HEADER SIGNALING PROTEIN 06-SEP-12 4GZ9 TITLE MOUSE NEUROPILIN-1, EXTRACELLULAR DOMAINS 1-4 (A1A2B1B2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-586; COMPND 5 SYNONYM: A5 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NRP1, NRP; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS MULTI-DOMAIN, CELL-CELL SIGNALING, PLEXIN, SEMAPHORIN, VEGF, KEYWDS 2 GLYCOSILATED, TRANSMEMBRANE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.J.C.JANSSEN,T.MALINAUSKAS,C.SIEBOLD,E.Y.JONES REVDAT 5 08-NOV-23 4GZ9 1 HETSYN REVDAT 4 29-JUL-20 4GZ9 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 26-DEC-12 4GZ9 1 JRNL REVDAT 2 07-NOV-12 4GZ9 1 JRNL REVDAT 1 17-OCT-12 4GZ9 0 JRNL AUTH B.J.C.JANSSEN,T.MALINAUSKAS,G.A.WEIR,M.Z.CADER,C.SIEBOLD, JRNL AUTH 2 E.Y.JONES JRNL TITL NEUROPILINS LOCK SECRETED SEMAPHORINS ONTO PLEXINS IN A JRNL TITL 2 TERNARY SIGNALING COMPLEX. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1293 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23104057 JRNL DOI 10.1038/NSMB.2416 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 42837 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 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 : 2241 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3058 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4472 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.61000 REMARK 3 B22 (A**2) : 1.61000 REMARK 3 B33 (A**2) : -2.42000 REMARK 3 B12 (A**2) : 0.81000 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): 0.238 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.201 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.542 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4709 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4394 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6393 ; 1.582 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9994 ; 0.761 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 561 ; 7.096 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 215 ;34.049 ;23.814 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 773 ;16.835 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;17.694 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 672 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5236 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1066 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 141 REMARK 3 RESIDUE RANGE : A 608 A 608 REMARK 3 RESIDUE RANGE : A 729 A 729 REMARK 3 ORIGIN FOR THE GROUP (A): -41.6623 92.3368 15.8478 REMARK 3 T TENSOR REMARK 3 T11: 0.4730 T22: 0.4799 REMARK 3 T33: 0.4585 T12: -0.0790 REMARK 3 T13: -0.2242 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 5.3572 L22: 5.1089 REMARK 3 L33: 5.3431 L12: 3.0529 REMARK 3 L13: 1.3565 L23: 2.2313 REMARK 3 S TENSOR REMARK 3 S11: -0.1953 S12: 0.6375 S13: 0.4560 REMARK 3 S21: -0.5499 S22: -0.0669 S23: 0.1981 REMARK 3 S31: -0.9301 S32: -0.2495 S33: 0.2622 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 142 A 264 REMARK 3 RESIDUE RANGE : A 607 A 607 REMARK 3 RESIDUE RANGE : A 728 A 728 REMARK 3 RESIDUE RANGE : A 601 A 606 REMARK 