HEADER SIGNALING PROTEIN 08-OCT-20 7KDC TITLE THE COMPLEX BETWEEN RHOD AND THE PLEXIN B2 RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO-RELATED GTP-BINDING PROTEIN RHOD; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RHO-RELATED PROTEIN HP1,RHOHP1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PLEXIN-B2; COMPND 8 CHAIN: C, D; COMPND 9 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: RHOD, ARHD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: PLXNB2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLEXIN, RHOD, GTPASE, AXON GUIDANCE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.KUO,Y.WANG,X.ZHANG REVDAT 4 18-OCT-23 7KDC 1 REMARK REVDAT 3 11-AUG-21 7KDC 1 REMARK REVDAT 2 04-AUG-21 7KDC 1 JRNL REVDAT 1 28-JUL-21 7KDC 0 JRNL AUTH Y.LIU,P.KE,Y.C.KUO,Y.WANG,X.ZHANG,C.SONG,Y.SHAN JRNL TITL A PUTATIVE STRUCTURAL MECHANISM UNDERLYING THE ANTITHETIC JRNL TITL 2 EFFECT OF HOMOLOGOUS RND1 AND RHOD GTPASES IN MAMMALIAN JRNL TITL 3 PLEXIN REGULATION. JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34114565 JRNL DOI 10.7554/ELIFE.64304 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3845 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 18763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 951 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 39.6300 - 5.9300 0.99 2546 134 0.1666 0.2227 REMARK 3 2 5.9300 - 4.7100 1.00 2570 144 0.2176 0.2311 REMARK 3 3 4.7100 - 4.1100 1.00 2548 140 0.2297 0.2946 REMARK 3 4 4.1100 - 3.7400 0.99 2595 131 0.2339 0.2757 REMARK 3 5 3.7400 - 3.4700 0.99 2548 128 0.2571 0.3630 REMARK 3 6 3.4700 - 3.2600 0.99 2574 139 0.2794 0.3774 REMARK 3 7 3.2600 - 3.1000 0.95 2431 135 0.3589 0.3762 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) : 0.448 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.723 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 107.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 123.4 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 : 0.002 4546 REMARK 3 ANGLE : 0.482 6217 REMARK 3 CHIRALITY : 0.043 720 REMARK 3 PLANARITY : 0.005 787 REMARK 3 DIHEDRAL : 18.491 621 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 15:194 OR RESID 201:202 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.7887 52.0295 4.0502 REMARK 3 T TENSOR REMARK 3 T11: 1.3027 T22: 1.2020 REMARK 3 T33: 0.7800 T12: 0.1018 REMARK 3 T13: 0.1407 T23: 0.0755 REMARK 3 L TENSOR REMARK 3 L11: 2.1960 L22: 3.0698 REMARK 3 L33: 2.3698 L12: 1.0483 REMARK 3 L13: -0.3085 L23: -1.7982 REMARK 3 S TENSOR REMARK 3 S11: 0.2391 S12: 0.0723 S13: 0.0600 REMARK 3 S21: 0.1699 S22: -0.3924 S23: -0.0091 REMARK 3 S31: -0.5624 S32: -0.0596 S33: 0.2046 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND ( RESID 15:194 OR RESID 201:202 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.8583 65.3284 -80.1343 REMARK 3 T TENSOR REMARK 3 T11: 1.0096 T22: 1.2377 REMARK 3 T33: 0.6520 T12: 0.0103 REMARK 3 T13: -0.0171 T23: -0.1812 