HEADER TRANSFERASE 17-JUN-14 4TRL TITLE STRUCTURE OF EPHRIN TYPE-A RECEPTOR 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-A RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 590-876; COMPND 5 SYNONYM: EPITHELIAL CELL KINASE,TYROSINE-PROTEIN KINASE RECEPTOR ECK; 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: EPHA2, ECK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ARCTICEXPRESS KEYWDS ACTIVE STATE, PHOSPHORYLATED, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.WEI,N.WANG REVDAT 3 27-DEC-23 4TRL 1 REMARK REVDAT 2 22-NOV-17 4TRL 1 SOURCE KEYWDS JRNL REMARK REVDAT 1 02-JUL-14 4TRL 0 SPRSDE 02-JUL-14 4TRL 4P2W JRNL AUTH Q.WEI,N.WANG JRNL TITL STRUCTURE OF EPHRIN TYPE-A RECEPTOR 2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 12226 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 584 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 30.0280 - 3.8899 0.99 3035 134 0.1815 0.2083 REMARK 3 2 3.8899 - 3.0885 1.00 2907 149 0.1909 0.2554 REMARK 3 3 3.0885 - 2.6984 1.00 2881 163 0.2328 0.3047 REMARK 3 4 2.6984 - 2.4520 0.98 2819 138 0.2709 0.3800 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.64 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 : 0.008 2189 REMARK 3 ANGLE : 1.190 2949 REMARK 3 CHIRALITY : 0.078 324 REMARK 3 PLANARITY : 0.004 369 REMARK 3 DIHEDRAL : 15.860 818 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 4TRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12263 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.69700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 0.2M LI2SO4, 20% (W/V) REMARK 280 PEG3350, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.98333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.96667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.96667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.98333 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13340 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 MET A 578 REMARK 465 GLY A 579 REMARK 465 SER A 580 REMARK 465 SER A 581 REMARK 465 HIS A 582 REMARK 465 HIS A 583 REMARK 465 HIS A 584 REMARK 465 HIS A 585 REMARK 465 HIS A 586 REMARK 465 HIS A 587 REMARK 465 SER A 588 REMARK 465 GLN A 589 REMARK 465 ASP A 590 REMARK 465 PRO A 591 REMARK 465 HIS A 592 REMARK 465 THR A 593 REMARK 465 TYR A 594 REMARK 465 GLU A 595 REMARK 465 ASP A 596 REMARK 465 PRO A 597 REMARK 465 ASN A 598 REMARK 465 SER A 635 REMARK 465 SER A 636 REMARK 465 GLY A 637 REMARK 465 LYS A 638 REMARK 465 LYS A 639 REMARK 465 ALA A 650 REMARK 465 GLU A 654 REMARK 465 ASP A 766 REMARK 465 ARG A 876 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 PHE A 604 59.85 -93.57 REMARK 500 ASP A 739 28.24 -145.19 REMARK 500 TRP A 819 -123.09 62.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 4TRL A 590 876 UNP P29317 EPHA2_HUMAN 590 876 SEQADV 4TRL MET A 578 UNP P29317 INITIATING METHIONINE SEQADV 4TRL GLY A 579 UNP P29317 EXPRESSION TAG SEQADV 4TRL SER A 580 UNP P29317 EXPRESSION TAG SEQADV 4TRL SER A 581 UNP P29317 EXPRESSION TAG SEQADV 4TRL HIS A 582 UNP P29317 EXPRESSION TAG SEQADV 4TRL HIS A 583 UNP P29317 EXPRESSION TAG SEQADV 4TRL HIS A 584 UNP P29317 EXPRESSION TAG SEQADV 4TRL HIS A 585 UNP P29317 EXPRESSION TAG SEQADV 4TRL HIS A 586 UNP P29317 EXPRESSION TAG SEQADV 4TRL HIS A 587 