HEADER TRANSFERASE 04-FEB-18 6FNL TITLE CRYSTAL STRUCTURE OF EPHRIN B4 (EPHB4) RECEPTOR PROTEIN KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEPATOMA TRANSMEMBRANE KINASE,TYROSINE-PROTEIN KINASE COMPND 5 TYRO11; COMPND 6 EC: 2.7.10.1; COMPND 7 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: EPHB4, HTK, MYK1, TYRO11; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN TYROSINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.KUDLINZKI,A.TROESTER,K.WITT,V.L.LINHARD,K.SAXENA,H.SCHWALBE REVDAT 3 17-JAN-24 6FNL 1 REMARK REVDAT 2 29-AUG-18 6FNL 1 JRNL REVDAT 1 08-AUG-18 6FNL 0 JRNL AUTH A.TROSTER,S.HEINZLMEIR,B.T.BERGER,S.L.GANDE,K.SAXENA, JRNL AUTH 2 S.SREERAMULU,V.LINHARD,A.H.NASIRI,M.BOLTE,S.MULLER,B.KUSTER, JRNL AUTH 3 G.MEDARD,D.KUDLINZKI,H.SCHWALBE JRNL TITL NVP-BHG712: EFFECTS OF REGIOISOMERS ON THE AFFINITY AND JRNL TITL 2 SELECTIVITY TOWARD THE EPHRIN FAMILY. JRNL REF CHEMMEDCHEM V. 13 1629 2018 JRNL REFN ESSN 1860-7187 JRNL PMID 29928781 JRNL DOI 10.1002/CMDC.201800398 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 73024 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.820 REMARK 3 FREE R VALUE TEST SET COUNT : 2056 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 43.1367 - 3.1292 0.99 4974 145 0.1611 0.1795 REMARK 3 2 3.1292 - 2.4838 0.99 4868 141 0.1886 0.2111 REMARK 3 3 2.4838 - 2.1699 1.00 4873 141 0.1816 0.1813 REMARK 3 4 2.1699 - 1.9715 1.00 4913 142 0.1851 0.2176 REMARK 3 5 1.9715 - 1.8302 0.99 4797 139 0.1898 0.2308 REMARK 3 6 1.8302 - 1.7223 0.99 4876 141 0.1948 0.2215 REMARK 3 7 1.7223 - 1.6360 0.99 4848 140 0.1937 0.2273 REMARK 3 8 1.6360 - 1.5648 0.99 4831 140 0.2280 0.2593 REMARK 3 9 1.5648 - 1.5045 0.98 4769 138 0.2555 0.2423 REMARK 3 10 1.5045 - 1.4526 0.99 4772 139 0.2768 0.3184 REMARK 3 11 1.4526 - 1.4072 0.98 4831 140 0.3168 0.2941 REMARK 3 12 1.4072 - 1.3670 0.98 4746 137 0.3903 0.3872 REMARK 3 13 1.3670 - 1.3310 0.98 4822 140 0.4889 0.5070 REMARK 3 14 1.3310 - 1.2985 0.94 4577 132 0.6973 0.7590 REMARK 3 15 1.2985 - 1.2690 0.72 3471 101 0.9380 0.8085 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.32 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 : 0.007 2207 REMARK 3 ANGLE : 0.834 2994 REMARK 3 CHIRALITY : 0.087 324 REMARK 3 PLANARITY : 0.006 393 REMARK 3 DIHEDRAL : 15.125 1357 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 6FNL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008522. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JAN-18 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS XDSAPP 2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74570 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.269 REMARK 200 RESOLUTION RANGE LOW (A) : 43.112 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.690 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.230 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: 2VWU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG5000 MME, 15 % GLYCEROL, 0.1 M REMARK 280 TRIS PH7.5, VAPOR DIFFUSION, SITTING 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 27.03050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 596 REMARK 465 MET A 597 REMARK 465 ASP A 598 REMARK 465 PRO A 599 REMARK 465 ASN A 600 REMARK 465 GLU A 601 REMARK 465 ALA A 602 REMARK 465 VAL A 603 REMARK 465 ARG A 604 REMARK 465 GLU A 605 REMARK 465 PHE A 606 REMARK 465 LEU A 761 REMARK 465 SER A 762 REMARK 465 ARG A 763 REMARK 465 PHE A 764 REMARK 465 LEU A 765 REMARK 465 GLU A 766 REMARK 465 GLU A 767 REMARK 465 ASN A 768 REMARK 465 SER A 769 REMARK 465 SER A 770 REMARK 465 ASP A 771 REMARK 465 PRO A 772 REMARK 465 THR A 773 REMARK 465 GLU A 774 REMARK 465 THR A 775 REMARK 465 SER A 776 REMARK 465 SER A 777 REMARK 465 LEU A 778 REMARK 465 GLY A 779 REMARK 465 GLY A 780 REMARK 465 ARG A 889 REMARK 465 GLU A 890 REMARK 465 ASN A 891 REMARK 465 GLY A 892 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 GLU A 619 136.93 -175.58 REMARK 500 ARG A 739 -12.97 75.96 REMARK 500 ASP A 758 76.75 73.02 REMARK 500 ASP A 758 76.75 71.94 REMARK 500 TRP A 822 -118.32 53.42 REMARK 500 ASP A 836 4.68 82.12 REMARK 500 ASN A 880 67.06 -119.