HEADER SIGNALING PROTEIN 28-NOV-19 6TKK TITLE NEUROPILIN 1-B1 DOMAIN IN A COMPLEX WITH THE C-TERMINAL VEGFB186 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ACE-ARG-PRO-GLN-PRO-ARG; COMPND 8 CHAIN: B; 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: NRP1, NRP, VEGF165R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS VEGF-BINDING, NRP1, ANGIOGENESIS, IMMUNOMODULATION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.ELDRID,L.YU,T.YELLAND,C.FOTINOU,S.DJORDJEVIC REVDAT 2 24-JAN-24 6TKK 1 REMARK REVDAT 1 16-DEC-20 6TKK 0 JRNL AUTH C.ELDRID,L.YU,T.YELLAND,C.FOTINOU,S.DJORDJEVIC JRNL TITL NEUROPILIN 1-B1 DOMAIN IN A COMPLEX WITH THE C-TERMINAL JRNL TITL 2 VEGFB186 PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.1 REMARK 3 NUMBER OF REFLECTIONS : 55869 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2785 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 48.8050 - 2.8800 0.99 3544 186 0.1614 0.1666 REMARK 3 2 2.8800 - 2.2900 1.00 3409 152 0.1649 0.1617 REMARK 3 3 2.2900 - 2.0000 1.00 3378 155 0.1429 0.1615 REMARK 3 4 2.0000 - 1.8100 1.00 3342 161 0.1388 0.1527 REMARK 3 5 1.8100 - 1.6800 0.99 3285 197 0.1335 0.1574 REMARK 3 6 1.6800 - 1.5800 1.00 3339 166 0.1188 0.1311 REMARK 3 7 1.5800 - 1.5100 1.00 3221 211 0.1135 0.1358 REMARK 3 8 1.5100 - 1.4400 1.00 3305 174 0.1080 0.1211 REMARK 3 9 1.4400 - 1.3800 0.99 3282 161 0.1043 0.1405 REMARK 3 10 1.3800 - 1.3400 0.99 3285 158 0.1076 0.1265 REMARK 3 11 1.3400 - 1.2900 0.99 3259 183 0.1054 0.1278 REMARK 3 12 1.2900 - 1.2600 0.98 3199 188 0.1076 0.1226 REMARK 3 13 1.2600 - 1.2200 0.93 3068 163 0.0995 0.1308 REMARK 3 14 1.2200 - 1.1900 0.81 2665 138 0.0987 0.1314 REMARK 3 15 1.1900 - 1.1700 0.69 2238 129 0.0974 0.1161 REMARK 3 16 1.1700 - 1.1400 0.56 1823 102 0.0967 0.1179 REMARK 3 17 1.1400 - 1.1200 0.43 1417 60 0.0952 0.1463 REMARK 3 18 1.1200 - 1.1000 0.32 1062 40 0.1034 0.1615 REMARK 3 19 1.1000 - 1.0800 0.22 700 46 0.1497 0.1395 REMARK 3 20 1.0800 - 1.0600 0.08 263 15 0.2901 0.2010 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.050 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.787 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.29 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 : 0.012 1381 REMARK 3 ANGLE : 1.299 1872 REMARK 3 CHIRALITY : 0.111 200 REMARK 3 PLANARITY : 0.010 239 REMARK 3 DIHEDRAL : 14.626 521 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6TKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-16 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060 REMARK 200 RESOLUTION RANGE LOW (A) : 48.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4RN5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16 % W/V PEG3350 AND 200 MM AMMONIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.99000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 A 271 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 LYS A 377 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 O HOH A 640 O HOH A 765 2.19 REMARK 500 O HOH A 699 O HOH A 734 2.19 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 LYS A 274 -143.94 -121.68 REMARK 500 MET A 276 47.50 -146.87 REMARK 500 ASN A 313 -146.66 60.46 REMARK 500 ASN A 376 17.96 58.51 REMARK 500 THR A 413 -53.72 75.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 DBREF 6TKK A 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 6TKK B 227 232 PDB 6TKK 6TKK 227 232 SEQADV 6TKK GLY A 270 UNP O14786 EXPRESSION TAG SEQADV 6TKK HIS A 271 UNP O14786 EXPRESSION TAG SEQADV 6TKK MET A 272 UNP O14786 EXPRESSION TAG SEQRES 1 A 158 GLY HIS MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 A 158 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 A 158 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 A 158 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 A 158 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 A 158 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 A 158 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 A 158 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 A 158 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 A 158 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 A 158 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 A 158 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 A 158 ILE THR SEQRES 1 B 6 ACE ARG PRO GLN PRO ARG HET ACE B 227 3 HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HETNAM ACE ACETYL GROUP HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ACE C2 H4 O FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *195(H2 O) HELIX 1 AA1 HIS A 287 ASP A 289 5 3 HELIX 2 AA2 SER A 298 ARG A 307 5 10 SHEET 1 A 4 ILE A 291 ALA A 293 0 SHEET 2 A 4 ILE A 326 ASP A 329 -1 SHEET 3 A 4 PHE A 403 PRO A 408 -1 SHEET 4 A 4 TYR A 358 SER A 363 -1 SHEET 1 B 3 LEU A 399 THR A 401 0 SHEET 2 B 3 ARG A 334 GLN A 342 -1 SHEET 3 B 3 ARG A 418 LYS A 425 -1 SHEET 1 C 2 ALA A 338 THR A 341 0 SHEET 2 C 2 VAL A 391 VAL A 394 -1 SHEET 1 D 2 TYR A 354 THR A 357 0 SHEET 2 D 2 THR A 410 GLU A 412 -1 SSBOND 1 CYS A 275 CYS A 424 1555 1555 2.14 LINK C ACE B 227 N ARG B 228 1555 1555 1.33 SITE 1 AC1 4 THR A 410 TRP A 411 EDO A 503 PRO B 229 SITE 1 AC2 8 LYS A 274 CYS A 275 PHE A 335 VAL A 390 SITE 2 AC2 8 PRO A 398 CYS A 424 HOH A 608 HOH A 703 SITE 1 AC3 6 TYR A 297 GLY A 318 EDO A 501 HOH A 622 SITE 2 AC3 6 HOH A 714 PRO B 229 CRYST1 38.880 39.980 97.610 90.00 90.00 90.00 P 21 21 21 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 0.025720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010245 0.00000