REMARK 3 L TENSOR REMARK 3 L11: 2.6917 L22: 3.4780 REMARK 3 L33: 2.0978 L12: 1.5114 REMARK 3 L13: 1.3710 L23: 0.6901 REMARK 3 S TENSOR REMARK 3 S11: -0.3030 S12: -0.3009 S13: 0.1084 REMARK 3 S21: -0.1607 S22: 0.2350 S23: 0.0238 REMARK 3 S31: -0.2822 S32: 0.6006 S33: 0.1117 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN C AND RESID 1463:1508 ) OR ( CHAIN D AND REMARK 3 RESID 1509:1565 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7806 66.0915 -51.8180 REMARK 3 T TENSOR REMARK 3 T11: 1.0719 T22: 1.2312 REMARK 3 T33: 0.7650 T12: 0.1140 REMARK 3 T13: -0.0355 T23: -0.1549 REMARK 3 L TENSOR REMARK 3 L11: 4.2290 L22: 2.7980 REMARK 3 L33: 0.1607 L12: 1.5622 REMARK 3 L13: 1.3114 L23: 0.1821 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: 0.6596 S13: -0.2932 REMARK 3 S21: -0.2186 S22: 0.1291 S23: -0.1249 REMARK 3 S31: 0.2338 S32: 0.4254 S33: -0.2210 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN C AND RESID 1509:1565 ) OR ( CHAIN D AND REMARK 3 RESID 1463:1508 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.5599 63.8308 -24.3155 REMARK 3 T TENSOR REMARK 3 T11: 0.9570 T22: 1.1004 REMARK 3 T33: 0.7721 T12: 0.1468 REMARK 3 T13: 0.1157 T23: 0.0947 REMARK 3 L TENSOR REMARK 3 L11: 1.2111 L22: 8.2576 REMARK 3 L33: 1.3885 L12: 0.2777 REMARK 3 L13: 0.8449 L23: -2.0503 REMARK 3 S TENSOR REMARK 3 S11: -0.1709 S12: -0.1106 S13: 0.0678 REMARK 3 S21: 0.7838 S22: 0.2738 S23: 0.6117 REMARK 3 S31: -0.4715 S32: -0.3675 S33: -0.2078 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 7KDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19325 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51400 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2REX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 22 % (W/V) PEG 3350, AND REMARK 280 100 MM MIB (PH 6.8, SODIUM MALONATE, IMIDAZOLE, AND BORIC ACID REMARK 280 MIXED AT 2:3:3 MOLAR RATIO)., VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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 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 45.58700 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 91.17400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 GLY A 4 REMARK 465 PRO A 5 REMARK 465 HIS A 6 REMARK 465 MET A 7 REMARK 465 GLY A 8 REMARK 465 GLU A 9 REMARK 465 GLU A 10 REMARK 465 ALA A 11 REMARK 465 PRO A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 GLY B 4 REMARK 465 PRO B 5 REMARK 465 HIS B 6 REMARK 465 MET B 7 REMARK 465 GLY B 8 REMARK 465 GLU B 9 REMARK 465 GLU B 10 REMARK 465 ALA B 11 REMARK 465 PRO B 12 REMARK 465 PRO B 13 REMARK 465 GLY B 14 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 GLU A 44 CG CD OE1 OE2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 ARG A 194 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 LYS B 121 CG CD CE NZ REMARK 470 LYS B 142 CG CD CE NZ REMARK 470 ARG B 194 CG CD NE CZ NH1 NH2 REMARK 470 GLU C1463 CG CD OE1 OE2 REMARK 470 TYR C1464 