HEADER SIGNALING PROTEIN 29-MAR-16 5J1X TITLE X-RAY STRUCTURE OF NEUROPILIN-1 B1 DOMAIN COMPLEXED WITH ARG-5 LIGAND. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR; 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: NRP1, NRP, VEGF165R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA-GAMI2-PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET15B-TEV; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B-TEV-NRP1B1 KEYWDS SIGNALING PROTEIN, NEUROPILIN-1, ANGIOGENESIS EXPDTA X-RAY DIFFRACTION AUTHOR C.FOTINOU,R.RANA,S.DJORDJEVIC,T.YELLAND REVDAT 6 13-NOV-24 5J1X 1 REMARK REVDAT 5 10-JAN-24 5J1X 1 REMARK REVDAT 4 11-JUL-18 5J1X 1 JRNL REVDAT 3 28-FEB-18 5J1X 1 JRNL REVDAT 2 29-NOV-17 5J1X 1 REMARK REVDAT 1 05-APR-17 5J1X 0 JRNL AUTH F.MOTA,C.FOTINOU,R.R.RANA,A.W.E.CHAN,T.YELLAND,M.T.AROOZ, JRNL AUTH 2 A.P.O'LEARY,J.HUTTON,P.FRANKEL,I.ZACHARY,D.SELWOOD, JRNL AUTH 3 S.DJORDJEVIC JRNL TITL ARCHITECTURE AND HYDRATION OF THE ARGININE-BINDING SITE OF JRNL TITL 2 NEUROPILIN-1. JRNL REF FEBS J. V. 285 1290 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 29430837 JRNL DOI 10.1111/FEBS.14405 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 33165 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1728 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2426 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4953 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 431 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.99000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 1.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.273 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.395 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5198 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4897 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7061 ; 1.517 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11303 ; 1.218 ; 2.977 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 632 ; 6.852 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 225 ;35.780 ;24.089 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 897 ;12.535 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;15.136 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 768 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5826 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1187 ; 0.007 ; 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): 2496 ; 0.991 ; 1.672 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2491 ; 0.988 ; 1.669 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3112 ; 1.716 ; 2.498 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3113 ; 1.715 ; 2.498 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2702 ; 1.290 ; 1.881 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2703 ; 1.290 ; 1.882 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3942 ; 2.182 ; 2.752 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5982 ; 4.283 ;14.094 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5983 ; 4.283 ;14.099 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 274 426 B 274 426 18386 0.08 0.05 REMARK 3 2 A 273 426 C 273 426 18346 0.10 0.05 REMARK 3 3 A 273 427 D 273 427 18442 0.11 0.05 REMARK 3 4 B 274 426 C 274 426 18570 0.09 0.05 REMARK 3 5 B 274 426 D 274 426 18494 0.10 0.05 REMARK 3 6 C 273 426 D 273 426 19102 0.07 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 427 REMARK 3 ORIGIN FOR THE GROUP (A): 40.1103 19.2466 21.2856 REMARK 3 T TENSOR REMARK 3 T11: 0.0126 T22: 0.0065 REMARK 3 T33: 0.0558 T12: -0.0003 REMARK 3 T13: -0.0107 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.7736 L22: 0.3021 REMARK 3 L33: 0.7840 L12: 0.1664 REMARK 3 L13: 0.3115 L23: 0.4396 REMARK 3 S TENSOR REMARK 3 S11: -0.0207 S12: 0.0311 S13: 0.0545 REMARK 3 S21: 0.0085 S22: -0.0075 S23: 0.0215 REMARK 3 S31: -0.0227 S32: -0.0057 S33: 0.0282 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 : B 274 B 427 REMARK 3 ORIGIN FOR THE GROUP (A): 34.1306 19.1390 60.8675 REMARK 3 T TENSOR REMARK 3 T11: 0.0368 T22: 0.0295 REMARK 3 T33: 0.0265 T12: 0.0135 REMARK 3 T13: -0.0265 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.6002 L22: 0.6270 REMARK 3 L33: 0.9376 L12: 0.1038 REMARK 3 L13: 0.3489 L23: 0.5684 REMARK 3 S TENSOR REMARK 3 S11: -0.0369 S12: 0.0649 S13: -0.0071 REMARK 3 S21: 0.0058 S22: -0.0621 S23: 0.0208 REMARK 3 S31: -0.1140 S32: -0.0771 