HEADER SIGNALING PROTEIN, MEMBRANE PROTEIN 05-FEB-07 2ORX TITLE STRUCTURAL BASIS FOR LIGAND BINDING AND HEPARIN MEDIATED ACTIVATION OF TITLE 2 NEUROPILIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: F5/8 TYPE C1 AND C2 DOMAINS, RESIDUES 273-586; COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: NRP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI-2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7HMT KEYWDS NEUROPILIN, VEGF, TUFTSIN, SIGNALING PROTEIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.W.VANDER KOOI,M.A.JUSINO,B.PERMAN,D.B.NEAU,H.D.BELLAMY,D.J.LEAHY REVDAT 5 30-AUG-23 2ORX 1 REMARK REVDAT 4 13-JUL-11 2ORX 1 VERSN REVDAT 3 24-FEB-09 2ORX 1 VERSN REVDAT 2 29-APR-08 2ORX 1 JRNL REVDAT 1 03-APR-07 2ORX 0 JRNL AUTH C.W.VANDER KOOI,M.A.JUSINO,B.PERMAN,D.B.NEAU,H.D.BELLAMY, JRNL AUTH 2 D.J.LEAHY JRNL TITL STRUCTURAL BASIS FOR LIGAND AND HEPARIN BINDING TO JRNL TITL 2 NEUROPILIN B DOMAINS JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 6152 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17405859 JRNL DOI 10.1073/PNAS.0700043104 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) : 29.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 15556 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 823 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) : 838 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.4390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2510 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 198 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) : 57.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : 0.49000 REMARK 3 B33 (A**2) : -0.09000 REMARK 3 B12 (A**2) : 0.00000 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): 0.380 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.261 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.192 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.425 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2572 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3478 ; 1.405 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 313 ; 7.356 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;33.824 ;23.583 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 452 ;17.661 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.322 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 366 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1958 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1182 ; 0.199 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1716 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 187 ; 0.185 ; 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): 42 ; 0.254 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.174 ; 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): 1601 ; 0.563 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2519 ; 0.920 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1131 ; 1.302 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 959 ; 1.956 ; 4.500 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 : 6 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 273 A 324 REMARK 3 ORIGIN FOR THE GROUP (A): 9.5500 -4.4990 -19.5220 REMARK 3 T TENSOR REMARK 3 T11: -.1949 T22: -.3928 REMARK 3 T33: -.2781 T12: -.1016 REMARK 3 T13: .0044 T23: .0999 REMARK 3 L TENSOR REMARK 3 L11: 1.9899 L22: 6.8449 REMARK 3 L33: 6.1586 L12: -.5165 REMARK 3 L13: .3891 L23: -3.4765 REMARK 3 S TENSOR REMARK 3 S11: .1381 S12: .2064 S13: .3203 REMARK 3 S21: .2498 S22: -.3497 S23: -.4633 REMARK 3 S31: -.2329 S32: .7071 