HEADER SIGNALING PROTEIN 28-MAY-09 3HM6 TITLE CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF HUMAN PLEXIN B1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLEXIN-B1; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: CYTOPLASMIC DOMAIN (UNP RESIDUES 1511-2135); COMPND 5 SYNONYM: SEMAPHORIN RECEPTOR SEP; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UNKNOWN PEPTIDE; COMPND 10 CHAIN: C; COMPND 11 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: PLXNB1, KIAA0407, PLXN5, SEP; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFBOH-LIC (GI:134105591); SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: PLXNB1, KIAA0407, PLXN5, SEP; SOURCE 16 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 17 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PFBOH-LIC (GI:134105591) KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, MEMBRANE, TRANSMEMBRANE, KEYWDS 2 RECEPTOR, CELL MEMBRANE, GLYCOPROTEIN, PHOSPHOPROTEIN, SECRETED, KEYWDS 3 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.TONG,H.HE,L.SHEN,W.TEMPEL,F.MACKENZIE,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 C.BOUNTRA,J.WEIGELT,A.BOCHKAREV,H.PARK,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 8 03-APR-24 3HM6 1 REMARK REVDAT 7 21-FEB-24 3HM6 1 REMARK REVDAT 6 13-OCT-21 3HM6 1 SOURCE DBREF SEQADV REVDAT 5 01-NOV-17 3HM6 1 REMARK REVDAT 4 13-JUL-11 3HM6 1 VERSN REVDAT 3 11-AUG-10 3HM6 1 JRNL REVDAT 2 24-NOV-09 3HM6 1 JRNL REVDAT 1 09-JUN-09 3HM6 0 JRNL AUTH Y.TONG,P.K.HOTA,J.Y.PENACHIONI,M.B.HAMANEH,S.KIM, JRNL AUTH 2 R.S.ALVIANI,L.SHEN,H.HE,W.TEMPEL,L.TAMAGNONE,H.W.PARK,M.BUCK JRNL TITL STRUCTURE AND FUNCTION OF THE INTRACELLULAR REGION OF THE JRNL TITL 2 PLEXIN-B1 TRANSMEMBRANE RECEPTOR. JRNL REF J.BIOL.CHEM. V. 284 35962 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19843518 JRNL DOI 10.1074/JBC.M109.056275 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 27598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.037 REMARK 3 FREE R VALUE TEST SET COUNT : 1390 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1846 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4078 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95300 REMARK 3 B22 (A**2) : 0.95300 REMARK 3 B33 (A**2) : -1.42900 REMARK 3 B12 (A**2) : 0.47600 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.362 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.255 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.216 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.659 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4159 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2741 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5661 ; 1.213 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6697 ; 0.899 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 523 ; 5.576 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;34.655 ;23.728 