PDB Short entry for 1E88 HEADER CELL ADHESION 18-SEP-00 1E88 TITLE SOLUTION STRUCTURE OF 6F11F22F2, A COMPACT THREE-MODULE FRAGMENT OF TITLE 2 THE GELATIN-BINDING DOMAIN OF HUMAN FIBRONECTIN CAVEAT 1E88 NAG A 161 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 6F11F22F2, RESIDUES 305-464; 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 CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PHAFFII GS115; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 644223; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: SECRETED; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: INTEGRATED PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPIC9K KEYWDS EXTRACELLULAR MATRIX GLYCOPROTEIN, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.R.PICKFORD,S.P.SMITH,D.STAUNTON,J.BOYD,I.D.CAMPBELL REVDAT 7 29-JUL-20 1E88 1 CAVEAT COMPND REMARK HETNAM REVDAT 7 2 1 LINK SITE REVDAT 6 14-FEB-18 1E88 1 SOURCE JRNL REMARK REVDAT 5 28-NOV-12 1E88 1 REMARK SEQADV REVDAT 4 19-OCT-11 1E88 1 HEADER COMPND KEYWDS REMARK REVDAT 4 2 1 HETSYN VERSN REVDAT 3 24-FEB-09 1E88 1 VERSN REVDAT 2 25-MAY-01 1E88 1 JRNL MODEL REVDAT 1 09-OCT-00 1E88 0 JRNL AUTH A.R.PICKFORD,S.P.SMITH,D.STAUNTON,J.BOYD,I.D.CAMPBELL JRNL TITL THE HAIRPIN STRUCTURE OF THE (6)F1(1)F2(2)F2 FRAGMENT FROM JRNL TITL 2 HUMAN FIBRONECTIN ENHANCES GELATIN BINDING JRNL REF EMBO J. V. 20 1519 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11285216 JRNL DOI 10.1093/EMBOJ/20.7.1519 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1E88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1290005363. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 2MM 6F11F22F2, 20MM PHOSPHATE REMARK 210 BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D [1H-1H] NOESY (60MS MIXIMG REMARK 210 TIME); 3D [1H-15N] NOESY (60MS REMARK 210 MIXING TIME); HMQC-J. REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2.3, NMRVIEW, CNS REMARK 210 METHOD USED : AB INITIO SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED BY HETERONUCLEAR NMR REMARK 210 SPECTROSCOPY ON UNIFORMLY 15N-LABELED 6F11F22F2. 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 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: 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 O TYR A 148 H ASP A 151 1.58 REMARK 500 H LEU A 121 O GLN A 146 1.58 REMARK 500 O CYS A 82 H SER A 95 1.58 REMARK 500 O LEU A 28 H GLN A 39 1.58 REMARK 500 O THR A 30 H SER A 37 1.58 REMARK 500 O CYS A 4 H TYR A 12 1.58 REMARK 500 H PHE A 120 O TYR A 127 1.59 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 HIS A 3 165.47 56.61 REMARK 500 1 ASP A 7 -44.57 85.49 REMARK 500 1 SER A 8 -22.64 158.37 REMARK 500 1 SER A 13 157.87 -41.14 REMARK 