S33: .2116 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 325 A 355 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9320 -4.2450 -16.7450 REMARK 3 T TENSOR REMARK 3 T11: -.0702 T22: -.4446 REMARK 3 T33: -.2744 T12: -.0830 REMARK 3 T13: .0232 T23: .0323 REMARK 3 L TENSOR REMARK 3 L11: 1.2420 L22: 9.2980 REMARK 3 L33: 2.0802 L12: -.6620 REMARK 3 L13: -.0019 L23: -.4741 REMARK 3 S TENSOR REMARK 3 S11: .1669 S12: .0648 S13: .4093 REMARK 3 S21: .1625 S22: -.3248 S23: -.3871 REMARK 3 S31: -.6104 S32: .2466 S33: .1579 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 356 A 425 REMARK 3 ORIGIN FOR THE GROUP (A): .4150 -11.5450 -15.3690 REMARK 3 T TENSOR REMARK 3 T11: -.1798 T22: -.4681 REMARK 3 T33: -.3479 T12: -.0628 REMARK 3 T13: .0476 T23: -.0170 REMARK 3 L TENSOR REMARK 3 L11: 3.0495 L22: 7.5100 REMARK 3 L33: 3.4063 L12: -.7980 REMARK 3 L13: -.0232 L23: -1.4606 REMARK 3 S TENSOR REMARK 3 S11: .1869 S12: .1894 S13: .1464 REMARK 3 S21: .4901 S22: -.1249 S23: .3794 REMARK 3 S31: -.1979 S32: -.0364 S33: -.0621 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 426 A 486 REMARK 3 ORIGIN FOR THE GROUP (A): 10.8590 -41.1480 -17.6410 REMARK 3 T TENSOR REMARK 3 T11: -.2367 T22: -.4102 REMARK 3 T33: -.2664 T12: .0234 REMARK 3 T13: .0620 T23: -.0912 REMARK 3 L TENSOR REMARK 3 L11: 1.9776 L22: 2.4139 REMARK 3 L33: 3.3435 L12: -.3668 REMARK 3 L13: .8954 L23: -.1023 REMARK 3 S TENSOR REMARK 3 S11: .0375 S12: .3057 S13: -.2097 REMARK 3 S21: -.0617 S22: .0406 S23: .2040 REMARK 3 S31: -.0445 S32: .2681 S33: -.0781 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 487 A 553 REMARK 3 ORIGIN FOR THE GROUP (A): 6.6760 -40.0430 -9.0920 REMARK 3 T TENSOR REMARK 3 T11: -.1720 T22: -.4002 REMARK 3 T33: -.2002 T12: -.0172 REMARK 3 T13: .1534 T23: -.0619 REMARK 3 L TENSOR REMARK 3 L11: 3.2383 L22: 3.9018 REMARK 3 L33: 2.3861 L12: -1.4077 REMARK 3 L13: 1.8529 L23: .0170 REMARK 3 S TENSOR REMARK 3 S11: -.0612 S12: -.1589 S13: -.3202 REMARK 3 S21: .3434 S22: .0526 S23: .3917 REMARK 3 S31: -.0099 S32: -.0785 S33: .0086 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 554 A 586 REMARK 3 ORIGIN FOR THE GROUP (A): 10.2870 -40.7800 -9.6980 REMARK 3 T TENSOR REMARK 3 T11: -.1263 T22: -.3552 REMARK 3 T33: -.1931 T12: -.0083 REMARK 3 T13: .0846 T23: -.0289 REMARK 3 L TENSOR REMARK 3 L11: .6239 L22: 2.3864 REMARK 3 L33: 1.6263 L12: .2230 REMARK 3 L13: -.4444 L23: 1.5772 REMARK 3 S TENSOR REMARK 3 S11: .1639 S12: -.1926 S13: -.2846 REMARK 3 S21: .3224 S22: .0674 S23: .1024 REMARK 3 S31: .0217 S32: -.0427 S33: -.2313 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 2ORX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CAMD REMARK 200 BEAMLINE : GCPCC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.38 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16862 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1KEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.6, 10% PEG 20K, 7% REMARK 280 ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 19.04700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.05750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.11050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.05750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.04700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.11050 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 CYS A 275 59.53 -152.92 REMARK 500 TRP A 301 45.37 -144.58 REMARK 500 ASN A 313 -136.53 62.43 REMARK 500 SER A 432 38.24 -142.20 REMARK 500 LEU A 464 -84.47 -34.77 REMARK 500 ARG A 506 -134.29 61.65 REMARK 500 ARG A 513 -136.46 -97.