3 ORIGIN FOR THE GROUP (A): -72.3945 62.0000 13.2667 REMARK 3 T TENSOR REMARK 3 T11: 0.0541 T22: 0.4014 REMARK 3 T33: 0.3372 T12: 0.0384 REMARK 3 T13: -0.0237 T23: -0.0880 REMARK 3 L TENSOR REMARK 3 L11: 7.2302 L22: 3.7769 REMARK 3 L33: 5.9030 L12: 0.9480 REMARK 3 L13: 3.2078 L23: 1.4511 REMARK 3 S TENSOR REMARK 3 S11: 0.2355 S12: -0.0370 S13: -0.3748 REMARK 3 S21: 0.3240 S22: -0.0281 S23: -0.7239 REMARK 3 S31: 0.2100 S32: 0.3814 S33: -0.2074 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 265 A 424 REMARK 3 ORIGIN FOR THE GROUP (A):-103.0745 52.2818 22.9430 REMARK 3 T TENSOR REMARK 3 T11: 0.0781 T22: 0.1627 REMARK 3 T33: 0.0527 T12: 0.0230 REMARK 3 T13: -0.0491 T23: -0.0650 REMARK 3 L TENSOR REMARK 3 L11: 1.8552 L22: 2.8676 REMARK 3 L33: 6.8155 L12: 0.9991 REMARK 3 L13: -0.6922 L23: -1.6519 REMARK 3 S TENSOR REMARK 3 S11: 0.0466 S12: 0.0663 S13: -0.0327 REMARK 3 S21: 0.0513 S22: 0.0493 S23: -0.0018 REMARK 3 S31: 0.4296 S32: -0.1433 S33: -0.0959 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 425 A 586 REMARK 3 ORIGIN FOR THE GROUP (A): -98.7828 75.9848 0.9437 REMARK 3 T TENSOR REMARK 3 T11: 0.0682 T22: 0.2121 REMARK 3 T33: 0.0691 T12: -0.0096 REMARK 3 T13: 0.0398 T23: -0.0498 REMARK 3 L TENSOR REMARK 3 L11: 2.7302 L22: 4.9120 REMARK 3 L33: 3.7351 L12: -1.5889 REMARK 3 L13: -0.5795 L23: -0.7361 REMARK 3 S TENSOR REMARK 3 S11: 0.1059 S12: 0.1053 S13: 0.2641 REMARK 3 S21: -0.0537 S22: 0.1790 S23: -0.1073 REMARK 3 S31: -0.4861 S32: 0.0348 S33: -0.2849 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4GZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9173 REMARK 200 MONOCHROMATOR : SINGLE BOUNCE MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45127 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 81.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 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: PHASER REMARK 200 STARTING MODEL: 2QQM, 2QQK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, 1.5M LITHIUM REMARK 280 SULPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 47.93000 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 GLU A 19 REMARK 465 THR A 20 REMARK 465 GLY A 21 REMARK 465 PHE A 22 REMARK 465 ARG A 23 REMARK 465 SER A 24 REMARK 465 ARG A 587 REMARK 465 THR A 588 REMARK 465 LYS A 589 REMARK 465 HIS A 590 REMARK 465 HIS A 591 REMARK 465 HIS A 592 REMARK 465 HIS A 593 REMARK 465 HIS A 594 REMARK 465 HIS A 595 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 GLU A 34 -79.03 -114.36 REMARK 500 HIS A 46 -61.47 -92.22 REMARK 500 ASP A 76 107.97 -161.17 REMARK 500 ASP A 81 49.17 -20.79 REMARK 500 GLU A 128 -156.32 -91.73 REMARK 500 THR A 129 145.39 -26.13 REMARK 500 LYS A 181 19.89 59.95 REMARK 500 SER A 198 -78.84 -65.27 REMARK 500 TYR A 208 -75.12 -102.49 REMARK 500 VAL A 220 -45.65 -131.20 REMARK 500 PRO A 233 -3.90 -48.46 REMARK 500 ILE A 253 118.52 36.91 REMARK 500 SER A 267 97.97 -62.25 REMARK 500 SER A 268 75.71 -116.80 REMARK 500 ASP A 272 69.30 -111.43 REMARK 500 ASN A 313 -152.44 61.81 REMARK 500 THR A 413 -19.18 18.11 REMARK 500 THR A 469 -91.95 -130.04 REMARK 500 ASN A 482 49.47 35.91 REMARK 500 ARG A 496 -30.18 -141.31 REMARK 500 LYS A 514 132.33 -175.