500 1 GLU A 40 153.87 -36.33 REMARK 500 1 THR A 41 51.33 -104.33 REMARK 500 1 VAL A 43 147.39 61.24 REMARK 500 1 GLN A 45 104.61 -36.50 REMARK 500 1 VAL A 57 59.45 -151.33 REMARK 500 1 ASN A 63 -8.33 76.55 REMARK 500 1 CYS A 70 162.01 -38.41 REMARK 500 1 THR A 84 51.77 -101.97 REMARK 500 1 THR A 85 117.96 -174.50 REMARK 500 1 ASN A 87 77.16 -101.99 REMARK 500 1 GLN A 90 -69.15 -94.60 REMARK 500 1 ASP A 99 40.79 30.65 REMARK 500 1 HIS A 100 48.65 35.25 REMARK 500 1 THR A 101 -167.00 38.86 REMARK 500 1 ASN A 110 -40.85 -142.00 REMARK 500 1 ASN A 112 90.83 -39.97 REMARK 500 1 LEU A 115 85.43 -60.59 REMARK 500 1 ASN A 123 19.94 54.30 REMARK 500 1 ASN A 124 29.32 89.97 REMARK 500 1 ASP A 129 139.91 -170.43 REMARK 500 1 CYS A 130 86.60 -48.97 REMARK 500 1 GLU A 133 99.43 -44.96 REMARK 500 1 ARG A 135 -89.69 -92.06 REMARK 500 1 ARG A 136 13.04 84.69 REMARK 500 1 ASN A 138 88.97 -45.23 REMARK 500 1 MET A 139 142.47 164.10 REMARK 500 1 TYR A 148 -75.96 -49.03 REMARK 500 2 HIS A 3 -178.11 46.47 REMARK 500 2 SER A 13 176.89 -54.75 REMARK 500 2 TRP A 18 134.79 -170.56 REMARK 500 2 GLN A 22 48.36 -92.39 REMARK 500 2 GLU A 40 165.59 -41.07 REMARK 500 2 THR A 41 -79.49 -39.93 REMARK 500 2 ALA A 42 99.08 42.44 REMARK 500 2 SER A 51 12.57 -142.95 REMARK 500 2 ASN A 63 -8.72 77.23 REMARK 500 2 SER A 69 166.77 165.93 REMARK 500 2 CYS A 70 151.72 -36.23 REMARK 500 2 GLU A 73 94.91 -36.46 REMARK 500 2 ASP A 77 15.10 -141.17 REMARK 500 2 THR A 84 41.64 -89.16 REMARK 500 2 THR A 85 128.88 -176.17 REMARK 500 2 ASP A 99 75.90 -59.03 REMARK 500 2 THR A 101 -165.21 37.54 REMARK 500 2 LEU A 103 105.40 -161.88 REMARK 500 2 LEU A 115 87.50 -65.88 REMARK 500 REMARK 500 THIS ENTRY HAS 668 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E8B RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF 6F11F22F2, A COMPACT THREE-MODULE FRAGMENT OF REMARK 900 THE GELATIN-BINDING DOMAIN OF HUMAN FIBRONECTIN DBREF 1E88 A 1 160 UNP P02751 FINC_HUMAN 305 464 SEQRES 1 A 160 TYR GLY HIS CYS VAL THR ASP SER GLY VAL VAL TYR SER SEQRES 2 A 160 VAL GLY MET GLN TRP LEU LYS THR GLN GLY ASN LYS GLN SEQRES 3 A 160 MET LEU CYS THR CYS LEU GLY ASN GLY VAL SER CYS GLN SEQRES 4 A 160 GLU THR ALA VAL THR GLN THR TYR GLY GLY ASN SER ASN SEQRES 5 A 160 GLY GLU PRO CYS VAL LEU PRO PHE THR TYR ASN GLY ARG SEQRES 6 A 160 THR PHE TYR SER CYS THR THR GLU GLY ARG GLN ASP GLY SEQRES 7 A 160 HIS LEU TRP CYS SER THR THR SER ASN TYR GLU GLN ASP SEQRES 8 A 160 GLN LYS TYR SER PHE CYS THR ASP HIS THR VAL LEU VAL SEQRES 9 A 160 GLN THR ARG GLY GLY ASN SER ASN GLY ALA LEU CYS HIS SEQRES 10 A 160 PHE PRO PHE LEU TYR ASN ASN HIS ASN TYR THR ASP CYS SEQRES 11 A 160 THR SER GLU GLY ARG ARG ASP ASN MET LYS TRP CYS GLY