S33: 0.0990 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 : C 272 C 427 REMARK 3 ORIGIN FOR THE GROUP (A): 51.3619 -3.6060 42.4283 REMARK 3 T TENSOR REMARK 3 T11: 0.0138 T22: 0.0282 REMARK 3 T33: 0.0068 T12: 0.0015 REMARK 3 T13: -0.0032 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.3286 L22: 0.8565 REMARK 3 L33: 0.8039 L12: -0.6605 REMARK 3 L13: -0.2584 L23: 0.2304 REMARK 3 S TENSOR REMARK 3 S11: 0.0891 S12: 0.0961 S13: 0.0054 REMARK 3 S21: 0.0003 S22: -0.0454 S23: 0.0043 REMARK 3 S31: 0.0129 S32: -0.0277 S33: -0.0437 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 : D 273 D 427 REMARK 3 ORIGIN FOR THE GROUP (A): 57.6529 -3.6171 2.2189 REMARK 3 T TENSOR REMARK 3 T11: 0.0117 T22: 0.0350 REMARK 3 T33: 0.0210 T12: 0.0109 REMARK 3 T13: -0.0053 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.6200 L22: 0.9364 REMARK 3 L33: 0.6875 L12: -0.3391 REMARK 3 L13: -0.1626 L23: 0.2127 REMARK 3 S TENSOR REMARK 3 S11: 0.0521 S12: 0.0896 S13: -0.0023 REMARK 3 S21: 0.0430 S22: 0.0072 S23: -0.0449 REMARK 3 S31: -0.0106 S32: -0.0588 S33: -0.0594 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 REMARK 4 REMARK 4 5J1X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47057 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.08600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: 1KEX REMARK 200 REMARK 200 REMARK: NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% W/V PEG3350, 0.2M NH4CL, PH 7.9, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 45.24000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 270 REMARK 465 HIS A 271 REMARK 465 MET A 272 REMARK 465 GLY B 270 REMARK 465 HIS B 271 REMARK 465 MET B 272 REMARK 465 PHE B 273 REMARK 465 GLY C 270 REMARK 465 HIS C 271 REMARK 465 GLY D 270 REMARK 465 HIS D 271 REMARK 465 MET D 272 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 68.68 -152.67 REMARK 500 SER A 298 -179.87 -172.81 REMARK 500 ASN A 313 -139.54 59.51 REMARK 500 THR A 413 -49.24 77.38 REMARK 500 SER B 298 -179.90 -172.00 REMARK 500 ASN B 313 -137.70 59.59 REMARK 500 THR B 413 -49.22 76.67 REMARK 500 CYS C 275 69.66 -150.62 REMARK 500 ASN C 313 -137.63 57.89 REMARK 500 THR C 413 -49.23 76.71 REMARK 500 CYS D 275 71.16 -151.72 REMARK 500 ASN D 313 -138.46 60.75 REMARK 500 THR D 413 -50.14 75.54 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 AR5 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AR5 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AR5 C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AR5 D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS D 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IJR RELATED DB: PDB REMARK 900 RELATED ID: 1KEX RELATED DB: PDB REMARK 900 RELATED ID: 3I97 RELATED DB: PDB REMARK 900 RELATED ID: 5IYY RELATED DB: PDB DBREF 5J1X A 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 5J1X B 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 5J1X C 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 5J1X D 273 427 UNP O14786 NRP1_HUMAN 273 427 SEQADV 5J1X GLY A 270 UNP O14786 EXPRESSION TAG SEQADV 5J1X HIS A 271 UNP O14786 EXPRESSION TAG SEQADV 5J1X MET A 272 UNP O14786 EXPRESSION TAG SEQADV 5J1X GLY B 270 UNP O14786 EXPRESSION TAG SEQADV 5J1X HIS B 271 UNP O14786 EXPRESSION TAG SEQADV 5J1X MET B 272 UNP O14786 EXPRESSION TAG SEQADV 5J1X GLY C 270 UNP O14786 EXPRESSION TAG SEQADV 5J1X HIS C 271 UNP O14786 EXPRESSION TAG SEQADV 5J1X MET C 272 UNP O14786 EXPRESSION TAG SEQADV 5J1X GLY D 270 UNP O14786 EXPRESSION TAG SEQADV 5J1X HIS D 271 UNP O14786 EXPRESSION TAG SEQADV 5J1X MET D 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 158 GLY HIS MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 B 158 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 B 158 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 B 158 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 B 158 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 B 158 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 B 158 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 B 158 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 B 158 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 B 158 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 B 158 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 B 158 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 B 158 ILE THR SEQRES 1 C 158 GLY