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 80 ASP A 81 -149.18 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 CA A 606 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 78 OE1 REMARK 620 2 ASP A 85 OD2 85.3 REMARK 620 3 ASP A 126 OD1 97.5 102.0 REMARK 620 4 GLU A 128 O 111.7 147.8 102.5 REMARK 620 5 THR A 129 O 81.8 86.4 171.5 70.0 REMARK 620 6 HOH A 729 O 164.5 81.9 93.8 76.0 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 605 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 195 OE1 REMARK 620 2 ASP A 209 OD2 83.8 REMARK 620 3 ASP A 209 OD1 92.3 53.0 REMARK 620 4 ASP A 250 OD1 90.0 117.6 65.4 REMARK 620 5 ALA A 252 O 95.4 161.1 145.8 81.3 REMARK 620 6 ILE A 253 O 84.3 90.2 143.1 150.9 70.9 REMARK 620 7 HOH A 728 O 177.5 95.3 89.0 92.6 84.7 93.3 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GZ8 RELATED DB: PDB REMARK 900 RELATED ID: 4GZA RELATED DB: PDB DBREF 4GZ9 A 22 586 UNP P97333 NRP1_MOUSE 22 586 SEQADV 4GZ9 GLU A 19 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 THR A 20 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 GLY A 21 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 ARG A 587 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 THR A 588 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 LYS A 589 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 HIS A 590 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 HIS A 591 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 HIS A 592 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 HIS A 593 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 HIS A 594 UNP P97333 EXPRESSION TAG SEQADV 4GZ9 HIS A 595 UNP P97333 EXPRESSION TAG SEQRES 1 A 577 GLU THR GLY PHE ARG SER ASP LYS CYS GLY GLY THR ILE SEQRES 2 A 577 LYS ILE GLU ASN PRO GLY TYR LEU THR SER PRO GLY TYR SEQRES 3 A 577 PRO HIS SER TYR HIS PRO SER GLU LYS CYS GLU TRP LEU SEQRES 4 A 577 ILE GLN ALA PRO GLU PRO TYR GLN ARG ILE MET ILE ASN SEQRES 5 A 577 PHE ASN PRO HIS PHE ASP LEU GLU ASP ARG ASP CYS LYS SEQRES 6 A 577 TYR ASP TYR VAL GLU VAL ILE ASP GLY GLU ASN GLU GLY SEQRES 7 A 577 GLY ARG LEU TRP GLY LYS PHE CYS GLY LYS ILE ALA PRO SEQRES 8 A 577 SER PRO VAL VAL SER SER GLY PRO PHE LEU PHE ILE LYS SEQRES 9 A 577 PHE VAL SER ASP TYR GLU THR HIS GLY ALA GLY PHE SER SEQRES 10 A 577 ILE ARG TYR GLU ILE PHE LYS ARG GLY PRO GLU CYS SER SEQRES 11 A 577 GLN ASN TYR THR ALA PRO THR GLY VAL ILE LYS SER PRO SEQRES 12 A 577 GLY PHE PRO GLU LYS TYR PRO ASN SER LEU GLU CYS THR SEQRES 13 A 577 TYR ILE ILE PHE ALA PRO LYS MET SER GLU ILE ILE LEU SEQRES 14 A 577 GLU PHE GLU SER PHE ASP LEU GLU GLN ASP SER ASN PRO SEQRES 15 A 577 PRO GLY GLY MET PHE CYS ARG TYR ASP ARG LEU GLU ILE SEQRES 16 A 577 TRP ASP GLY PHE PRO GLU VAL GLY PRO HIS ILE GLY ARG SEQRES 17 A 577 TYR CYS GLY GLN LYS THR PRO GLY ARG ILE ARG SER SER SEQRES 18 A 577 SER GLY VAL LEU SER MET VAL PHE TYR THR ASP SER ALA SEQRES 19 A 577 ILE ALA LYS GLU GLY PHE SER ALA ASN TYR SER VAL LEU SEQRES 20 A 577 GLN SER SER ILE SER GLU ASP PHE LYS CYS MET GLU ALA SEQRES 