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP C1475 CG OD1 OD2 REMARK 470 LYS C1484 CG CD CE NZ REMARK 470 ARG C1555 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1564 CG CD CE NZ REMARK 470 GLU D1463 CG CD OE1 OE2 REMARK 470 TYR D1464 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP D1475 CG OD1 OD2 REMARK 470 LYS D1484 CG CD CE NZ REMARK 470 LYS D1564 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2G GNP B 201 O HOH B 301 1.95 REMARK 500 O2G GNP A 201 O HOH A 301 2.17 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 VAL A 50 -71.46 -96.32 REMARK 500 PHE A 118 -72.39 -87.29 REMARK 500 LYS A 135 41.84 -97.77 REMARK 500 HIS A 176 6.86 59.89 REMARK 500 VAL B 50 -68.14 -90.29 REMARK 500 PRO B 83 -8.65 -58.11 REMARK 500 PHE B 118 -77.24 -102.13 REMARK 500 HIS B 176 15.27 56.58 REMARK 500 ASN B 178 18.32 59.51 REMARK 500 LEU C1467 110.07 -161.39 REMARK 500 ASP C1534 -152.51 -131.15 REMARK 500 LEU D1467 117.90 -160.25 REMARK 500 ASP D1534 -157.63 -143.31 REMARK 500 THR D1548 -169.92 -111.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 31 OG1 REMARK 620 2 THR A 49 OG1 72.4 REMARK 620 3 GNP A 201 O2G 145.9 104.4 REMARK 620 4 GNP A 201 O2B 76.7 147.1 94.9 REMARK 620 5 HOH A 301 O 82.8 92.6 63.2 72.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 31 OG1 REMARK 620 2 THR B 49 OG1 78.2 REMARK 620 3 GNP B 201 O2G 146.0 108.3 REMARK 620 4 GNP B 201 O2B 72.5 149.4 91.8 REMARK 620 5 HOH B 301 O 89.6 93.1 57.2 78.4 REMARK 620 N 1 2 3 4 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ORIGINAL SEQUENCE FOR CHAINS C AND D INCLUDED RESIDUES 1274 TO REMARK 999 1842 OF UNP PLXB2_MOUSE B2RXS4, HOWEVER, PROTEOLYTIC CLEAVAGE REMARK 999 OCCURS DURING INCUBATION AT AN UNKNOWN SITE. THUS, THE REPORTED REMARK 999 SEQUENCE CORRESPONDS TO THE PORTION OBSERVED IN THE COORDINATES, REMARK 999 WHICH IS RESIDUES 1463 TO 1565 OF UNP PLXB2_MOUSE B2RXS4. DBREF 7KDC A 8 194 UNP O00212 RHOD_HUMAN 8 194 DBREF 7KDC B 8 194 UNP O00212 RHOD_HUMAN 8 194 DBREF 7KDC C 1463 1565 UNP B2RXS4 PLXB2_MOUSE 1463 1565 DBREF 7KDC D 1463 1565 UNP B2RXS4 PLXB2_MOUSE 1463 1565 SEQADV 7KDC GLY A 4 UNP O00212 EXPRESSION TAG SEQADV 7KDC PRO A 5 UNP O00212 EXPRESSION TAG SEQADV 7KDC HIS A 6 UNP O00212 EXPRESSION TAG SEQADV 7KDC MET A 7 UNP O00212 EXPRESSION TAG SEQADV 7KDC LEU A 75 UNP O00212 GLN 75 ENGINEERED MUTATION SEQADV 7KDC ARG A 134 UNP O00212 CYS 134 VARIANT SEQADV 7KDC GLY B 4 UNP O00212 EXPRESSION TAG SEQADV 7KDC PRO B 5 UNP O00212 EXPRESSION TAG SEQADV 7KDC HIS B 6 UNP O00212 EXPRESSION TAG SEQADV 7KDC MET B 7 UNP O00212 EXPRESSION TAG SEQADV 7KDC LEU B 75 UNP O00212 GLN 75 ENGINEERED MUTATION SEQADV 7KDC ARG B 134 UNP O00212 CYS 134 VARIANT SEQRES 1 A 191 GLY PRO HIS MET GLY GLU GLU ALA PRO PRO GLY VAL ARG SEQRES 2 A 191 SER VAL LYS VAL VAL LEU VAL GLY ASP GLY GLY CYS GLY SEQRES 3 A 191 LYS THR SER LEU LEU MET VAL PHE ALA ASP GLY ALA PHE SEQRES 4 A 191 PRO GLU SER TYR THR PRO THR VAL PHE GLU