HEADER TRANSFERASE 13-OCT-98 1NUK TITLE CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE EPHB2 RECEPTOR TITLE 2 TYROSINE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (TYROSINE-PROTEIN KINASE RECEPTOR EPH); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN; COMPND 5 SYNONYM: NUK; COMPND 6 EC: 2.7.1.112; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: AD494 KEYWDS TRANSFERASE, EPH RECEPTOR TYROSINE KINASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-P.HIMANEN,M.HENKEMEYER,D.B.NIKOLOV REVDAT 3 27-DEC-23 1NUK 1 REMARK REVDAT 2 24-FEB-09 1NUK 1 VERSN REVDAT 1 13-OCT-99 1NUK 0 JRNL AUTH J.P.HIMANEN,M.HENKEMEYER,D.B.NIKOLOV JRNL TITL CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE JRNL TITL 2 RECEPTOR TYROSINE KINASE EPHB2. JRNL REF NATURE V. 396 486 1998 JRNL REFN ISSN 0028-0836 JRNL PMID 9853759 JRNL DOI 10.1038/24904 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 4554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 340 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1362 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.90 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.970 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4214 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 56.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 79.45000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.57500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.72500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.57500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.57500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 119.17500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.57500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.57500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.72500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.57500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.57500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 119.17500 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 79.45000 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 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 GLU A 59 REMARK 465 ASN A 60 REMARK 465 MET A 61 REMARK 465 LEU A 160 REMARK 465 GLY A 161 REMARK 465 GLY A 162 REMARK 465 ARG A 163 REMARK 465 LYS A 204 REMARK 465 CYS A 205 REMARK 465 PRO A 206 REMARK 465 ARG A 207 REMARK 465 ILE A 208 REMARK 465 ILE A 209 REMARK 465 GLN A 210 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 TYR A 57 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 62 OD1 ND2 REMARK 470 VAL A 164 CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 31 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 MET A 32 123.92 -4.23 REMARK 500 SER A 34 -71.86 170.53 REMARK 500 THR A 36 -5.82 -48.41 REMARK 500 THR A 38 66.97 26.37 REMARK 500 ALA A 39 125.95 63.57 REMARK 500 GLU A 40 105.34 53.86 REMARK 500 HIS A 46 -82.71 -81.78 REMARK 500 SER A 55 90.59 -69.83 REMARK 500 CYS A 70 34.05 -166.05 REMARK 500 SER A 76 82.07 35.00 REMARK 500 THR A 83 -172.19 -64.17 REMARK 500 ARG A 87 106.49 -59.09 REMARK 500 ARG A 89 72.96 36.42 REMARK 500 ALA A 91 138.11 60.91 REMARK 500 PHE A 100 141.49 -172.89 REMARK 500 PRO A 109 -84.47 -32.47 REMARK 500 GLU A 117 22.60 -140.82 REMARK 500 ASP A 129 -81.14 -47.00 REMARK 500 LEU A 130 -13.84 57.28 REMARK 500 PHE A 135 -110.95 -47.25 REMARK 500 PRO A 136 100.05 -33.19 REMARK 500 TRP A 138 48.95 -75.37 REMARK 500 GLU A 140 3.32 -68.10 REMARK 500 ASN A 141 -79.61 -76.21 REMARK 500 VAL A 146 -72.68 -63.79 REMARK 500 GLU A 153 -4.79 60.19 REMARK 500 PRO A 176 -87.75 -16.96 REMARK 500 VAL A 177 95.19 47.08 REMARK 500 TYR A 189 40.03 -167.60 REMARK 500 MET A 193 129.64 179.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 1NUK A 28 210 UNP P54763 EPHB2_MOUSE 27 209 SEQRES 1 A 183 GLU GLU THR LEU MET ASP SER THR THR ALA THR ALA GLU SEQRES 2 A 183 LEU GLY TRP MET VAL HIS PRO PRO SER GLY TRP GLU GLU SEQRES 3 A 183 VAL SER GLY TYR ASP GLU ASN MET ASN THR ILE ARG THR SEQRES 4 A 183 TYR GLN VAL CYS ASN VAL PHE GLU SER SER GLN ASN ASN SEQRES 5 A 183 TRP LEU ARG THR LYS PHE ILE ARG ARG ARG GLY ALA HIS SEQRES 6 A 183 ARG ILE HIS VAL GLU MET LYS PHE SER VAL ARG ASP CYS SEQRES 7 A 183 SER SER ILE PRO SER VAL PRO GLY SER CYS LYS GLU THR SEQRES 8 A 183 PHE ASN LEU TYR TYR TYR GLU ALA ASP PHE ASP LEU ALA SEQRES 9 A 183 THR LYS THR PHE PRO ASN TRP MET GLU ASN PRO TRP VAL SEQRES 10 A 183 LYS VAL ASP THR ILE ALA ALA ASP GLU SER PHE SER GLN SEQRES 11 A 183 VAL ASP LEU GLY GLY ARG VAL MET LYS ILE ASN THR GLU SEQRES 12 A 183 VAL ARG SER PHE GLY PRO VAL SER ARG ASN GLY PHE TYR SEQRES 13 A 183 LEU ALA PHE GLN ASP TYR GLY GLY CYS MET SER LEU ILE SEQRES 14 A 183 ALA VAL ARG VAL PHE TYR ARG LYS CYS PRO ARG ILE ILE SEQRES 15 A 183 GLN HELIX 1 1 THR A 35 ALA A 37 5 3 SHEET 1 A 5 GLU A 53 GLY A 56 0 SHEET 2 A 5 ILE A 64 CYS A 70 -1 N THR A 66 O VAL A 54 SHEET 3 A 5 CYS A 192 PHE A 201 -1 N LEU A 195 O TYR A 67 SHEET 4 A 5 HIS A 95 SER A 101 -1 N SER A 101 O SER A 194 SHEET 5 A 5 ASN A 168 SER A 173 -1 N ARG A 172 O VAL A 96 SHEET 1 B 4 ASN A 79 ARG A 82 0 SHEET 2 B 4 GLY A 181 ASP A 188 -1 N ASP A 188 O ASN A 79 SHEET 3 B 4 PHE A 119 ALA A 126 -1 N ALA A 126 O GLY A 181 SHEET 4 B 4 VAL A 144 ILE A 149 -1 N ILE A 149 O PHE A 119 SSBOND 1 CYS A 70 CYS A 192 1555 1555 2.02 SSBOND 2 CYS A 105 CYS A 115 1555 1555 2.03 CRYST1 55.150 55.150 158.900 90.00 90.00 90.00 P 41 21 2 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 0.018132 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006293 0.00000