HEADER PROTEIN BINDING 16-DEC-98 2FNB TITLE NMR STRUCTURE OF THE FIBRONECTIN ED-B DOMAIN, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FIBRONECTIN); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TYPE III DOMAIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ED-B, FIBRONECTIN, TYPEIII DOMAIN, ANGIOGENESIS, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.FATTORUSSO,M.PELLECCHIA,F.VITI,P.NERI,D.NERI,K.WUTHRICH REVDAT 4 27-APR-16 2FNB 1 ATOM REMARK VERSN REVDAT 3 24-FEB-09 2FNB 1 VERSN REVDAT 2 29-DEC-99 2FNB 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 23-DEC-98 2FNB 0 JRNL AUTH R.FATTORUSSO,M.PELLECCHIA,F.VITI,P.NERI,D.NERI,K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE HUMAN ONCOFOETAL FIBRONECTIN ED-B JRNL TITL 2 DOMAIN, A SPECIFIC MARKER FOR ANGIOGENESIS. JRNL REF STRUCTURE FOLD.DES. V. 7 381 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10196121 JRNL DOI 10.1016/S0969-2126(99)80051-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL VERSION 2.6 REMARK 3 AUTHORS : LUGINBUHL, GUNTERT, BILLETER,WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 2FNB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-99. REMARK 100 THE RCSB ID CODE IS RCSB008408. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 63 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 REMARK 210 REMARK 210 REMARK: SEE JRNL ARTICLE FOR DETAILS 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 18 ASP A 11 OD1 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 OD1 ASP A 74 HG1 THR A 92 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 9 VAL A 41 CG1 - CB - CG2 ANGL. DEV. = -10.8 DEGREES REMARK 500 10 ARG A 25 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 11 TYR A 62 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 12 VAL A 41 CG1 - CB - CG2 ANGL. DEV. = -10.3 DEGREES REMARK 500 16 VAL A 41 CG1 - CB - CG2 ANGL. DEV. = -9.9 DEGREES 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 5 -77.75 -135.16 REMARK 500 1 ASN A 30 40.49 -79.73 REMARK 500 1 SER A 32 -22.63 159.31 REMARK 500 1 THR A 33 -3.57 -165.06 REMARK 500 1 ILE A 48 105.53 -45.69 REMARK 500 1 ILE A 50 -82.79 -122.81 REMARK 500 1 SER A 57 -22.02 154.19 REMARK 500 1 ASN A 82 104.63 -34.58 REMARK 500 2 SER A 21 171.96 170.48 REMARK 500 2 SER A 32 38.52 -63.39 REMARK 500 2 THR A 33 -12.42 -169.27 REMARK 500 2 ALA A 44 99.29 -65.09 REMARK 500 2 ILE A 48 106.13 -43.09 REMARK 500 2 ILE A 50 -82.13 -84.06 REMARK 500 2 SER A 57 -41.45 153.64 REMARK 500 2 ASN A 82 108.72 -34.69 REMARK 500 3 ARG A 2 22.24 -68.16 REMARK 500 3 SER A 4 75.05 -171.26 REMARK 500 3 GLU A 5 -106.06 -135.78 REMARK 500 3 LEU A 9 83.89 -66.93 REMARK 500 3 SER A 21 153.18 177.05 REMARK 500 3 THR A 33 -4.16 -160.08 REMARK 500 3 GLU A 46 17.04 -150.83 REMARK 500 3 ILE A 48 106.24 -45.55 REMARK 500 3 SER A 57 -43.07 155.23 REMARK 500 3 ASN A 82 110.43 -37.69 REMARK 500 4 ARG A 2 -28.64 -164.40 REMARK 500 4 SER A 4 -165.24 -78.18 REMARK 500 4 GLU A 5 -80.27 -99.14 REMARK 500 4 LEU A 9 75.85 -67.90 REMARK 500 4 ASN A 30 41.44 -75.33 REMARK 500 4 ILE A 48 106.68 -46.13 REMARK 500 4 ILE A 50 -80.03 -93.64 REMARK 500 