INCLUDES THE REMARK 3 REFLECTIONS UNTIL 2.08 A BUT AUTHOR DID NOT USE THE DATA FOR REMARK 3 RESOLUTION 2.6-2.08A, THAT IS NOT GOOD FOR REFINEMENT. REMARK 4 REMARK 4 4ET7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000072038. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5385 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 41.361 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.12 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 1.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 3CKH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.1M TRIS-HCL PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 7.5 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 40.58300 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 40.58300 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 27.52000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.36050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.52000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.36050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.58300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.52000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.36050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.58300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.52000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.36050 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 57 REMARK 465 SER A 58 REMARK 465 ALA A 233 REMARK 465 PRO A 234 REMARK 465 SER A 235 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 ASN A 81 -175.42 -68.05 REMARK 500 CYS A 102 56.56 -149.79 REMARK 500 LYS A 103 57.50 -91.81 REMARK 500 GLU A 106 -145.82 -97.28 REMARK 500 SER A 124 -33.44 -135.50 REMARK 500 ASP A 160 105.58 -44.48 REMARK 500 ASN A 165 -78.84 -105.22 REMARK 500 ILE A 166 -35.38 -35.99 REMARK 500 GLU A 168 79.33 -110.27 REMARK 500 GLU A 185 6.43 -67.43 REMARK 500 ASP A 187 145.35 -19.21 REMARK 500 SER A 206 -69.38 -96.20 REMARK 500 LYS A 207 -168.92 -69.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CKH RELATED DB: PDB REMARK 900 THE SAME SUB-CLASS PROTEIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN SEQUENCE IS DERIVED FROM THE EPHA5 ISOFORM B (NP_872272) REMARK 999 WHICH HAS GLU AT POSITION 232. DBREF 4ET7 A 59 235 UNP P54756 EPHA5_HUMAN 59 235 SEQADV 4ET7 GLY A 57 UNP P54756 EXPRESSION TAG SEQADV 4ET7 SER A 58 UNP P54756 EXPRESSION TAG SEQADV 4ET7 GLU A 232 UNP P54756 LYS 232 SEE REMARK 999 SEQADV 4ET7 ALA A 233 UNP P54756 CYS 233 ENGINEERED MUTATION SEQRES 1 A 179 GLY SER ASN GLU VAL ASN LEU LEU ASP SER ARG THR VAL SEQRES 2 A 179 MET GLY ASP LEU GLY TRP ILE ALA PHE PRO LYS ASN GLY SEQRES 3 A 179 TRP GLU GLU ILE GLY GLU VAL ASP GLU ASN TYR ALA PRO SEQRES 4 A 179 ILE HIS THR TYR GLN VAL CYS LYS VAL MET GLU GLN ASN SEQRES 5 A 179 GLN ASN ASN TRP LEU LEU THR SER TRP ILE SER ASN GLU SEQRES 6 A 179 GLY ALA SER ARG ILE PHE ILE GLU LEU LYS PHE THR LEU SEQRES 7 A 179 ARG ASP CYS ASN SER LEU PRO GLY GLY LEU GLY THR CYS SEQRES 8 A 179 LYS GLU THR PHE ASN MET TYR TYR PHE GLU SER ASP ASP SEQRES 9 A 179 GLN ASN GLY ARG ASN ILE LYS GLU ASN GLN TYR ILE LYS SEQRES 10 A 179 ILE ASP THR ILE ALA ALA ASP GLU SER PHE THR GLU LEU SEQRES 11 A 179 ASP LEU GLY ASP ARG VAL MET LYS LEU ASN THR GLU VAL SEQRES 12 A 179 ARG ASP VAL GLY PRO LEU SER LYS LYS GLY PHE TYR LEU SEQRES 13 A 179 ALA PHE GLN ASP VAL GLY ALA CYS ILE ALA LEU VAL SER SEQRES 14 A 179 VAL ARG VAL TYR TYR LYS GLU ALA PRO SER FORMUL 2 HOH *36(H2 O) HELIX 1 1 ASP A 136 LEU A 140 5 5 HELIX 2 2 ASN A 165 ASN A 169 5 5 SHEET 1 A 4 VAL A 61 ASP A 65 0 SHEET 2 A 4 ILE A 221 TYR A 230 -1 O VAL A 228 N LEU A 63 SHEET 3 A 4 PRO A 95 VAL A 101 -1 N TYR A 99 O LEU A 223 SHEET 4 A 4 GLU A 84 VAL A 89 -1 N GLU A 88 O ILE A 96 SHEET 1 B 4 VAL A 61 ASP A 65 0 SHEET 2 B 4 ILE A 221 TYR A 230 -1 O VAL A 228 N LEU A 63 SHEET 3 B 4 ILE A 126 LEU A 134 -1 N GLU A 129 O ARG A 227 SHEET 4 B 4 ASN A 196 VAL A 202 -1 O ARG A 200 N ILE A 128 SHEET 1 C 4 ILE A 76 PHE A 78 0 SHEET 2 C 4 ASN A 111 LEU A 114 -1 O TRP A 112 N PHE A 78 SHEET 3 C 4 GLY A 209 ASP A 216 -1 O ASP A 216 N ASN A 111 SHEET 4 C 4 ILE A 118 SER A 119 -1 N ILE A 118 O PHE A 210 SHEET 1 D 5 ILE A 76 PHE A 78 0 SHEET 2 D 5 ASN A 111 LEU A 114 -1 O TRP A 112 N PHE A 78 SHEET 3 D 5 GLY A 209 ASP A 216 -1 O ASP A 216 N ASN A 111 SHEET 4 D 5 THR A 150 GLU A 157 -1 N TYR A 154 O ALA A 213 SHEET 5 D 5 ILE A 172 ALA A 178 -1 O ILE A 174 N MET A 153 SSBOND 1 CYS A 102 CYS A 220 1555 1555 2.04 SSBOND 2 CYS A 137 CYS A 147 1555 1555 2.04 CISPEP 1 PHE A 78 PRO A 79 0 3.30 CRYST1 55.040 82.721 81.166 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 0.018169 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012320 0.00000