HEADER SIGNALING PROTEIN 23-APR-09 3H6N TITLE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN OF PLEXIN D1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLEXIN-D1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN (UNP RESIDUES 1553-1678); COMPND 5 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: PLXND1, KIAA0620; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, MEMBRANE, TRANSMEMBRANE, KEYWDS 2 RECEPTOR, ALTERNATIVE SPLICING, CELL MEMBRANE, GLYCOPROTEIN, KEYWDS 3 POLYMORPHISM, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.TONG,L.NEDYALKOVA,W.TEMPEL,F.MACKENZIE,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 C.BOUNTRA,J.WEIGELT,A.BOCHKAREV,M.BUCK,H.PARK,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 3 30-OCT-24 3H6N 1 REMARK SEQADV LINK REVDAT 2 01-NOV-17 3H6N 1 REMARK REVDAT 1 19-MAY-09 3H6N 0 JRNL AUTH Y.TONG,L.NEDYALKOVA,W.TEMPEL,F.MACKENZIE,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,C.BOUNTRA,J.WEIGELT,A.BOCHKAREV,M.BUCK,H.PARK JRNL TITL CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN OF PLEXIN D1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 7229 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) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.662 REMARK 3 FREE R VALUE TEST SET COUNT : 337 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 505 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 775 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.70600 REMARK 3 B22 (A**2) : 1.44400 REMARK 3 B33 (A**2) : 0.04600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.26500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.228 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.191 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.569 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.887 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 789 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 506 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1075 ; 1.095 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1237 ; 0.748 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 103 ; 6.012 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;33.446 ;24.688 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 122 ;14.389 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;20.348 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 126 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 892 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 154 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 519 ; 0.983 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 207 ; 0.217 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 825 ; 1.651 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 270 ; 1.305 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 250 ; 1.814 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1553 A 1656 REMARK 3 ORIGIN FOR THE GROUP (A): 16.5258 16.6552 14.8903 REMARK 3 T TENSOR REMARK 3 T11: 0.0439 T22: 0.0751 REMARK 3 T33: 0.0843 T12: -0.0152 REMARK 3 T13: 0.0303 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 3.2374 L22: 2.1422 REMARK 3 L33: 4.8958 L12: 0.4764 REMARK 3 L13: 2.8561 L23: 0.6545 REMARK 3 S TENSOR REMARK 3 S11: -0.1521 S12: -0.0408 S13: -0.0478 REMARK 3 S21: -0.1307 S22: 0.0831 S23: 0.0034 REMARK 3 S31: 0.1086 S32: -0.1199 S33: 0.0690 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. U VALUES: WITH TLS ADDED. PHENIX, ARP/WARP, COOT AND REMARK 3 MOLPROBITY WERE ALSO USED DURING REFINEMENT. REMARK 4 REMARK 4 3H6N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7245 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.39M SODIUM CITRATE, 0.1M SODIUM REMARK 280 CACODYLATE. THE PROTEIN STOCK SOLUTION WAS ADJUSTED TO CONTAIN REMARK 280 15 MM TCEP, SUPPLEMENTED WITH 1:100 (W/W) CHYMOTRYPSIN, PH 5.