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 675 ;14.896 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.721 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 667 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4590 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 828 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 945 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2644 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2037 ; 0.175 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2059 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.139 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.201 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 56 ; 0.274 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.088 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2713 ; 1.932 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1056 ; 0.454 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4239 ; 2.886 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1656 ; 1.923 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1422 ; 2.695 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 1563 X 2129 REMARK 3 RESIDUE RANGE : C 1007 C 1033 REMARK 3 ORIGIN FOR THE GROUP (A): -20.2896 29.0521 -16.9473 REMARK 3 T TENSOR REMARK 3 T11: -0.0253 T22: -0.3137 REMARK 3 T33: -0.2068 T12: -0.1049 REMARK 3 T13: 0.0063 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 1.1305 L22: 1.4759 REMARK 3 L33: 2.6048 L12: -0.0362 REMARK 3 L13: -0.5348 L23: -0.3424 REMARK 3 S TENSOR REMARK 3 S11: -0.1482 S12: 0.0084 S13: -0.0426 REMARK 3 S21: -0.2278 S22: 0.0892 S23: -0.1182 REMARK 3 S31: 0.4391 S32: -0.0207 S33: 0.0590 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. ATOMIC B-FACTORS ARE RESIDUALS FROM TLS REFINEMENT. REMARK 3 CHAIN C LIKELY REPRESENTS PART OF THE PROTEIN CONSTRUCT'S N- REMARK 3 TERMINUS. DENSITY WAS DISCONTINUOUS AND THE AMINO ACID SEQUENCE REMARK 3 OF THE FRAGMENT COULD NOT BE ASSIGNED. O, COOT, MOLPROBITY WERE REMARK 3 ALSO USED FOR REFINEMENT. REMARK 4 REMARK 4 3HM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053304. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27657 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57700 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: SAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: FOR PHASING, NATIVE CRYSTALS WERE INCUBATED OVER REMARK 200 -NIGHT IN AN ARTIFICIAL MOTHER LIQUOR CONTAINING 0.001 M REMARK 200 THIMEROSAL. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG-2000 MME, 0.1M TRIS, 0.2M REMARK 280 TMAO, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 71.46600 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 142.93200 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 142.93200 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 71.46600 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, C 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 400 REMARK 400 COMPOUND REMARK 400 ACCORDING TO THE AUTHORS CHAIN C LIKELY REPRESENTS PART OF THE REMARK 400 PROTEIN CONSTRUCT'S N-TERMINUS. DENSITY WAS DISCONTINUOUS AND THE REMARK 400 AMINO ACID SEQUENCE OF THE FRAGMENT COULD NOT BE ASSIGNED. 