4 SER A 57 -29.42 166.29 REMARK 500 4 ASN A 82 112.75 -39.64 REMARK 500 5 GLU A 5 -100.96 -77.18 REMARK 500 5 ILE A 17 48.09 -76.10 REMARK 500 5 ASN A 30 48.61 37.86 REMARK 500 5 SER A 32 -104.45 -178.45 REMARK 500 5 ILE A 34 128.25 -34.21 REMARK 500 5 ALA A 44 95.37 -67.31 REMARK 500 5 ILE A 48 105.13 -45.53 REMARK 500 5 PHE A 51 175.95 54.59 REMARK 500 5 SER A 57 -41.21 157.22 REMARK 500 5 ILE A 81 -164.85 -115.85 REMARK 500 5 ASN A 82 99.82 -39.56 REMARK 500 6 SER A 4 93.66 -69.16 REMARK 500 6 SER A 21 161.96 179.14 REMARK 500 6 ASN A 30 43.55 -75.76 REMARK 500 6 SER A 32 -61.07 165.99 REMARK 500 REMARK 500 THIS ENTRY HAS 200 RAMACHANDRAN OUTLIERS. 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 GLN A 93 GLN A 94 5 149.82 REMARK 500 ARG A 2 GLY A 3 15 -149.40 REMARK 500 SER A 4 GLU A 5 19 -148.87 REMARK 500 THR A 33 ILE A 34 20 146.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 2 0.11 SIDE CHAIN REMARK 500 1 TYR A 37 0.09 SIDE CHAIN REMARK 500 1 TYR A 62 0.08 SIDE CHAIN REMARK 500 2 ARG A 2 0.09 SIDE CHAIN REMARK 500 3 TYR A 61 0.08 SIDE CHAIN REMARK 500 4 TYR A 61 0.07 SIDE CHAIN REMARK 500 4 TYR A 62 0.08 SIDE CHAIN REMARK 500 5 TYR A 61 0.08 SIDE CHAIN REMARK 500 5 TYR A 62 0.12 SIDE CHAIN REMARK 500 8 ARG A 2 0.09 SIDE CHAIN REMARK 500 8 ARG A 38 0.08 SIDE CHAIN REMARK 500 9 ARG A 25 0.09 SIDE CHAIN REMARK 500 10 ARG A 38 0.11 SIDE CHAIN REMARK 500 10 TYR A 62 0.12 SIDE CHAIN REMARK 500 11 ARG A 2 0.09 SIDE CHAIN REMARK 500 11 ARG A 38 0.10 SIDE CHAIN REMARK 500 12 TYR A 61 0.07 SIDE CHAIN REMARK 500 12 TYR A 62 0.08 SIDE CHAIN REMARK 500 13 ARG A 2 0.09 SIDE CHAIN REMARK 500 13 TYR A 62 0.07 SIDE CHAIN REMARK 500 15 ARG A 25 0.17 SIDE CHAIN REMARK 500 16 ARG A 25 0.12 SIDE CHAIN REMARK 500 16 ARG A 38 0.10 SIDE CHAIN REMARK 500 17 TYR A 37 0.08 SIDE CHAIN REMARK 500 17 ARG A 38 0.11 SIDE CHAIN REMARK 500 20 ARG A 25 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 5 PHE A 51 24.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL DBREF 2FNB A 1 95 UNP P02751 FINC_HUMAN 1261 1355 SEQADV 2FNB MET A 1 UNP P02751 THR 1261 CONFLICT SEQADV 2FNB ARG A 2 UNP P02751 VAL 1262 CONFLICT SEQADV 2FNB GLY A 3 UNP P02751 VAL 1263 CONFLICT SEQADV 2FNB SER A 4 UNP P02751 PRO 1264 CONFLICT SEQRES 1 A 95 MET ARG GLY SER GLU VAL PRO GLN LEU THR ASP LEU SER SEQRES 2 A 95 PHE VAL ASP ILE THR ASP SER SER ILE GLY LEU ARG TRP SEQRES 3 A 95 THR PRO LEU ASN SER SER THR ILE ILE GLY TYR ARG ILE SEQRES 4 A 95 THR VAL VAL ALA ALA GLY GLU GLY ILE PRO ILE PHE GLU SEQRES 5 A 95 ASP PHE VAL ASP SER SER VAL GLY TYR TYR THR VAL THR SEQRES 6 A 95 GLY LEU GLU PRO GLY ILE ASP TYR ASP ILE SER VAL ILE SEQRES 7 A 95 THR LEU ILE ASN GLY GLY GLU SER ALA PRO THR THR LEU SEQRES 8 A 95 THR GLN GLN THR SHEET 1 A 3 SER A 13 VAL A 15 0 SHEET 2 A 3 ILE A 22 ARG A 25 -1 N ARG A 25 O SER A 13 SHEET 3 A 3 TYR A 61 VAL A 64 -1 N VAL A 64 O ILE A 22 SHEET 1 B 4 GLU A 52 PHE A 54 0 SHEET 2 B 4 GLY A 36 ALA A 44 -1 N ILE A 39 O ASP A 53 SHEET 3 B 4 ASP A 72 LEU A 80 -1 N LEU A 80 O GLY A 36 SHEET 4 B 4 LEU A 91 GLN A 94 -1 N GLN A 93 O TYR A 73 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 MODEL 1