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 6FNL A 598 892 UNP P54760 EPHB4_HUMAN 598 892 SEQADV 6FNL GLY A 596 UNP P54760 EXPRESSION TAG SEQADV 6FNL MET A 597 UNP P54760 EXPRESSION TAG SEQADV 6FNL GLU A 774 UNP P54760 TYR 774 ENGINEERED MUTATION SEQADV 6FNL VAL A 803 UNP P54760 ALA 803 ENGINEERED MUTATION SEQADV 6FNL ILE A 870 UNP P54760 VAL 870 ENGINEERED MUTATION SEQRES 1 A 297 GLY MET ASP PRO ASN GLU ALA VAL ARG GLU PHE ALA LYS SEQRES 2 A 297 GLU ILE ASP VAL SER TYR VAL LYS ILE GLU GLU VAL ILE SEQRES 3 A 297 GLY ALA GLY GLU PHE GLY GLU VAL CYS ARG GLY ARG LEU SEQRES 4 A 297 LYS ALA PRO GLY LYS LYS GLU SER CYS VAL ALA ILE LYS SEQRES 5 A 297 THR LEU LYS GLY GLY TYR THR GLU ARG GLN ARG ARG GLU SEQRES 6 A 297 PHE LEU SER GLU ALA SER ILE MET GLY GLN PHE GLU HIS SEQRES 7 A 297 PRO ASN ILE ILE ARG LEU GLU GLY VAL VAL THR ASN SER SEQRES 8 A 297 MET PRO VAL MET ILE LEU THR GLU PHE MET GLU ASN GLY SEQRES 9 A 297 ALA LEU ASP SER PHE LEU ARG LEU ASN ASP GLY GLN PHE SEQRES 10 A 297 THR VAL ILE GLN LEU VAL GLY MET LEU ARG GLY ILE ALA SEQRES 11 A 297 SER GLY MET ARG TYR LEU ALA GLU MET SER TYR VAL HIS SEQRES 12 A 297 ARG ASP LEU ALA ALA ARG ASN ILE LEU VAL ASN SER ASN SEQRES 13 A 297 LEU VAL CYS LYS VAL SER ASP PHE GLY LEU SER ARG PHE SEQRES 14 A 297 LEU GLU GLU ASN SER SER ASP PRO THR GLU THR SER SER SEQRES 15 A 297 LEU GLY GLY LYS ILE PRO ILE ARG TRP THR ALA PRO GLU SEQRES 16 A 297 ALA ILE ALA PHE ARG LYS PHE THR SER ALA SER ASP VAL SEQRES 17 A 297 TRP SER TYR GLY ILE VAL MET TRP GLU VAL MET SER PHE SEQRES 18 A 297 GLY GLU ARG PRO TYR TRP ASP MET SER ASN GLN ASP VAL SEQRES 19 A 297 ILE ASN ALA ILE GLU GLN ASP TYR ARG LEU PRO PRO PRO SEQRES 20 A 297 PRO ASP CYS PRO THR SER LEU HIS GLN LEU MET LEU ASP SEQRES 21 A 297 CYS TRP GLN LYS ASP ARG ASN ALA ARG PRO ARG PHE PRO SEQRES 22 A 297 GLN ILE VAL SER ALA LEU ASP LYS MET ILE ARG ASN PRO SEQRES 23 A 297 ALA SER LEU LYS ILE VAL ALA ARG GLU ASN GLY FORMUL 2 HOH *265(H2 O) HELIX 1 AA1 ASP A 611 SER A 613 5 3 HELIX 2 AA2 THR A 654 GLY A 669 1 16 HELIX 3 AA3 ALA A 700 ASN A 708 1 9 HELIX 4 AA4 THR A 713 MET A 734 1 22 HELIX 5 AA5 ALA A 742 ARG A 744 5 3 HELIX 6 AA6 PRO A 783 THR A 787 5 5 HELIX 7 AA7 ALA A 788 ARG A 795 1 8 HELIX 8 AA8 THR A 798 SER A 815 1 18 HELIX 9 AA9 SER A 825 GLN A 835 1 11 HELIX 10 AB1 PRO A 846 TRP A 857 1 12 HELIX 11 AB2 ASP A 860 ARG A 864 5 5 HELIX 12 AB3 ARG A 866 ASN A 880 1 15 HELIX 13 AB4 PRO A 881 LYS A 885 5 5 SHEET 1 AA1 5 VAL A 615 ALA A 623 0 SHEET 2 AA1 5 GLU A 628 LEU A 634 -1 O ARG A 631 N GLU A 618 SHEET 3 AA1 5 SER A 642 LEU A 649 -1 O ILE A 646 N CYS A 630 SHEET 4 AA1 5 VAL A 689 GLU A 694 -1 O ILE A 691 N LYS A 647 SHEET 5 AA1 5 LEU A 679 VAL A 683 -1 N GLY A 681 O LEU A 692 SHEET 1 AA2 2 ILE A 746 VAL A 748 0 SHEET 2 AA2 2 CYS A 754 VAL A 756 -1 O LYS A 755 N LEU A 747 CISPEP 1 MET A 687 PRO A 688 0 3.37 CRYST1 46.138 54.061 62.119 90.00 110.87 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 0.021674 0.000000 0.008264 0.00000 SCALE2 0.000000 0.018498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017228 0.00000