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 X 1492 REMARK 465 GLY X 1493 REMARK 465 SER X 1494 REMARK 465 SER X 1495 REMARK 465 HIS X 1496 REMARK 465 HIS X 1497 REMARK 465 HIS X 1498 REMARK 465 HIS X 1499 REMARK 465 HIS X 1500 REMARK 465 HIS X 1501 REMARK 465 SER X 1502 REMARK 465 SER X 1503 REMARK 465 GLY X 1504 REMARK 465 LEU X 1505 REMARK 465 VAL X 1506 REMARK 465 PRO X 1507 REMARK 465 ARG X 1508 REMARK 465 GLY X 1509 REMARK 465 SER X 1510 REMARK 465 TYR X 1511 REMARK 465 ARG X 1512 REMARK 465 ARG X 1513 REMARK 465 LYS X 1514 REMARK 465 SER X 1515 REMARK 465 LYS X 1516 REMARK 465 GLN X 1517 REMARK 465 ALA X 1518 REMARK 465 LEU X 1519 REMARK 465 ARG X 1520 REMARK 465 ASP X 1521 REMARK 465 TYR X 1522 REMARK 465 LYS X 1523 REMARK 465 LYS X 1524 REMARK 465 VAL X 1525 REMARK 465 GLN X 1526 REMARK 465 ILE X 1527 REMARK 465 GLN X 1528 REMARK 465 LEU X 1529 REMARK 465 GLU X 1530 REMARK 465 ASN X 1531 REMARK 465 LEU X 1532 REMARK 465 GLU X 1533 REMARK 465 SER X 1534 REMARK 465 SER X 1535 REMARK 465 VAL X 1536 REMARK 465 ARG X 1537 REMARK 465 ASP X 1538 REMARK 465 ARG X 1539 REMARK 465 CYS X 1540 REMARK 465 LYS X 1541 REMARK 465 LYS X 1542 REMARK 465 GLU X 1543 REMARK 465 PHE X 1544 REMARK 465 THR X 1545 REMARK 465 ASP X 1546 REMARK 465 LEU X 1547 REMARK 465 MET X 1548 REMARK 465 THR X 1549 REMARK 465 GLU X 1550 REMARK 465 MET X 1551 REMARK 465 THR X 1552 REMARK 465 ASP X 1553 REMARK 465 LEU X 1554 REMARK 465 THR X 1555 REMARK 465 SER X 1556 REMARK 465 ASP X 1557 REMARK 465 LEU X 1558 REMARK 465 LEU X 1559 REMARK 465 GLY X 1560 REMARK 465 SER X 1561 REMARK 465 GLY X 1562 REMARK 465 ARG X 1581 REMARK 465 GLU X 1582 REMARK 465 VAL X 1757 REMARK 465 GLY X 1758 REMARK 465 PRO X 1759 REMARK 465 GLY X 1760 REMARK 465 ALA X 1761 REMARK 465 GLY X 1762 REMARK 465 GLU X 1763 REMARK 465 LEU X 1853 REMARK 465 THR X 1854 REMARK 465 LYS X 1855 REMARK 465 HIS X 1856 REMARK 465 VAL X 1857 REMARK 465 LEU X 1858 REMARK 465 ARG X 1859 REMARK 465 GLU X 1860 REMARK 465 ASN X 1861 REMARK 465 GLN X 1862 REMARK 465 ASP X 1863 REMARK 465 TYR X 1864 REMARK 465 VAL X 1865 REMARK 465 PRO X 1866 REMARK 465 GLY X 1867 REMARK 465 GLU X 1868 REMARK 465 ARG X 1869 REMARK 465 THR X 1870 REMARK 465 PRO X 1871 REMARK 465 MET X 1872 REMARK 465 LEU X 1873 REMARK 465 GLU X 1874 REMARK 465 ASP X 1875 REMARK 465 VAL X 1876 REMARK 465 ASP X 1877 REMARK 465 GLU X 1878 REMARK 465 ASP X 1891 REMARK 465 GLU X 1892 REMARK 465 PRO X 1893 REMARK 465 GLU X 1894 REMARK 465 PRO X 1895 REMARK 465 PRO X 1896 REMARK 465 ARG X 1897 REMARK 465 PRO X 1898 REMARK 465 ARG X 1899 REMARK 465 ARG X 1900 