ARG TYR MET SEQRES 5 A 191 VAL ASN LEU GLN VAL LYS GLY LYS PRO VAL HIS LEU HIS SEQRES 6 A 191 ILE TRP ASP THR ALA GLY LEU ASP ASP TYR ASP ARG LEU SEQRES 7 A 191 ARG PRO LEU PHE TYR PRO ASP ALA SER VAL LEU LEU LEU SEQRES 8 A 191 CYS PHE ASP VAL THR SER PRO ASN SER PHE ASP ASN ILE SEQRES 9 A 191 PHE ASN ARG TRP TYR PRO GLU VAL ASN HIS PHE CYS LYS SEQRES 10 A 191 LYS VAL PRO ILE ILE VAL VAL GLY CYS LYS THR ASP LEU SEQRES 11 A 191 ARG LYS ASP LYS SER LEU VAL ASN LYS LEU ARG ARG ASN SEQRES 12 A 191 GLY LEU GLU PRO VAL THR TYR HIS ARG GLY GLN GLU MET SEQRES 13 A 191 ALA ARG SER VAL GLY ALA VAL ALA TYR LEU GLU CYS SER SEQRES 14 A 191 ALA ARG LEU HIS ASP ASN VAL HIS ALA VAL PHE GLN GLU SEQRES 15 A 191 ALA ALA GLU VAL ALA LEU SER SER ARG SEQRES 1 B 191 GLY PRO HIS MET GLY GLU GLU ALA PRO PRO GLY VAL ARG SEQRES 2 B 191 SER VAL LYS VAL VAL LEU VAL GLY ASP GLY GLY CYS GLY SEQRES 3 B 191 LYS THR SER LEU LEU MET VAL PHE ALA ASP GLY ALA PHE SEQRES 4 B 191 PRO GLU SER TYR THR PRO THR VAL PHE GLU ARG TYR MET SEQRES 5 B 191 VAL ASN LEU GLN VAL LYS GLY LYS PRO VAL HIS LEU HIS SEQRES 6 B 191 ILE TRP ASP THR ALA GLY LEU ASP ASP TYR ASP ARG LEU SEQRES 7 B 191 ARG PRO LEU PHE TYR PRO ASP ALA SER VAL LEU LEU LEU SEQRES 8 B 191 CYS PHE ASP VAL THR SER PRO ASN SER PHE ASP ASN ILE SEQRES 9 B 191 PHE ASN ARG TRP TYR PRO GLU VAL ASN HIS PHE CYS LYS SEQRES 10 B 191 LYS VAL PRO ILE ILE VAL VAL GLY CYS LYS THR ASP LEU SEQRES 11 B 191 ARG LYS ASP LYS SER LEU VAL ASN LYS LEU ARG ARG ASN SEQRES 12 B 191 GLY LEU GLU PRO VAL THR TYR HIS ARG GLY GLN GLU MET SEQRES 13 B 191 ALA ARG SER VAL GLY ALA VAL ALA TYR LEU GLU CYS SER SEQRES 14 B 191 ALA ARG LEU HIS ASP ASN VAL HIS ALA VAL PHE GLN GLU SEQRES 15 B 191 ALA ALA GLU VAL ALA LEU SER SER ARG SEQRES 1 C 103 GLU TYR ALA PRO LEU THR VAL SER VAL ILE VAL GLN ASP SEQRES 2 C 103 GLU GLY ILE ASP ALA ILE PRO VAL LYS VAL LEU ASN CYS SEQRES 3 C 103 ASP THR ILE SER GLN VAL LYS GLU LYS ILE ILE ASP GLN SEQRES 4 C 103 VAL TYR ARG THR GLN PRO CYS SER CYS TRP PRO LYS PRO SEQRES 5 C 103 ASP SER VAL VAL LEU GLU TRP ARG PRO GLY SER THR ALA SEQRES 6 C 103 GLN ILE LEU SER ASP LEU ASP LEU THR SER GLN ARG GLU SEQRES 7 C 103 GLY ARG TRP LYS ARG ILE ASN THR LEU MET HIS TYR ASN SEQRES 8 C 103 VAL ARG ASP GLY ALA THR LEU ILE LEU SER LYS VAL SEQRES 1 D 103 GLU TYR ALA PRO LEU THR VAL SER VAL ILE VAL GLN ASP SEQRES 2 D 103 GLU GLY ILE ASP ALA ILE PRO VAL LYS VAL LEU ASN CYS SEQRES 3 D 103 ASP THR ILE SER GLN VAL LYS GLU LYS ILE ILE ASP GLN SEQRES 4 D 103 VAL TYR ARG THR GLN PRO CYS SER CYS TRP PRO LYS PRO SEQRES 5 D 103 ASP SER VAL VAL LEU GLU TRP ARG PRO GLY SER THR ALA SEQRES 6 D 103 GLN ILE LEU SER ASP LEU ASP LEU THR SER GLN ARG GLU SEQRES 7 D 103 GLY ARG TRP LYS ARG ILE ASN THR LEU MET HIS TYR ASN SEQRES 8 D 103 VAL ARG ASP GLY ALA THR LEU ILE LEU SER LYS VAL HET GNP A 201 32 HET MG A 202 1 HET MG A 203 1 HET GNP B 201 32 HET MG B 202 1 HET MG B 203 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 