HEADER SIGNALING PROTEIN 01-SEP-06 2I85 TITLE NMR SOLUTION STRUCTURE OF HUMAN EPHRINB2 ECTODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN-B2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN, RESIDUES 1-142; COMPND 5 SYNONYM: EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5, LERK-5, HTK COMPND 6 LIGAND, HTK-L; 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 CELL_LINE: HELA CELLS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-32A KEYWDS EPHRINB2 ECTODOMAIN, NMR SOLUTION STRUCTURE, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR X.RAN,J.FAN,J.SONG REVDAT 3 09-MAR-22 2I85 1 REMARK REVDAT 2 24-FEB-09 2I85 1 VERSN REVDAT 1 04-SEP-07 2I85 0 JRNL AUTH X.RAN,J.FAN,J.SONG JRNL TITL NMR SOLUTION STRUCTURE OF HUMAN EPHRINB2 ECTODOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, AMBER REMARK 3 AUTHORS : GUNTERT, P. (CYANA), CASE DA ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2I85 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039257. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 293 REMARK 210 PH : NULL; NULL REMARK 210 IONIC STRENGTH : 6.8; 6.8 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5MM EPHRINB2 ECTODOMAIN U REMARK 210 -15N,13C; 20MM PHOSPHATE REMARK 210 BUFFER(PH 6.8); 90% H2O, 10% D2O; REMARK 210 0.5MM EPHRINB2 ECTODOMAIN U-15N, REMARK 210 13C; 20MM PHOSPHATE BUFFER(PH REMARK 210 6.8); 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-EDITED HSQC-TOCSY; 15N REMARK 210 -EDITED HSQC-NOESY; HNCACB; REMARK 210 CBCA(CO)NH; HNCO; 13C-NOESY; REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNTION LESS THAN 2 REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 SER A 3 73.49 -155.26 REMARK 500 1 TYR A 10 70.05 -116.71 REMARK 500 1 TRP A 11 -59.04 77.29 REMARK 500 1 ASN A 12 64.40 -166.68 REMARK 500 1 LEU A 19 68.65 36.30 REMARK 500 1 LYS A 40 158.53 62.12 REMARK 500 1 ASP A 42 -87.59 -159.94 REMARK 500 1 GLN A 48 76.82 51.41 REMARK 500 1 THR A 72 -45.04 -176.73 REMARK 500 1 ASN A 76 -65.85 83.48 REMARK 500 1 CYS A 77 93.45 166.83 REMARK 500 1 PRO A 80 49.15 -76.83 REMARK 500 1 ASP A 81 -19.03 -161.37 REMARK 500 1 GLN A 82 -143.83 57.79 REMARK 500 1 THR A 131 -62.71 -139.39 REMARK 500 1 ALA A 133 92.51 53.56 REMARK 500 1 MET A 134 72.59 -112.31 REMARK 500 2 SER A 3 -39.73 -150.58 REMARK 500 2 ILE A 4 -55.36 -142.62 REMARK 500 2 VAL A 5 93.51 57.97 REMARK 500 2 TYR A 10 56.96 -115.58 REMARK 500 2 TRP A 11 -58.02 65.38 REMARK 500 2 SER A 13 -34.08 72.85 REMARK 500 2 SER A 14 -166.24 54.77 REMARK 500 2 PHE A 18 55.78 37.53 REMARK 500 2 LEU A 19 72.66 52.21 REMARK 500 2 ILE A 30 98.39 -60.53 REMARK 500 2 ASP A 42 -100.53 -150.51 REMARK 500 2 THR A 45 45.94 -153.65 REMARK 500 2 VAL A 46 -33.24 -39.66 REMARK 500 2 ASN A 76 60.84 -109.30 REMARK 500 2 CYS A 77 35.21 -69.07 REMARK 500 2 GLN A 91 109.29 -41.82 REMARK 500 2 GLU A 92 -71.60 -80.60 REMARK 500 2 ASN A 105 29.49 47.75 REMARK 500 2 THR A 113 72.65 -106.97 REMARK 500 2 GLN A 124 29.56 -65.22 REMARK 500 2 THR A 131 -45.51 -144.39 REMARK 500 2 ALA A 133 92.38 70.27 REMARK 500 3 SER A 3 113.93 -162.33 REMARK 500 3 VAL A 5 105.76 57.94 REMARK 500 3 TRP A 11 -49.29 71.05 REMARK 500 3 LEU A 19 66.47 35.34 REMARK 500 3 ASP A 42 -56.94 -172.00 REMARK 500 3 THR A 72 -47.30 178.94 REMARK 500 3 LEU A 75 -157.93 -135.37 REMARK 500 3 ASN A 76 -67.99 76.43 REMARK 500 3 CYS A 77 78.20 -168.97 REMARK 500 3 LYS A 79 161.71 61.85 REMARK 500 3 ASP A 81 87.27 -153.18 REMARK 500 REMARK 500 THIS ENTRY HAS 213 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 55 0.08 SIDE CHAIN REMARK 500 2 TYR A 108 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IKO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SAME PROTEIN FROM MOUSE DBREF 2I85 A 1 142 UNP P52799 EFNB2_HUMAN 25 166 SEQRES 1 A 142 SER LYS SER ILE VAL LEU GLU PRO ILE TYR TRP ASN SER SEQRES 2 A 142 SER ASN SER LYS PHE LEU PRO GLY GLN GLY LEU VAL LEU SEQRES 3 A 142 TYR PRO GLN ILE GLY ASP LYS LEU ASP ILE ILE CYS PRO SEQRES 4 A 142 LYS VAL ASP SER LYS THR VAL GLY GLN TYR GLU TYR TYR SEQRES 5 A 142 LYS VAL TYR MET VAL ASP LYS ASP GLN ALA ASP ARG CYS SEQRES 6 A 142 THR ILE LYS LYS GLU ASN THR PRO LEU LEU ASN CYS ALA SEQRES 7 A 142 LYS PRO ASP GLN ASP ILE LYS PHE THR ILE LYS PHE GLN SEQRES 8 A 142 GLU PHE SER PRO ASN LEU TRP GLY LEU GLU PHE GLN LYS SEQRES 9 A 142 ASN LYS ASP TYR TYR ILE ILE SER THR SER ASN GLY SER SEQRES 10 A 142 LEU GLU GLY LEU ASP ASN GLN GLU GLY GLY VAL CYS GLN SEQRES 11 A 142 THR ARG ALA MET LYS ILE LEU MET LYS VAL GLY GLN HELIX 1 1 ASP A 58 CYS A 65 1 8 HELIX 2 2 SER A 117 LEU A 121 5 5 SHEET 1 A 3 LEU A 6 TYR A 10 0 SHEET 2 A 3 LYS A 33 CYS A 38 1 O LYS A 33 N LEU A 6 SHEET 3 A 3 ILE A 84 LYS A 89 -1 O ILE A 88 N LEU A 34 SHEET 1 B 5 GLY A 23 LEU A 26 0 SHEET 2 B 5 LYS A 135 VAL A 140 1 O LEU A 137 N LEU A 26 SHEET 3 B 5 LYS A 106 ILE A 111 -1 N ILE A 110 O ILE A 136 SHEET 4 B 5 TYR A 52 MET A 56 -1 N TYR A 55 O ILE A 111 SHEET 5 B 5 LEU A 75 CYS A 77 -1 O CYS A 77 N TYR A 52 SSBOND 1 CYS A 38 CYS A 77 1555 1555 2.01 SSBOND 2 CYS A 65 CYS A 129 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1