REMARK 465 GLY X 1901 REMARK 465 SER X 1902 REMARK 465 LEU X 1903 REMARK 465 ARG X 1904 REMARK 465 GLY X 1905 REMARK 465 GLY X 1906 REMARK 465 GLU X 1907 REMARK 465 ARG X 1908 REMARK 465 GLU X 1909 REMARK 465 ARG X 1910 REMARK 465 ALA X 1911 REMARK 465 LYS X 1912 REMARK 465 ALA X 1913 REMARK 465 HIS X 2025 REMARK 465 LYS X 2026 REMARK 465 LEU X 2027 REMARK 465 GLY X 2028 REMARK 465 ARG X 2029 REMARK 465 ASP X 2030 REMARK 465 ASN X 2130 REMARK 465 LYS X 2131 REMARK 465 VAL X 2132 REMARK 465 THR X 2133 REMARK 465 ASP X 2134 REMARK 465 LEU X 2135 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 HIS X1586 CG ND1 CD2 CE1 NE2 REMARK 470 ARG X1632 NE CZ NH1 NH2 REMARK 470 ARG X1677 CG CD NE CZ NH1 NH2 REMARK 470 ARG X1678 CZ NH1 NH2 REMARK 470 ARG X1712 CD NE CZ NH1 NH2 REMARK 470 HIS X1716 ND1 CD2 CE1 NE2 REMARK 470 ARG X1741 NE CZ NH1 NH2 REMARK 470 GLU X1742 CG CD OE1 OE2 REMARK 470 ASP X1743 CG OD1 OD2 REMARK 470 VAL X1744 CG1 CG2 REMARK 470 GLN X1765 CG CD OE1 NE2 REMARK 470 VAL X1767 CG1 CG2 REMARK 470 LYS X1770 CG CD CE NZ REMARK 470 LEU X1788 CG CD1 CD2 REMARK 470 LYS X1790 CD CE NZ REMARK 470 GLN X1796 CG CD OE1 NE2 REMARK 470 VAL X1811 CG1 CG2 REMARK 470 GLU X1825 CG CD OE1 OE2 REMARK 470 GLN X1827 CD OE1 NE2 REMARK 470 GLN X1837 CD OE1 NE2 REMARK 470 LYS X1840 CD CE NZ REMARK 470 VAL X1847 CG1 CG2 REMARK 470 GLU X1916 CG CD OE1 OE2 REMARK 470 ILE X1917 CG1 CG2 CD1 REMARK 470 ARG X1921 CG CD NE CZ NH1 NH2 REMARK 470 ASP X2024 CG OD1 OD2 REMARK 470 GLN X2058 CD OE1 NE2 REMARK 470 GLN X2065 CD OE1 NE2 REMARK 470 GLU X2108 CG CD OE1 OE2 REMARK 470 LYS X2114 CG CD CE NZ REMARK 470 MET X2115 CG SD CE REMARK 470 GLN X2123 CD OE1 NE2 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 LYS X1670 -125.03 -114.09 REMARK 500 TYR X1789 61.25 -110.43 REMARK 500 LEU X1794 -38.08 -36.27 REMARK 500 GLN X1796 43.34 -97.03 REMARK 500 HIS X1885 -74.30 -123.98 REMARK 500 LEU X1981 -72.10 -134.26 REMARK 500 ARG X1984 -38.34 -131.35 REMARK 500 ASN X2077 47.25 -85.05 REMARK 500 GLU X2108 20.03 -78.07 REMARK 500 UNK C1032 39.30 -78.50 REMARK 500 REMARK 500 REMARK: NULL DBREF 3HM6 X 1511 2135 UNP O43157 PLXB1_HUMAN 1511 2135 DBREF 3HM6 C 1007 1033 PDB 3HM6 3HM6 1007 1033 SEQADV 3HM6 MET X 1492 UNP O43157 INITIATING METHIONINE SEQADV 3HM6 GLY X 1493 UNP O43157 EXPRESSION TAG SEQADV 3HM6 SER X 1494 UNP O43157 EXPRESSION TAG SEQADV 3HM6 SER X 1495 UNP O43157 EXPRESSION TAG SEQADV 3HM6 HIS X 1496 UNP O43157 EXPRESSION TAG SEQADV 3HM6 HIS X 1497 UNP O43157 EXPRESSION TAG SEQADV 3HM6 HIS X 1498 UNP O43157 EXPRESSION TAG SEQADV 3HM6 HIS X 1499 UNP O43157 EXPRESSION TAG SEQADV 3HM6 HIS X 1500 UNP O43157 EXPRESSION TAG SEQADV 3HM6 HIS X 1501 UNP O43157 EXPRESSION TAG SEQADV 3HM6 SER X 1502 UNP O43157 EXPRESSION TAG SEQADV 3HM6 SER X 1503 UNP O43157 EXPRESSION TAG SEQADV 3HM6 GLY X 1504 UNP O43157 EXPRESSION TAG SEQADV 3HM6 LEU X 1505 UNP O43157 EXPRESSION TAG