HIS MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 C 158 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 C 158 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 C 158 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 C 158 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 C 158 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 C 158 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 C 158 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 C 158 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 C 158 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 C 158 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 C 158 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 C 158 ILE THR SEQRES 1 D 158 GLY HIS MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 D 158 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 D 158 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 D 158 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 D 158 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 D 158 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 D 158 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 D 158 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 D 158 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 D 158 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 D 158 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 D 158 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 D 158 ILE THR HET AR5 A 501 19 HET AR5 B 501 19 HET AR5 C 501 19 HET AR5 D 501 19 HET DMS D 502 4 HETNAM AR5 N~2~-(TERT-BUTOXYCARBONYL)-L-ARGININE HETNAM DMS DIMETHYL SULFOXIDE FORMUL 5 AR5 4(C11 H22 N4 O4) FORMUL 9 DMS C2 H6 O S FORMUL 10 HOH *431(H2 O) HELIX 1 AA1 HIS A 287 ASP A 289 5 3 HELIX 2 AA2 SER A 298 ARG A 307 5 10 HELIX 3 AA3 HIS B 287 ASP B 289 5 3 HELIX 4 AA4 SER B 298 ARG B 307 5 10 HELIX 5 AA5 HIS C 287 ASP C 289 5 3 HELIX 6 AA6 SER C 298 ARG C 307 5 10 HELIX 7 AA7 HIS D 287 ASP D 289 5 3 HELIX 8 AA8 SER D 298 ARG D 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 CYS A 424 -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 SHEET 1 E 5 ILE B 291 ALA B 293 0 SHEET 2 E 5 ILE B 326 ASP B 329 -1 SHEET 3 E 5 PHE B 403 PRO B 408 -1 SHEET 4 E 5 TYR B 358 SER B 363 -1 SHEET 5 E 5 TRP B 369 THR B 371 -1 SHEET 1 F 3 LEU B 399 THR B 401 0 SHEET 2 F 3 ARG B 334 GLN B 342 -1 SHEET 3 F 3 ARG B 418 CYS B 424 -1 SHEET 1 G 2 ALA B 338 THR B 341 0 SHEET 2 G 2 VAL B 391 VAL B 394 -1 SHEET 1 H 2 TYR B 354 THR B 357 0 SHEET 2 H 2 THR B 410 GLU B 412 -1 SHEET 1 I 4 ILE C 291 ALA C 293 0 SHEET 2 I 4 ILE C 326 ASP C 329 -1 SHEET 3 I 4 PHE C 403 PRO C 408 -1 SHEET 4 I 4 TYR C 358 SER C 363 -1 SHEET 1 J 3 LEU C 399 THR C 401 0 SHEET 2 J 3 ARG C 334 GLN C 342 -1 SHEET 3 J 3 ARG C 418 CYS C 424 -1 SHEET 1 K 2 ALA C 338 THR C 341 0 SHEET 2 K 2 VAL C 391 VAL C 394 -1 SHEET 1 L 2 TYR C 354 THR C 357 0 SHEET 2 L 2 THR C 410 GLU C 412 -1 SHEET 1 M 4 ILE D 291 ALA D 293 0 SHEET 2 M 4 ILE D 326 ASP D 329 -1 SHEET 3 M 4 PHE D 403 PRO D 408 -1 SHEET 4 M 4 TYR D 358 SER D 363 -1 SHEET 1 N 3 LEU D 399 THR D 401 0 SHEET 2 N 3 ARG D 334 GLN D 342 -1 SHEET 3 N 3 ARG D 418 CYS D 424 -1 SHEET 1 O 2 ALA D 338 THR D 341 0 SHEET 2 O 2 VAL D 391 VAL D 394 -1 SHEET 1 P 2 TYR D 354 THR D 357 0 SHEET 2 P 2 THR D 410 GLU D 412 -1 SSBOND 1 CYS A 275 CYS A 424 1555 1555 2.08 SSBOND 2 CYS B 275 CYS B 424 1555 1555 2.03 SSBOND 3 CYS C 275 CYS C 424 1555 1555 2.08 SSBOND 4 CYS D 275 CYS D 424 1555 1555 2.09 SITE 1 AC1 12 TYR A 297 TRP A 301 THR A 316 ASP A 320 SITE 2 AC1 12 SER A 346 THR A 349 TYR A 353 GLY A 414 SITE 3 AC1 12 ILE A 415 HOH A 602 HOH A 624 MET D 276 SITE 1 AC2 12 TYR B 297 TRP B 301 THR B 316 ASP B 320 SITE 2 AC2 12 SER B 346 THR B 349 TYR B 353 GLY B 414 SITE 3 AC2 12 ILE B 415 HOH B 603 HOH B 641 MET C 276 SITE 1 AC3 9 THR C 316 ASP C 320 SER C 346 THR C 349 SITE 2 AC3 9 LYS C 351 TYR C 353 GLY C 414 ILE C 415 SITE 3 AC3 9 HOH C 638 SITE 1 AC4 11 TRP D 301 THR D 316 ASP D 320 SER D 346 SITE 2 AC4 11 THR D 349 TYR D 353 GLY D 414 ILE D 415 SITE 3 AC4 11 HOH D 601 HOH D 643 HOH D 649 SITE 1 AC5 3 TYR D 322 THR D 410 TRP D 411 CRYST1 41.590 90.480 81.890 90.00 99.64 90.00 P 1 21 1 8 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 0.024044 0.000000 0.004084 0.00000 SCALE2 0.000000 0.011052 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012386 0.00000