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 2ORX A 273 586 UNP Q9QWJ9 NRP1_RAT 273 586 SEQRES 1 A 314 PHE LYS CYS MET GLU ALA LEU GLY MET GLU SER GLY GLU SEQRES 2 A 314 ILE HIS SER ASP GLN ILE THR ALA SER SER GLN TYR GLY SEQRES 3 A 314 THR ASN TRP SER VAL GLU ARG SER ARG LEU ASN TYR PRO SEQRES 4 A 314 GLU ASN GLY TRP THR PRO GLY GLU ASP SER TYR ARG GLU SEQRES 5 A 314 TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG PHE VAL THR SEQRES 6 A 314 ALA VAL GLY THR GLN GLY ALA ILE SER LYS GLU THR LYS SEQRES 7 A 314 LYS LYS TYR TYR VAL LYS THR TYR ARG VAL ASP ILE SER SEQRES 8 A 314 SER ASN GLY GLU ASP TRP ILE THR LEU LYS GLU GLY ASN SEQRES 9 A 314 LYS ALA ILE ILE PHE GLN GLY ASN THR ASN PRO THR ASP SEQRES 10 A 314 VAL VAL PHE GLY VAL PHE PRO LYS PRO LEU ILE THR ARG SEQRES 11 A 314 PHE VAL ARG ILE LYS PRO ALA SER TRP GLU THR GLY ILE SEQRES 12 A 314 SER MET ARG PHE GLU VAL TYR GLY CYS LYS ILE THR ASP SEQRES 13 A 314 TYR PRO CYS SER GLY MET LEU GLY MET VAL SER GLY LEU SEQRES 14 A 314 ILE SER ASP SER GLN ILE THR ALA SER ASN GLN GLY ASP SEQRES 15 A 314 ARG ASN TRP MET PRO GLU ASN ILE ARG LEU VAL THR SER SEQRES 16 A 314 ARG THR GLY TRP ALA LEU PRO PRO SER PRO HIS PRO TYR SEQRES 17 A 314 ILE ASN GLU TRP LEU GLN VAL ASP LEU GLY ASP GLU LYS SEQRES 18 A 314 ILE VAL ARG GLY VAL ILE ILE GLN GLY GLY LYS HIS ARG SEQRES 19 A 314 GLU ASN LYS VAL PHE MET ARG LYS PHE LYS ILE ALA TYR SEQRES 20 A 314 SER ASN ASN GLY SER ASP TRP LYS MET ILE MET ASP ASP SEQRES 21 A 314 SER LYS ARG LYS ALA LYS SER PHE GLU GLY ASN ASN ASN SEQRES 22 A 314 TYR ASP THR PRO GLU LEU ARG ALA PHE THR PRO LEU SER SEQRES 23 A 314 THR ARG PHE ILE ARG ILE TYR PRO GLU ARG ALA THR HIS SEQRES 24 A 314 SER GLY LEU GLY LEU ARG MET GLU LEU LEU GLY CYS GLU SEQRES 25 A 314 VAL GLU FORMUL 2 HOH *198(H2 O) HELIX 1 1 HIS A 287 ASP A 289 5 3 HELIX 2 2 GLY A 298 SER A 306 5 9 HELIX 3 3 SER A 443 SER A 445 5 3 HELIX 4 4 MET A 458 ARG A 463 5 6 SHEET 1 A 6 GLU A 277 ALA A 278 0 SHEET 2 A 6 ARG A 418 CYS A 424 -1 O GLY A 423 N GLU A 277 SHEET 3 A 6 ILE A 326 GLN A 342 -1 N ALA A 338 O TYR A 422 SHEET 4 A 6 VAL A 391 TRP A 411 -1 O ARG A 402 N LEU A 330 SHEET 5 A 6 VAL A 355 SER A 363 -1 N THR A 357 O ALA A 409 SHEET 6 A 6 TRP A 369 THR A 371 -1 O ILE A 370 N ILE A 362 SHEET 1 B 5 ILE A 291 ALA A 293 0 SHEET 2 B 5 ILE A 326 GLN A 342 -1 O GLN A 327 N THR A 292 SHEET 3 B 5 VAL A 391 TRP A 411 -1 O ARG A 402 N LEU A 330 SHEET 4 B 5 VAL A 355 SER A 363 -1 N THR A 357 O ALA A 409 SHEET 5 B 5 PHE A 381 GLN A 382 -1 O PHE A 381 N TYR A 358 SHEET 1 C 2 ALA A 344 ILE A 345 0 SHEET 2 C 2 LYS A 352 TYR A 353 -1 O TYR A 353 N ALA A 344 SHEET 1 D 2 LYS A 373 GLU A 374 0 SHEET 2 D 2 LYS A 377 ALA A 378 -1 O LYS A 377 N GLU A 374 SHEET 1 E 4 GLY A 433 MET A 434 0 SHEET 2 E 4 LEU A 574 CYS A 583 -1 O GLY A 582 N GLY A 433 SHEET 3 E 4 LEU A 485 GLN A 501 -1 N ILE A 494 O CYS A 583 SHEET 4 E 4 TRP A 471 LEU A 473 0 SHEET 1 F 6 ILE A 447 ALA A 449 0 SHEET 2 F 6 LEU A 485 GLN A 501 -1 O GLN A 486 N THR A 448 SHEET 3 F 6 LEU A 574 CYS A 583 -1 O CYS A 583 N ILE A 494 SHEET 4 F 6 GLU A 550 PRO A 566 0 SHEET 5 F 6 PHE A 515 SER A 520 -1 N LYS A 516 O TYR A 565 SHEET 6 F 6 LYS A 527 MET A 528 -1 O LYS A 527 N TYR A 519 SHEET 1 G 2 GLY A 503 HIS A 505 0 SHEET 2 G 2 ASN A 508 VAL A 510 -1 O ASN A 508 N HIS A 505 SSBOND 1 CYS A 275 CYS A 424 1555 1555 2.05 SSBOND 2 CYS A 431 CYS A 583 1555 1555 2.04 CRYST1 38.094 92.221 120.115 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 0.026251 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008325 0.00000