SEQADV 3HM6 VAL X 1506 UNP O43157 EXPRESSION TAG SEQADV 3HM6 PRO X 1507 UNP O43157 EXPRESSION TAG SEQADV 3HM6 ARG X 1508 UNP O43157 EXPRESSION TAG SEQADV 3HM6 GLY X 1509 UNP O43157 EXPRESSION TAG SEQADV 3HM6 SER X 1510 UNP O43157 EXPRESSION TAG SEQADV 3HM6 THR X 1625 UNP O43157 SER 1625 ENGINEERED MUTATION SEQRES 1 X 644 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 X 644 LEU VAL PRO ARG GLY SER TYR ARG ARG LYS SER LYS GLN SEQRES 3 X 644 ALA LEU ARG ASP TYR LYS LYS VAL GLN ILE GLN LEU GLU SEQRES 4 X 644 ASN LEU GLU SER SER VAL ARG ASP ARG CYS LYS LYS GLU SEQRES 5 X 644 PHE THR ASP LEU MET THR GLU MET THR ASP LEU THR SER SEQRES 6 X 644 ASP LEU LEU GLY SER GLY ILE PRO PHE LEU ASP TYR LYS SEQRES 7 X 644 VAL TYR ALA GLU ARG ILE PHE PHE PRO GLY HIS ARG GLU SEQRES 8 X 644 SER PRO LEU HIS ARG ASP LEU GLY VAL PRO GLU SER ARG SEQRES 9 X 644 ARG PRO THR VAL GLU GLN GLY LEU GLY GLN LEU SER ASN SEQRES 10 X 644 LEU LEU ASN SER LYS LEU PHE LEU THR LYS PHE ILE HIS SEQRES 11 X 644 THR LEU GLU THR GLN ARG THR PHE SER ALA ARG ASP ARG SEQRES 12 X 644 ALA TYR VAL ALA SER LEU LEU THR VAL ALA LEU HIS GLY SEQRES 13 X 644 LYS LEU GLU TYR PHE THR ASP ILE LEU ARG THR LEU LEU SEQRES 14 X 644 SER ASP LEU VAL ALA GLN TYR VAL ALA LYS ASN PRO LYS SEQRES 15 X 644 LEU MET LEU ARG ARG THR GLU THR VAL VAL GLU LYS LEU SEQRES 16 X 644 LEU THR ASN TRP MET SER ILE CYS LEU TYR THR PHE VAL SEQRES 17 X 644 ARG ASP SER VAL GLY GLU PRO LEU TYR MET LEU PHE ARG SEQRES 18 X 644 GLY ILE LYS HIS GLN VAL ASP LYS GLY PRO VAL ASP SER SEQRES 19 X 644 VAL THR GLY LYS ALA LYS TYR THR LEU ASN ASP ASN ARG SEQRES 20 X 644 LEU LEU ARG GLU ASP VAL GLU TYR ARG PRO LEU THR LEU SEQRES 21 X 644 ASN ALA LEU LEU ALA VAL GLY PRO GLY ALA GLY GLU ALA SEQRES 22 X 644 GLN GLY VAL PRO VAL LYS VAL LEU ASP CYS ASP THR ILE SEQRES 23 X 644 SER GLN ALA LYS GLU LYS MET LEU ASP GLN LEU TYR LYS SEQRES 24 X 644 GLY VAL PRO LEU THR GLN ARG PRO ASP PRO ARG THR LEU SEQRES 25 X 644 ASP VAL GLU TRP ARG SER GLY VAL ALA GLY HIS LEU ILE SEQRES 26 X 644 LEU SER ASP GLU ASP VAL THR SER GLU VAL GLN GLY LEU SEQRES 27 X 644 TRP ARG ARG LEU ASN THR LEU GLN HIS TYR LYS VAL PRO SEQRES 28 X 644 ASP GLY ALA THR VAL ALA LEU VAL PRO CYS LEU THR LYS SEQRES 29 X 644 HIS VAL LEU ARG GLU ASN GLN ASP TYR VAL PRO GLY GLU SEQRES 30 X 644 ARG THR PRO MET LEU GLU ASP VAL ASP GLU GLY GLY ILE SEQRES 31 X 644 ARG PRO TRP HIS LEU VAL LYS PRO SER ASP GLU PRO GLU SEQRES 32 X 644 PRO PRO ARG PRO ARG ARG GLY SER LEU ARG GLY GLY GLU SEQRES 33 X 644 ARG GLU ARG ALA LYS ALA ILE PRO GLU ILE TYR LEU THR SEQRES 34 X 644 ARG LEU LEU SER MET LYS GLY THR LEU GLN LYS PHE VAL SEQRES 35 X 644 ASP ASP LEU PHE GLN VAL ILE LEU SER THR SER ARG PRO SEQRES 36 X 644 VAL PRO LEU ALA VAL LYS TYR PHE PHE ASP LEU LEU ASP SEQRES 37 X 644 GLU GLN ALA GLN GLN HIS GLY ILE SER ASP GLN ASP THR SEQRES 38 X 644 ILE HIS ILE TRP LYS THR ASN SER LEU PRO LEU ARG PHE SEQRES 39 X 644 TRP