21 A 577 LEU GLY MET GLU SER GLY GLU ILE HIS SER ASP GLN ILE SEQRES 22 A 577 THR ALA SER SER GLN TYR GLY THR ASN TRP SER VAL GLU SEQRES 23 A 577 ARG SER ARG LEU ASN TYR PRO GLU ASN GLY TRP THR PRO SEQRES 24 A 577 GLY GLU ASP SER TYR LYS GLU TRP ILE GLN VAL ASP LEU SEQRES 25 A 577 GLY LEU LEU ARG PHE VAL THR ALA VAL GLY THR GLN GLY SEQRES 26 A 577 ALA ILE SER LYS GLU THR LYS LYS LYS TYR TYR VAL LYS SEQRES 27 A 577 THR TYR ARG VAL ASP ILE SER SER ASN GLY GLU ASP TRP SEQRES 28 A 577 ILE SER LEU LYS GLU GLY ASN LYS ALA ILE ILE PHE GLN SEQRES 29 A 577 GLY ASN THR ASN PRO THR ASP VAL VAL LEU GLY VAL PHE SEQRES 30 A 577 SER LYS PRO LEU ILE THR ARG PHE VAL ARG ILE LYS PRO SEQRES 31 A 577 VAL SER TRP GLU THR GLY ILE SER MET ARG PHE GLU VAL SEQRES 32 A 577 TYR GLY CYS LYS ILE THR ASP TYR PRO CYS SER GLY MET SEQRES 33 A 577 LEU GLY MET VAL SER GLY LEU ILE SER ASP SER GLN ILE SEQRES 34 A 577 THR ALA SER ASN GLN ALA ASP ARG ASN TRP MET PRO GLU SEQRES 35 A 577 ASN ILE ARG LEU VAL THR SER ARG THR GLY TRP ALA LEU SEQRES 36 A 577 PRO PRO SER PRO HIS PRO TYR THR ASN GLU TRP LEU GLN SEQRES 37 A 577 VAL ASP LEU GLY ASP GLU LYS ILE VAL ARG GLY VAL ILE SEQRES 38 A 577 ILE GLN GLY GLY LYS HIS ARG GLU ASN LYS VAL PHE MET SEQRES 39 A 577 ARG LYS PHE LYS ILE ALA TYR SER ASN ASN GLY SER ASP SEQRES 40 A 577 TRP LYS THR ILE MET ASP ASP SER LYS ARG LYS ALA LYS SEQRES 41 A 577 SER PHE GLU GLY ASN ASN ASN TYR ASP THR PRO GLU LEU SEQRES 42 A 577 ARG THR PHE SER PRO LEU SER THR ARG PHE ILE ARG ILE SEQRES 43 A 577 TYR PRO GLU ARG ALA THR HIS SER GLY LEU GLY LEU ARG SEQRES 44 A 577 MET GLU LEU LEU GLY CYS GLU VAL GLU ARG THR LYS HIS SEQRES 45 A 577 HIS HIS HIS HIS HIS MODRES 4GZ9 ASN A 150 ASN GLYCOSYLATION SITE MODRES 4GZ9 ASN A 261 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG A 604 14 HET CA A 605 1 HET CA A 606 1 HET SO4 A 607 5 HET SO4 A 608 5 HET EDO A 609 4 HET EDO A 610 4 HET EDO A 611 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 4 CA 2(CA 2+) FORMUL 6 SO4 2(O4 S 2-) FORMUL 8 EDO 3(C2 H6 O2) FORMUL 11 HOH *29(H2 O) HELIX 1 1 ASP A 79 LYS A 83 5 5 HELIX 2 2 PRO A 180 SER A 183 5 4 HELIX 3 3 HIS A 287 ASP A 289 5 3 HELIX 4 4 GLY A 298 SER A 306 5 9 HELIX 5 5 LYS A 425 TYR A 429 5 5 HELIX 6 6 SER A 443 SER A 445 5 3 HELIX 7 7 MET A 458 ARG A 463 5 6 SHEET 1 A 5 GLY A 29 LYS A 32 0 SHEET 2 A 5 LYS A 53 GLN A 59 1 O LEU A 57 N GLY A 29 SHEET 3 A 5 PHE A 118 VAL A 124 -1 O ILE A 121 N TRP A 56 SHEET 4 A 5 TYR A 86 ASP A 91 -1 N GLU A 88 O LYS A 122 SHEET 5 A 5 ARG A 98 PHE A 103 -1 O ARG A 98 N ASP A 91 SHEET 1 B 4 GLY A 37 THR A 40 0 SHEET 2 B 4 SER A 135 ILE A 140 -1 O ILE A 136 N LEU A 39 SHEET 3 B 4 ILE A 67 PHE A 71 -1 N MET A 68 O GLU A 139 SHEET 4 B 4 VAL A 112 VAL A 113 -1 O VAL A 112 N ILE A 69 SHEET 1 C 5 GLU A 146 TYR A 151 0 SHEET 2 C 5 GLU A 172 PHE A 178 1 O PHE A 178 N TYR A 151 SHEET 3 C 5 VAL A 242 TYR A 248 -1 O MET A 245 N TYR A 175 SHEET 4 C 5 ARG A 210 TRP A 214 -1 N TRP A 214 O SER A 244 SHEET 5 C 5 HIS A 223 TYR A 227 -1 O ILE A 224 N ILE A 213 SHEET 1 D 4 THR A 155 LYS A 159 0 SHEET 2 D 4 GLY A 257 VAL A 264 -1 O ALA A 260 N ILE A 158 SHEET 3 D 4 ILE