HEADER CELL ADHESION PROTEIN 11-FEB-98 2MFN
TITLE SOLUTION NMR STRUCTURE OF LINKED CELL ATTACHMENT MODULES OF MOUSE
TITLE 2 FIBRONECTIN CONTAINING THE RGD AND SYNERGY REGIONS, 10 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FIBRONECTIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: 184 AMINO ACID FRAGMENT, 9TH AND 10TH TYPE-III REPEATS;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 CELL_LINE: BL21;
SOURCE 6 GENE: POTENTIAL;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PRSET;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: BL21
KEYWDS CELL ADHESION PROTEIN, RGD, EXTRACELLULAR MATRIX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR V.COPIE,Y.TOMITA,S.K.AKIYAMA,S.AOTA,K.M.YAMADA,R.M.VENABLE,
AUTHOR 2 R.W.PASTOR,S.KRUEGER,D.A.TORCHIA
REVDAT 3 16-MAR-22 2MFN 1 REMARK
REVDAT 2 24-FEB-09 2MFN 1 VERSN
REVDAT 1 29-APR-98 2MFN 0
JRNL AUTH V.COPIE,Y.TOMITA,S.K.AKIYAMA,S.AOTA,K.M.YAMADA,R.M.VENABLE,
JRNL AUTH 2 R.W.PASTOR,S.KRUEGER,D.A.TORCHIA
JRNL TITL SOLUTION STRUCTURE AND DYNAMICS OF LINKED CELL ATTACHMENT
JRNL TITL 2 MODULES OF MOUSE FIBRONECTIN CONTAINING THE RGD AND SYNERGY
JRNL TITL 3 REGIONS: COMPARISON WITH THE HUMAN FIBRONECTIN CRYSTAL
JRNL TITL 4 STRUCTURE.
JRNL REF J.MOL.BIOL. V. 277 663 1998
JRNL REFN ISSN 0022-2836
JRNL PMID 9533887
JRNL DOI 10.1006/JMBI.1998.1616
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.8
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE.
REMARK 4
REMARK 4 2MFN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000178351.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308
REMARK 210 PH : 4.2
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : TRIPLE RESONANCE FOR ASSIGNMENT
REMARK 210 OF PROTEIN: CBCA(CO)NH; CBCANH;
REMARK 210 HBHA(CO)NH; C (CO)NH; H(CCO)NH;
REMARK 210 HCCH-TOCSY; HOHAHA; 15N; 13C-
REMARK 210 HSQC; 2D; 3D; 4D-NOESY.
REMARK 210 QUANTITATIVE J CORRELATION FOR
REMARK 210 COUPLING CONSTANTS; HNHA; HNHB;
REMARK 210 HAHB; CCO-SED; CN-SED; LRCC;
REMARK 210 LRCH.
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : DMX500; AMX500; AMX600
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR
REMARK 210 METHOD USED : TORSION-ANGLE MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : NO NOE VIOLATIONS GREATER THAN
REMARK 210 0.5 A,NO DIHEDRAL ANGLE
REMARK 210 RESTRAINT VIOLATIONS > 5, RMSD
REMARK 210 FOR BOND DEVIATIONS FROM
REMARK 210 IDEALITY < 0.05 A, RMSD FOR
REMARK 210 ANGLE DEVIATIONS FROM IDEALITY <
REMARK 210 5 AND RMSD FOR IMPROPER ANGLES
REMARK 210 DEVIATIONS FROM IDEALITY < 5
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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 HG SER A 103 OH TYR A 182 1.32
REMARK 500 O VAL A 140 H GLY A 142 1.38
REMARK 500 O GLY A 130 H ASN A 132 1.42
REMARK 500 OG1 THR A 129 H GLY A 130 1.43
REMARK 500 H THR A 125 O THR A 161 1.50
REMARK 500 H ASN A 63 OH TYR A 68 1.50
REMARK 500 O SER A 133 H VAL A 135 1.57
REMARK 500 H ARG A 123 O TYR A 163 1.57
REMARK 500 OG1 THR A 104 O SER A 107 2.16
REMARK 500 OG SER A 10 OE1 GLN A 88 2.18
REMARK 500 OG1 THR A 14 O SER A 17 2.18
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 THR A 6 -153.29 -150.57
REMARK 500 1 PRO A 25 176.15 -59.17
REMARK 500 1 VAL A 91 171.68 -43.47
REMARK 500 1 PRO A 95 -165.97 -58.45
REMARK 500 1 PRO A 115 -162.18 -60.87
REMARK 500 1 THR A 129 -89.10 -21.37
REMARK 500 1 PRO A 134 44.33 -65.91
REMARK 500 1 PRO A 141 44.23 -59.80
REMARK 500 1 ASN A 151 44.98 77.15
