PDB Short entry for 2N6F HEADER HEPARIN-BINDING PROTEIN 20-AUG-15 2N6F TITLE STRUCTURE OF PLEIOTROPHIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLEIOTROPHIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 33-168; COMPND 5 SYNONYM: PTN, HEPARIN-BINDING BRAIN MITOGEN, HBBM, HEPARIN-BINDING COMPND 6 GROWTH FACTOR 8, HBGF-8, HEPARIN-BINDING GROWTH-ASSOCIATED MOLECULE, COMPND 7 HB-GAM, HEPARIN-BINDING NEURITE OUTGROWTH-PROMOTING FACTOR 1, HBNF-1, COMPND 8 OSTEOBLAST-SPECIFIC FACTOR 1, OSF-1; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: TWO DOMAINS CONNECTED BY A FLEXIBLE LINKER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HBNF1, NEGF1, PTN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-15B KEYWDS CYTOKINE, GLYCOSAMINOGLYCAN-BINDING PROTEIN, MITOGEN, ANGIOGENESIS, KEYWDS 2 HEPARIN-BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.O.RYAN,D.SHEN,X.WANG REVDAT 3 14-JUN-23 2N6F 1 REMARK REVDAT 2 04-MAY-16 2N6F 1 JRNL REVDAT 1 20-APR-16 2N6F 0 JRNL AUTH E.RYAN,D.SHEN,X.WANG JRNL TITL STRUCTURAL STUDIES REVEAL AN IMPORTANT ROLE FOR THE JRNL TITL 2 PLEIOTROPHIN C-TERMINUS IN MEDIATING INTERACTIONS WITH JRNL TITL 3 CHONDROITIN SULFATE. JRNL REF FEBS J. V. 283 1488 2016 JRNL REFN ISSN 1742-464X JRNL PMID 26896299 JRNL DOI 10.1111/FEBS.13686 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT WITH THE DEFAULT REMARK 3 PROTOCOL REMARK 4 REMARK 4 2N6F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000104480. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 PTN, 10 % V/V D2O, 10 MM MES, REMARK 210 150 MM SODIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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: CLOSE CONTACTS 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 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 1 GLU A 4 177.04 66.07 REMARK 500 1 LYS A 5 81.41 56.99 REMARK 500 1 PRO A 6 -131.77 -93.38 REMARK 500 1 GLU A 7 108.31 69.23 REMARK 500 1 THR A 26 -66.64 85.98 REMARK 500 1 SER A 27 121.69 68.23 REMARK 500 1 CYS A 30 88.91 76.91 REMARK 500 1 CYS A 44 79.74 61.23 REMARK 500 1 TRP A 59 89.51 66.78 REMARK 500 1 LYS A 60 -169.97 -101.11 REMARK 500 1 ALA A 65 -79.87 -156.20 REMARK 500 1 CYS A 77 126.58 -21.33 REMARK 500 1 SER A 121 -166.86 61.25 REMARK 500 1 LYS A 133 -88.61 62.72 REMARK 500 1 MET A 134 21.11 -146.99 REMARK 500 1 LEU A 135 86.68 66.84 REMARK 500 2 PRO A 6 -137.48 -86.81 REMARK 500 2 GLU A 7 78.63 61.76 REMARK 500 2 LYS A 8 -74.44 -164.24 REMARK 500 2 LYS A 9 135.83 67.52 REMARK 500 2 CYS A 15 -77.32 92.70 REMARK 500 2 CYS A 30 88.45 59.41 REMARK 500 2 GLN A 62 24.66 -142.65 REMARK 500 2 PHE A 63 -37.30 75.95 REMARK 500 2 ALA A 65 -75.99 -114.06 REMARK 500 2 ALA A 73 116.85 71.74 REMARK 500 2 CYS A 77 102.24 79.53 REMARK 500 2 LEU A 112 86.99 57.94 REMARK 500 2 LYS A 114 89.20 -152.80 REMARK 500 2 PRO A 117 89.73 -61.70 REMARK 500 2 SER A 121 -165.42 -127.68 REMARK 500 2 LYS A 122 -1.72 75.80 REMARK 500 2 LEU A 135 135.31 70.36 REMARK 500 3 GLU A 4 35.96 -93.43 REMARK 500 3 LYS A 5 77.23 63.36 REMARK 500 3 PRO A 6 -85.44 -92.06 REMARK 500 3 LYS A 8 -48.56 74.44 REMARK 500 3 LYS A 12 94.18 57.40 REMARK 500 3 CYS A 15 81.32 70.50 REMARK 500 3 CYS A 30 92.15 166.02 REMARK 500 3 CYS A 44 70.85 60.51 REMARK 500 3 GLN A 46 100.56 66.74 REMARK 500 3 CYS A 57 -51.18 73.43 REMARK 500 3 CYS A 77 102.06 59.99 REMARK 500 3 LEU A 112 74.84 60.60 REMARK 500 3 PRO A 115 -161.54 -76.76 REMARK 500 3 LYS A 116 -40.52 -160.03 REMARK 500 3 SER A 121 34.05 -99.23 REMARK 500 4 LYS A 5 88.53 54.50 REMARK 500 4 PRO A 6 -91.14 -68.91 REMARK 500 REMARK 500 THIS ENTRY HAS 181 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25762 RELATED DB: BMRB DBREF 2N6F A 1 136 UNP P21246 PTN_HUMAN 33 168 SEQRES 1 A 136 GLY LYS LYS GLU LYS PRO GLU LYS LYS VAL LYS LYS SER SEQRES 2 A 136 ASP CYS GLY GLU TRP GLN TRP SER VAL CYS VAL PRO THR SEQRES 3 A 136 SER GLY ASP CYS GLY LEU GLY THR ARG GLU GLY THR ARG SEQRES 4 A 136 THR GLY ALA GLU CYS LYS GLN THR MET LYS THR GLN ARG SEQRES 5 A 136 CYS LYS ILE PRO CYS ASN TRP LYS LYS GLN PHE GLY ALA SEQRES 6 A 136 GLU CYS LYS TYR GLN PHE GLN ALA TRP GLY GLU CYS ASP SEQRES 7 A 136 LEU ASN THR ALA LEU LYS THR ARG THR GLY SER LEU LYS SEQRES 8 A 136 ARG ALA LEU HIS ASN ALA GLU CYS GLN LYS THR VAL THR SEQRES 9 A 136 ILE SER LYS PRO CYS GLY LYS LEU THR LYS PRO LYS PRO SEQRES 10 A 136 GLN ALA GLU SER LYS LYS LYS LYS LYS GLU GLY LYS LYS SEQRES 11 A 136 GLN GLU LYS MET LEU ASP SHEET 1 A 3 GLY A 16 TRP A 20 0 SHEET 2 A 3 THR A 34 THR A 40 -1 O THR A 38 N GLN A 19 SHEET 3 A 3 GLN A 46 ARG A 52 -1 O GLN A 51 N ARG A 35 SHEET 1 B 3 LYS A 68 GLN A 72 0 SHEET 2 B 3 LEU A 83 ARG A 92 -1 O THR A 87 N GLN A 72 SHEET 3 B 3 THR A 102 PRO A 108 -1 O LYS A 107 N LYS A 84 SSBOND 1 CYS A 15 CYS A 44 1555 1555 2.04 SSBOND 2 CYS A 23 CYS A 53 1555 1555 2.03 SSBOND 3 CYS A 30 CYS A 57 1555 1555 2.03 SSBOND 4 CYS A 67 CYS A 99 1555 1555 2.03 SSBOND 5 CYS A 77 CYS A 109 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000