A 185 ASP A 193 -1 N ILE A 186 O SER A 263 SHEET 4 D 4 ILE A 236 SER A 238 -1 O SER A 238 N ILE A 185 SHEET 1 E 6 GLU A 277 ALA A 278 0 SHEET 2 E 6 ARG A 418 CYS A 424 -1 O GLY A 423 N GLU A 277 SHEET 3 E 6 ILE A 326 GLN A 342 -1 N GLN A 342 O ARG A 418 SHEET 4 E 6 VAL A 391 GLU A 412 -1 O ILE A 406 N ILE A 326 SHEET 5 E 6 LYS A 352 SER A 363 -1 N ASP A 361 O ARG A 405 SHEET 6 E 6 ALA A 344 ILE A 345 -1 N ALA A 344 O TYR A 353 SHEET 1 F 5 ILE A 291 ALA A 293 0 SHEET 2 F 5 ILE A 326 GLN A 342 -1 O GLN A 327 N THR A 292 SHEET 3 F 5 VAL A 391 GLU A 412 -1 O ILE A 406 N ILE A 326 SHEET 4 F 5 LYS A 352 SER A 363 -1 N ASP A 361 O ARG A 405 SHEET 5 F 5 ILE A 370 SER A 371 -1 O ILE A 370 N ILE A 362 SHEET 1 G 3 ALA A 344 ILE A 345 0 SHEET 2 G 3 LYS A 352 SER A 363 -1 O TYR A 353 N ALA A 344 SHEET 3 G 3 PHE A 381 GLN A 382 -1 O PHE A 381 N TYR A 358 SHEET 1 H 4 GLY A 433 MET A 434 0 SHEET 2 H 4 LEU A 574 CYS A 583 -1 O GLY A 582 N GLY A 433 SHEET 3 H 4 LEU A 485 GLN A 501 -1 N ILE A 499 O GLU A 579 SHEET 4 H 4 ILE A 447 ALA A 449 -1 N THR A 448 O GLN A 486 SHEET 1 I 6 TRP A 471 LEU A 473 0 SHEET 2 I 6 LEU A 574 CYS A 583 -1 O LEU A 576 N TRP A 471 SHEET 3 I 6 LEU A 485 GLN A 501 -1 N ILE A 499 O GLU A 579 SHEET 4 I 6 GLU A 550 ALA A 569 -1 O LEU A 557 N VAL A 495 SHEET 5 I 6 MET A 512 SER A 520 -1 N LYS A 514 O GLU A 567 SHEET 6 I 6 PHE A 540 GLU A 541 -1 O PHE A 540 N PHE A 515 SHEET 1 J 5 ILE A 447 ALA A 449 0 SHEET 2 J 5 LEU A 485 GLN A 501 -1 O GLN A 486 N THR A 448 SHEET 3 J 5 GLU A 550 ALA A 569 -1 O LEU A 557 N VAL A 495 SHEET 4 J 5 MET A 512 SER A 520 -1 N LYS A 514 O GLU A 567 SHEET 5 J 5 LYS A 527 THR A 528 -1 O LYS A 527 N TYR A 519 SHEET 1 K 2 GLY A 503 LYS A 504 0 SHEET 2 K 2 LYS A 509 VAL A 510 -1 O VAL A 510 N GLY A 503 SSBOND 1 CYS A 27 CYS A 54 1555 1555 2.06 SSBOND 2 CYS A 82 CYS A 104 1555 1555 2.06 SSBOND 3 CYS A 147 CYS A 173 1555 1555 2.05 SSBOND 4 CYS A 206 CYS A 228 1555 1555 2.08 SSBOND 5 CYS A 275 CYS A 424 1555 1555 2.11 SSBOND 6 CYS A 431 CYS A 583 1555 1555 2.13 LINK ND2 ASN A 150 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 261 C1 NAG A 604 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.43 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.46 LINK OE1 GLU A 78 CA CA A 606 1555 1555 2.44 LINK OD2 ASP A 85 CA CA A 606 1555 1555 2.32 LINK OD1 ASP A 126 CA CA A 606 1555 1555 2.37 LINK O GLU A 128 CA CA A 606 1555 1555 2.42 LINK O THR A 129 CA CA A 606 1555 1555 2.30 LINK OE1 GLU A 195 CA CA A 605 1555 1555 2.36 LINK OD2 ASP A 209 CA CA A 605 1555 1555 2.28 LINK OD1 ASP A 209 CA CA A 605 1555 1555 2.57 LINK OD1 ASP A 250 CA CA A 605 1555 1555 2.33 LINK O ALA A 252 CA CA A 605 1555 1555 2.25 LINK O ILE A 253 CA CA A 605 1555 1555 2.23 LINK CA CA A 605 O HOH A 728 1555 1555 2.37 LINK CA CA A 606 O HOH A 729 1555 1555 2.33 CISPEP 1 TYR A 44 PRO A 45 0 7.04 CISPEP 2 PHE A 163 PRO A 164 0 9.85 CRYST1 245.359 245.359 47.930 90.00 90.00 120.00 P 3 2 1 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 0.004076 0.002353 0.000000 0.00000 SCALE2 0.000000 0.004706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020864 0.00000