5 GNP 2(C10 H17 N6 O13 P3) FORMUL 6 MG 4(MG 2+) FORMUL 11 HOH *8(H2 O) HELIX 1 AA1 GLY A 29 ASP A 39 1 11 HELIX 2 AA2 LEU A 75 ASP A 79 5 5 HELIX 3 AA3 LEU A 81 TYR A 86 5 6 HELIX 4 AA4 SER A 100 ARG A 110 1 11 HELIX 5 AA5 ARG A 110 PHE A 118 1 9 HELIX 6 AA6 LYS A 130 LYS A 135 5 6 HELIX 7 AA7 ASP A 136 ASN A 146 1 11 HELIX 8 AA8 THR A 152 GLY A 164 1 13 HELIX 9 AA9 SER A 172 HIS A 176 5 5 HELIX 10 AB1 ASN A 178 SER A 193 1 16 HELIX 11 AB2 GLY B 29 ASP B 39 1 11 HELIX 12 AB3 LEU B 75 ASP B 79 5 5 HELIX 13 AB4 LEU B 81 TYR B 86 5 6 HELIX 14 AB5 SER B 100 ARG B 110 1 11 HELIX 15 AB6 ARG B 110 PHE B 118 1 9 HELIX 16 AB7 LYS B 130 LYS B 135 5 6 HELIX 17 AB8 ASP B 136 ASN B 146 1 11 HELIX 18 AB9 THR B 152 GLY B 164 1 13 HELIX 19 AC1 SER B 172 HIS B 176 5 5 HELIX 20 AC2 ASN B 178 SER B 193 1 16 HELIX 21 AC3 THR C 1490 TYR C 1503 1 14 HELIX 22 AC4 LYS C 1513 ASP C 1515 5 3 HELIX 23 AC5 THR D 1490 ARG D 1504 1 15 HELIX 24 AC6 LYS D 1513 ASP D 1515 5 3 SHEET 1 AA1 6 GLU A 52 VAL A 60 0 SHEET 2 AA1 6 LYS A 63 ASP A 71 -1 O ILE A 69 N TYR A 54 SHEET 3 AA1 6 ARG A 16 GLY A 24 1 N VAL A 20 O HIS A 68 SHEET 4 AA1 6 VAL A 91 ASP A 97 1 O CYS A 95 N VAL A 23 SHEET 5 AA1 6 ILE A 124 CYS A 129 1 O ILE A 125 N LEU A 92 SHEET 6 AA1 6 ALA A 167 GLU A 170 1 O LEU A 169 N VAL A 126 SHEET 1 AA2 6 PHE B 51 VAL B 60 0 SHEET 2 AA2 6 LYS B 63 THR B 72 -1 O ILE B 69 N TYR B 54 SHEET 3 AA2 6 SER B 17 GLY B 24 1 N VAL B 20 O TRP B 70 SHEET 4 AA2 6 VAL B 91 ASP B 97 1 O CYS B 95 N VAL B 23 SHEET 5 AA2 6 ILE B 124 CYS B 129 1 O ILE B 125 N LEU B 92 SHEET 6 AA2 6 ALA B 167 GLU B 170 1 O LEU B 169 N GLY B 128 SHEET 1 AA3 5 ILE C1481 LEU C1486 0 SHEET 2 AA3 5 PRO C1466 VAL C1473 -1 N LEU C1467 O VAL C1485 SHEET 3 AA3 5 THR D1559 LYS D1564 1 O LEU D1562 N ILE C1472 SHEET 4 AA3 5 VAL D1517 TRP D1521 -1 N VAL D1518 O SER D1563 SHEET 5 AA3 5 GLN D1528 LEU D1530 -1 O LEU D1530 N LEU D1519 SHEET 1 AA4 5 GLN C1528 ILE C1529 0 SHEET 2 AA4 5 VAL C1517 TRP C1521 -1 N TRP C1521 O GLN C1528 SHEET 3 AA4 5 THR C1559 LYS C1564 -1 O SER C1563 N VAL C1518 SHEET 4 AA4 5 PRO D1466 VAL D1473 1 O ILE D1472 N LEU C1562 SHEET 5 AA4 5 ILE D1481 LEU D1486 -1 O VAL D1485 N LEU D1467 SSBOND 1 CYS C 1508 CYS D 1510 1555 1555 2.03 SSBOND 2 CYS C 1510 CYS D 1508 1555 1555 2.03 LINK OG1 THR A 31 MG MG A 202 1555 1555 2.06 LINK OG1 THR A 49 MG MG A 202 1555 1555 2.08 LINK O2G GNP A 201 MG MG A 202 1555 1555 2.07 LINK O2B GNP A 201 MG MG A 202 1555 1555 2.11 LINK MG MG A 202 O HOH A 301 1555 1555 2.07 LINK OG1 THR B 31 MG MG B 202 1555 1555 2.04 LINK OG1 THR B 49 MG MG B 202 1555 1555 2.09 LINK O2G GNP B 201 MG MG B 202 1555 1555 2.00 LINK O2B GNP B 201 MG MG B 202 1555 1555 2.17 LINK MG MG B 202 O HOH B 301 1555 1555 2.07 CRYST1 82.810 82.810 136.761 90.00 90.00 120.00 P 31 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 0.012076 0.006972 0.000000 0.00000 SCALE2 0.000000 0.013944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007312 0.00000