SEQRES 12 A 160 THR THR GLN ASN TYR ASP ALA ASP GLN LYS PHE GLY PHE SEQRES 13 A 160 CYS PRO MET ALA MODRES 1E88 ASN A 126 ASN GLYCOSYLATION SITE HET NAG A 161 28 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG C8 H15 N O6 HELIX 1 1 ASN A 87 GLN A 92 1 6 HELIX 2 2 ASN A 147 GLN A 152 1 6 SHEET 1 A 2 CYS A 4 THR A 6 0 SHEET 2 A 2 VAL A 10 TYR A 12 -1 N TYR A 12 O CYS A 4 SHEET 1 B 3 MET A 16 THR A 21 0 SHEET 2 B 3 GLN A 26 CYS A 31 -1 N CYS A 31 O MET A 16 SHEET 3 B 3 VAL A 36 GLU A 40 -1 N GLN A 39 O LEU A 28 SHEET 1 C 2 PHE A 60 TYR A 62 0 SHEET 2 C 2 ARG A 65 PHE A 67 -1 N PHE A 67 O PHE A 60 SHEET 1 D 2 TRP A 81 SER A 83 0 SHEET 2 D 2 TYR A 94 PHE A 96 -1 N SER A 95 O CYS A 82 SHEET 1 E 2 PHE A 120 TYR A 122 0 SHEET 2 E 2 HIS A 125 TYR A 127 -1 N TYR A 127 O PHE A 120 SHEET 1 F 2 TRP A 141 GLY A 143 0 SHEET 2 F 2 PHE A 154 PHE A 156 -1 N GLY A 155 O CYS A 142 SSBOND 1 CYS A 4 CYS A 31 1555 1555 2.03 SSBOND 2 CYS A 29 CYS A 38 1555 1555 2.03 SSBOND 3 CYS A 56 CYS A 82 1555 1555 2.03 SSBOND 4 CYS A 70 CYS A 97 1555 1555 2.03 SSBOND 5 CYS A 116 CYS A 142 1555 1555 2.03 SSBOND 6 CYS A 130 CYS A 157 1555 1555 2.03 LINK ND2 ASN A 126 C1 NAG A 161 1555 1555 1.46 CISPEP 1 LEU A 58 PRO A 59 1 0.04 CISPEP 2 PHE A 118 PRO A 119 1 0.01 CISPEP 3 LEU A 58 PRO A 59 2 0.13 CISPEP 4 PHE A 118 PRO A 119 2 0.12 CISPEP 5 LEU A 58 PRO A 59 3 0.13 CISPEP 6 PHE A 118 PRO A 119 3 0.03 CISPEP 7 LEU A 58 PRO A 59 4 0.06 CISPEP 8 PHE A 118 PRO A 119 4 -0.01 CISPEP 9 LEU A 58 PRO A 59 5 0.06 CISPEP 10 PHE A 118 PRO A 119 5 0.09 CISPEP 11 LEU A 58 PRO A 59 6 0.04 CISPEP 12 PHE A 118 PRO A 119 6 -0.12 CISPEP 13 LEU A 58 PRO A 59 7 -0.03 CISPEP 14 PHE A 118 PRO A 119 7 0.15 CISPEP 15 LEU A 58 PRO A 59 8 0.10 CISPEP 16 PHE A 118 PRO A 119 8 0.11 CISPEP 17 LEU A 58 PRO A 59 9 0.02 CISPEP 18 PHE A 118 PRO A 119 9 0.05 CISPEP 19 LEU A 58 PRO A 59 10 0.10 CISPEP 20 PHE A 118 PRO A 119 10 0.16 CISPEP 21 LEU A 58 PRO A 59 11 -0.02 CISPEP 22 PHE A 118 PRO A 119 11 0.10 CISPEP 23 LEU A 58 PRO A 59 12 0.06 CISPEP 24 PHE A 118 PRO A 119 12 0.12 CISPEP 25 LEU A 58 PRO A 59 13 0.11 CISPEP 26 PHE A 118 PRO A 119 13 0.01 CISPEP 27 LEU A 58 PRO A 59 14 0.18 CISPEP 28 PHE A 118 PRO A 119 14 0.15 CISPEP 29 LEU A 58 PRO A 59 15 0.14 CISPEP 30 PHE A 118 PRO A 119 15 0.93 CISPEP 31 LEU A 58 PRO A 59 16 -0.01 CISPEP 32 PHE A 118 PRO A 119 16 0.11 CISPEP 33 LEU A 58 PRO A 59 17 0.21 CISPEP 34 PHE A 118 PRO A 119 17 0.03 CISPEP 35 LEU A 58 PRO A 59 18 0.07 CISPEP 36 PHE A 118 PRO A 119 18 0.20 CISPEP 37 LEU A 58 PRO A 59 19 0.15 CISPEP 38 PHE A 118 PRO A 119 19 -0.17 CISPEP 39 LEU A 58 PRO A 59 20 -0.03 CISPEP 40 PHE A 118 PRO A 119 20 0.18 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