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.88850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.52550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.88850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.52550 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 60.31074 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.07846 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 1552 REMARK 465 LYS A 1657 REMARK 465 LYS A 1658 REMARK 465 ASP A 1659 REMARK 465 ASN A 1660 REMARK 465 THR A 1661 REMARK 465 LEU A 1662 REMARK 465 GLY A 1663 REMARK 465 ARG A 1664 REMARK 465 VAL A 1665 REMARK 465 LYS A 1666 REMARK 465 ASP A 1667 REMARK 465 LEU A 1668 REMARK 465 ASP A 1669 REMARK 465 THR A 1670 REMARK 465 GLU A 1671 REMARK 465 LYS A 1672 REMARK 465 TYR A 1673 REMARK 465 PHE A 1674 REMARK 465 HIS A 1675 REMARK 465 LEU A 1676 REMARK 465 VAL A 1677 REMARK 465 LEU A 1678 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 LYS A1554 CG CD CE NZ REMARK 470 LYS A1593 CD CE NZ REMARK 470 GLU A1604 CG CD OE1 OE2 REMARK 470 GLU A1609 CG CD OE1 OE2 REMARK 470 SER A1613 OG REMARK 470 SER A1614 OG REMARK 470 THR A1615 OG1 CG2 REMARK 470 GLN A1616 CG CD OE1 NE2 REMARK 470 ARG A1621 CD NE CZ NH1 NH2 REMARK 470 VAL A1629 CG1 CG2 REMARK 470 GLU A1630 CG CD OE1 OE2 REMARK 470 ASP A1631 CG OD1 OD2 REMARK 470 LYS A1635 CG CD CE NZ REMARK 470 LYS A1643 CE NZ REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE ELECTRON DENSITY SUGGESTS THE MODIFICATION OF THE SULFHYDRYL REMARK 600 GROUPS OF CYS-1565 AND CYS-1592, POSSIBLY BY A REACTION INVOLVING REMARK 600 CACODYLATE, SIMILAR TO SCOTT ET AL (1993, CHEM RES TOXICOL 6:102) REMARK 600 AND GOLDGUR ET AL (1998, PROC NATL ACAD SCI USA 95:9150). ONLY THE REMARK 600 PUTATIVE ARSENIC ATOMS OF THE MODIFICATION HAVE BEEN MODELED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARS A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARS A 2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SOLVENT CONTENT AND MATTHEWS COEFFICIENT WERE CALCULATED BASED ON REMARK 999 THE PURIFIED PROTEIN CONSTRUCT. HOWEVER, THE PROTEASE ADDED FOR REMARK 999 CRYSTALLIZATION MAY HAVE REDUCED THE CHAIN LENGTH OF THE TARGET REMARK 999 PROTEIN. DBREF 3H6N A 1553 1678 UNP Q9Y4D7 PLXD1_HUMAN 1553 1678 SEQADV 3H6N GLY A 1552 UNP Q9Y4D7 EXPRESSION TAG SEQRES 1 A 127 GLY ALA LYS PRO ARG ASN LEU ASN VAL SER PHE GLN GLY SEQRES 2 A 127 CYS GLY MSE ASP SER LEU SER VAL ARG ALA MSE ASP THR SEQRES 3 A 127 ASP THR LEU THR GLN VAL LYS GLU LYS ILE LEU GLU ALA SEQRES 4 A 127 PHE CYS LYS ASN VAL PRO TYR SER GLN TRP PRO ARG ALA SEQRES 5 A 127 GLU ASP VAL ASP LEU GLU TRP PHE ALA SER SER THR GLN SEQRES 6 A 127 SER TYR ILE LEU ARG ASP LEU ASP ASP THR SER VAL VAL SEQRES 7 A 127 GLU ASP GLY ARG LYS LYS LEU ASN THR LEU ALA HIS TYR SEQRES 8 A 127 LYS ILE PRO GLU GLY ALA SER LEU ALA MSE SER LEU ILE SEQRES 9 A 127 ASP LYS LYS ASP ASN THR LEU GLY ARG VAL LYS ASP LEU SEQRES 10 A 127 ASP THR GLU LYS TYR PHE HIS LEU VAL LEU MODRES 3H6N MSE A 1567 MET SELENOMETHIONINE MODRES 3H6N MSE A 1575 MET SELENOMETHIONINE MODRES 3H6N MSE A 1652 MET SELENOMETHIONINE HET MSE A1567 8 HET MSE A1575 8 HET MSE A1652 8 HET ARS A 1 1 HET ARS A 2 1 HET UNX A1679 1 HETNAM MSE SELENOMETHIONINE HETNAM ARS ARSENIC HETNAM UNX UNKNOWN ATOM OR ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 ARS 2(AS) FORMUL 4 UNX X FORMUL 5 HOH *11(H2 O) HELIX 1 1 THR A 1579 CYS A 1592 1 14 HELIX 2 2 PRO A 1596 TRP A 1600 5 5 HELIX 3 3 ARG A 1602 GLU A 1604 5 3 SHEET 1 A 5 LEU A1570 MSE A1575 0 SHEET 2 A 5 PRO A1555 GLN A1563 -1 N ARG A1556 O ALA A1574 SHEET 3 A 5 SER A1649 LEU A1654 1 O MSE A1652 N SER A1561 SHEET 4 A 5 VAL A1606 PHE A1611 -1 N GLU A1609 O ALA A1651 SHEET 5 A 5 SER A1617 ILE A1619 -1 O TYR A1618 N TRP A1610 SHEET 1 B 2 VAL A1629 GLU A1630 0 SHEET 2 B 2 ARG A1633 LYS A1634 -1 O ARG A1633 N GLU A1630 LINK C GLY A1566 N MSE A1567 1555 1555 1.33 LINK C MSE A1567 N ASP A1568 1555 1555 1.33 LINK C ALA A1574 N MSE A1575 1555 1555 1.33 LINK C MSE A1575 N ASP A1576 1555 1555 1.34 LINK C ALA A1651 N MSE A1652 1555 1555 1.33 LINK C MSE A1652 N SER A1653 1555 1555 1.34 SITE 1 AC1 1 CYS A1592 SITE 1 AC2 1 CYS A1565 CRYST1 81.777 27.051 52.653 90.00 114.06 90.00 C 1 2 1 4 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 0.012228 0.000000 0.005460 0.00000 SCALE2 0.000000 0.036967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020799 0.00000