UNP P29317 EXPRESSION TAG SEQADV 4TRL SER A 588 UNP P29317 EXPRESSION TAG SEQADV 4TRL GLN A 589 UNP P29317 EXPRESSION TAG SEQRES 1 A 299 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 299 PRO HIS THR TYR GLU ASP PRO ASN GLN ALA VAL LEU LYS SEQRES 3 A 299 PHE THR THR GLU ILE HIS PRO SER CYS VAL THR ARG GLN SEQRES 4 A 299 LYS VAL ILE GLY ALA GLY GLU PHE GLY GLU VAL TYR LYS SEQRES 5 A 299 GLY MET LEU LYS THR SER SER GLY LYS LYS GLU VAL PRO SEQRES 6 A 299 VAL ALA ILE LYS THR LEU LYS ALA GLY TYR THR GLU LYS SEQRES 7 A 299 GLN ARG VAL ASP PHE LEU GLY GLU ALA GLY ILE MET GLY SEQRES 8 A 299 GLN PHE SER HIS HIS ASN ILE ILE ARG LEU GLU GLY VAL SEQRES 9 A 299 ILE SER LYS TYR LYS PRO MET MET ILE ILE THR GLU TYR SEQRES 10 A 299 MET GLU ASN GLY ALA LEU ASP LYS PHE LEU ARG GLU LYS SEQRES 11 A 299 ASP GLY GLU PHE SER VAL LEU GLN LEU VAL GLY MET LEU SEQRES 12 A 299 ARG GLY ILE ALA ALA GLY MET LYS TYR LEU ALA ASN MET SEQRES 13 A 299 ASN TYR VAL HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU SEQRES 14 A 299 VAL ASN SER ASN LEU VAL CYS LYS VAL SER ASP PHE GLY SEQRES 15 A 299 LEU SER ARG VAL LEU GLU ASP ASP PRO GLU ALA THR PTR SEQRES 16 A 299 THR THR SER GLY GLY LYS ILE PRO ILE ARG TRP THR ALA SEQRES 17 A 299 PRO GLU ALA ILE SER TYR ARG LYS PHE THR SER ALA SER SEQRES 18 A 299 ASP VAL TRP SER PHE GLY ILE VAL MET TRP GLU VAL MET SEQRES 19 A 299 THR TYR GLY GLU ARG PRO TYR TRP GLU LEU SER ASN HIS SEQRES 20 A 299 GLU VAL MET LYS ALA ILE ASN ASP GLY PHE ARG LEU PRO SEQRES 21 A 299 THR PRO MET ASP CYS PRO SER ALA ILE TYR GLN LEU MET SEQRES 22 A 299 MET GLN CYS TRP GLN GLN GLU ARG ALA ARG ARG PRO LYS SEQRES 23 A 299 PHE ALA ASP ILE VAL SER ILE LEU ASP LYS LEU ILE ARG MODRES 4TRL PTR A 772 TYR MODIFIED RESIDUE HET PTR A 772 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 PTR C9 H12 N O6 P FORMUL 2 HOH *43(H2 O) HELIX 1 AA1 HIS A 609 SER A 611 5 3 HELIX 2 AA2 GLN A 656 GLY A 668 1 13 HELIX 3 AA3 ALA A 699 LYS A 707 1 9 HELIX 4 AA4 SER A 712 MET A 733 1 22 HELIX 5 AA5 ALA A 741 ARG A 743 5 3 HELIX 6 AA6 PRO A 780 THR A 784 5 5 HELIX 7 AA7 ALA A 785 TYR A 791 1 7 HELIX 8 AA8 THR A 795 THR A 812 1 18 HELIX 9 AA9 SER A 822 ASN A 831 1 10 HELIX 10 AB1 PRO A 843 TRP A 854 1 12 HELIX 11 AB2 GLU A 857 ARG A 861 5 5 HELIX 12 AB3 LYS A 863 ILE A 875 1 13 SHEET 1 AA1 5 VAL A 613 ALA A 621 0 SHEET 2 AA1 5 GLU A 626 LEU A 632 -1 O VAL A 627 N ILE A 619 SHEET 3 AA1 5 VAL A 641 THR A 647 -1 O VAL A 643 N GLY A 630 SHEET 4 AA1 5 MET A 689 GLU A 693 -1 O ILE A 690 N LYS A 646 SHEET 5 AA1 5 LEU A 678 ILE A 682 -1 N GLY A 680 O ILE A 691 SHEET 1 AA2 2 TYR A 735 VAL A 736 0 SHEET 2 AA2 2 ARG A 762 VAL A 763 -1 O ARG A 762 N VAL A 736 SHEET 1 AA3 2 ILE A 745 VAL A 747 0 SHEET 2 AA3 2 CYS A 753 VAL A 755 -1 O LYS A 754 N LEU A 746 SHEET 1 AA4 2 PTR A 772 THR A 773 0 SHEET 2 AA4 2 LYS A 793 PHE A 794 -1 O PHE A 794 N PTR A 772 LINK C THR A 771 N PTR A 772 1555 1555 1.33 LINK C PTR A 772 N THR A 773 1555 1555 1.33 CISPEP 1 ALA A 600 VAL A 601 0 -6.52 CISPEP 2 LYS A 603 PHE A 604 0 -1.19 CISPEP 3 LYS A 686 PRO A 687 0 -4.47 CRYST1 74.028 74.028 101.950 90.00 90.00 120.00 P 31 2 1 6 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 0.013508 0.007799 0.000000 0.00000 SCALE2 0.000000 0.015598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009809 0.00000