ILE ASN ILE ILE LYS ASN PRO GLN PHE VAL PHE ASP SEQRES 40 X 644 VAL GLN THR SER ASP ASN MET ASP ALA VAL LEU LEU VAL SEQRES 41 X 644 ILE ALA GLN THR PHE MET ASP ALA CYS THR LEU ALA ASP SEQRES 42 X 644 HIS LYS LEU GLY ARG ASP SER PRO ILE ASN LYS LEU LEU SEQRES 43 X 644 TYR ALA ARG ASP ILE PRO ARG TYR LYS ARG MET VAL GLU SEQRES 44 X 644 ARG TYR TYR ALA ASP ILE ARG GLN THR VAL PRO ALA SER SEQRES 45 X 644 ASP GLN GLU MET ASN SER VAL LEU ALA GLU LEU SER TRP SEQRES 46 X 644 ASN TYR SER GLY ASP LEU GLY ALA ARG VAL ALA LEU HIS SEQRES 47 X 644 GLU LEU TYR LYS TYR ILE ASN LYS TYR TYR ASP GLN ILE SEQRES 48 X 644 ILE THR ALA LEU GLU GLU ASP GLY THR ALA GLN LYS MET SEQRES 49 X 644 GLN LEU GLY TYR ARG LEU GLN GLN ILE ALA ALA ALA VAL SEQRES 50 X 644 GLU ASN LYS VAL THR ASP LEU SEQRES 1 C 27 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 2 C 27 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 3 C 27 UNK HET UNX X 1 1 HET UNX X 2 1 HET UNX X 3 1 HET UNX X 4 1 HET UNX X 5 1 HET UNX X 6 1 HET UNX X 7 1 HET UNX X 8 1 HET UNX X 9 1 HET UNX X 10 1 HET UNX X 11 1 HET UNX X 12 1 HET UNX X 13 1 HET UNX X 14 1 HET UNX X 15 1 HET UNX X 16 1 HET UNX X 17 1 HET UNX X 18 1 HET UNX X 19 1 HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 UNX 19(X) FORMUL 22 HOH *37(H2 O) HELIX 1 1 ASP X 1567 PHE X 1577 1 11 HELIX 2 2 PRO X 1592 SER X 1594 5 3 HELIX 3 3 ARG X 1595 ASN X 1611 1 17 HELIX 4 4 SER X 1612 GLN X 1626 1 15 HELIX 5 5 SER X 1630 LEU X 1645 1 16 HELIX 6 6 LYS X 1648 ALA X 1669 1 22 HELIX 7 7 LYS X 1670 MET X 1675 5 6 HELIX 8 8 THR X 1681 SER X 1702 1 22 HELIX 9 9 VAL X 1703 LYS X 1720 1 18 HELIX 10 10 THR X 1776 TYR X 1789 1 14 HELIX 11 11 PRO X 1793 ARG X 1797 5 5 HELIX 12 12 ASP X 1799 ARG X 1801 5 3 HELIX 13 13 PRO X 1915 SER X 1942 1 28 HELIX 14 14 PRO X 1948 HIS X 1965 1 18 HELIX 15 15 ASP X 1969 LEU X 1981 1 13 HELIX 16 16 PHE X 1985 ASN X 1992 1 8 HELIX 17 17 PRO X 1993 VAL X 1996 5 4 HELIX 18 18 SER X 2002 THR X 2021 1 20 HELIX 19 19 PRO X 2032 TYR X 2038 1 7 HELIX 20 20 ASP X 2041 THR X 2059 1 19 HELIX 21 21 SER X 2063 ASN X 2077 1 15 HELIX 22 22 GLY X 2083 TYR X 2098 1 16 HELIX 23 23 TYR X 2098 GLU X 2108 1 11 HELIX 24 24 ASP X 2109 MET X 2115 1 7 HELIX 25 25 GLN X 2116 GLU X 2129 1 14 HELIX 26 26 UNK C 1007 UNK C 1032 1 26 SHEET 1 A 5 VAL X1767 LEU X1772 0 SHEET 2 A 5 PRO X1748 LEU X1754 -1 N ALA X1753 O VAL X1767 SHEET 3 A 5 THR X1846 PRO X1851 1 O VAL X1847 N LEU X1754 SHEET 4 A 5 LEU X1803 ARG X1808 -1 N ASP X1804 O VAL X1850 SHEET 5 A 5 HIS X1814 LEU X1817 -1 O LEU X1815 N TRP X1807 SHEET 1 B 3 VAL X1826 GLN X1827 0 SHEET 2 B 3 TRP X1830 ARG X1832 -1 O TRP X1830 N GLN X1827 SHEET 3 B 3 ARG X1882 TRP X1884 1 O ARG X1882 N ARG X1831 CRYST1 74.346 74.346 214.398 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 0.013451 0.007766 0.000000 0.00000 SCALE2 0.000000 0.015531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004664 0.00000