REMARK 500 1 THR A 166 -65.30 -108.52
REMARK 500 1 PRO A 172 99.03 -66.34
REMARK 500 2 PRO A 5 72.65 -58.81
REMARK 500 2 THR A 6 -153.73 -79.55
REMARK 500 2 ASN A 76 38.45 -140.49
REMARK 500 2 PRO A 95 -170.37 -58.78
REMARK 500 2 ASP A 97 36.22 72.60
REMARK 500 2 PRO A 115 -160.65 -60.63
REMARK 500 2 THR A 129 -35.39 -28.91
REMARK 500 2 THR A 166 -65.38 -123.13
REMARK 500 3 PRO A 5 79.91 -59.04
REMARK 500 3 THR A 6 -159.56 -85.90
REMARK 500 3 VAL A 91 171.26 -37.21
REMARK 500 3 PRO A 95 -158.61 -61.70
REMARK 500 3 ASP A 97 35.08 74.96
REMARK 500 3 PRO A 115 -163.42 -63.31
REMARK 500 3 PRO A 141 50.56 -58.87
REMARK 500 3 ARG A 168 -109.98 -114.87
REMARK 500 3 PRO A 172 82.61 -65.74
REMARK 500 3 LYS A 176 100.10 -39.07
REMARK 500 4 THR A 6 -144.36 -156.20
REMARK 500 4 PRO A 25 -179.50 -59.79
REMARK 500 4 GLU A 39 -97.27 -72.66
REMARK 500 4 PRO A 45 95.47 -61.75
REMARK 500 4 VAL A 91 166.62 -45.72
REMARK 500 4 PRO A 115 -178.22 -60.22
REMARK 500 4 PRO A 134 87.15 -57.21
REMARK 500 4 PRO A 172 98.57 -62.06
REMARK 500 5 THR A 6 -150.65 -143.54
REMARK 500 5 PRO A 25 -164.57 -61.58
REMARK 500 5 VAL A 91 155.97 -41.71
REMARK 500 5 ASP A 93 14.61 58.62
REMARK 500 5 PRO A 115 -166.33 -60.03
REMARK 500 5 THR A 129 157.95 -33.08
REMARK 500 5 ASN A 151 49.74 71.69
REMARK 500 5 PRO A 172 87.66 -64.02
REMARK 500 6 THR A 6 -155.75 -120.00
REMARK 500 6 SER A 11 -162.32 -172.75
REMARK 500 6 PRO A 25 179.28 -58.69
REMARK 500 6 VAL A 91 170.21 -55.33
REMARK 500 6 PRO A 95 81.31 -63.68
REMARK 500
REMARK 500 THIS ENTRY HAS 90 RAMACHANDRAN OUTLIERS.
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 26 0.10 SIDE CHAIN
REMARK 500 1 ARG A 35 0.32 SIDE CHAIN
REMARK 500 1 ARG A 44 0.20 SIDE CHAIN
REMARK 500 1 ARG A 46 0.31 SIDE CHAIN
REMARK 500 1 ARG A 54 0.18 SIDE CHAIN
REMARK 500 1 ARG A 78 0.17 SIDE CHAIN
REMARK 500 1 ARG A 96 0.31 SIDE CHAIN
REMARK 500 1 ARG A 123 0.24 SIDE CHAIN
REMARK 500 1 ARG A 168 0.30 SIDE CHAIN
REMARK 500 2 ARG A 26 0.18 SIDE CHAIN
REMARK 500 2 ARG A 35 0.14 SIDE CHAIN
REMARK 500 2 ARG A 44 0.24 SIDE CHAIN
REMARK 500 2 ARG A 46 0.09 SIDE CHAIN
REMARK 500 2 ARG A 49 0.20 SIDE CHAIN
REMARK 500 2 ARG A 54 0.16 SIDE CHAIN
REMARK 500 2 ARG A 78 0.13 SIDE CHAIN
REMARK 500 2 ARG A 120 0.26 SIDE CHAIN
REMARK 500 2 ARG A 123 0.21 SIDE CHAIN
REMARK 500 2 ARG A 168 0.18 SIDE CHAIN
REMARK 500 3 ARG A 26 0.18 SIDE CHAIN
REMARK 500 3 ARG A 35 0.22 SIDE CHAIN
REMARK 500 3 ARG A 44 0.18 SIDE CHAIN
REMARK 500 3 ARG A 46 0.32 SIDE CHAIN
REMARK 500 3 ARG A 54 0.24 SIDE CHAIN
REMARK 500 3 ARG A 78 0.26 SIDE CHAIN
REMARK 500 3 ARG A 96 0.18 SIDE CHAIN
REMARK 500 3 ARG A 120 0.30 SIDE CHAIN
REMARK 500 3 ARG A 123 0.27 SIDE CHAIN
REMARK 500 4 ARG A 46 0.18 SIDE CHAIN
REMARK 500 4 ARG A 49 0.20 SIDE CHAIN
REMARK 500 4 ARG A 54 0.12 SIDE CHAIN
REMARK 500 4 ARG A 78 0.31 SIDE CHAIN
REMARK 500 4 ARG A 96 0.32 SIDE CHAIN
REMARK 500 4 ARG A 120 0.28 SIDE CHAIN
REMARK 500 4 ARG A 123 0.15 SIDE CHAIN
REMARK 500 4 ARG A 168 0.14 SIDE CHAIN
REMARK 500 5 ARG A 26 0.24 SIDE CHAIN
REMARK 500 5 ARG A 35 0.30 SIDE CHAIN
REMARK 500 5 ARG A 44 0.17 SIDE CHAIN
REMARK 500 5 ARG A 46 0.12 SIDE CHAIN
REMARK 500 5 ARG A 49 0.32 SIDE CHAIN
REMARK 500 5 ARG A 54 0.27 SIDE CHAIN
REMARK 500 5 ARG A 78 0.26 SIDE CHAIN
REMARK 500 5 ARG A 96 0.09 SIDE CHAIN
REMARK 500 5 ARG A 120 0.26 SIDE CHAIN
REMARK 500 5 ARG A 123 0.20 SIDE CHAIN
REMARK 500 5 ARG A 168 0.32 SIDE CHAIN
REMARK 500 6 ARG A 26 0.31 SIDE CHAIN
REMARK 500 6 ARG A 35 0.31 SIDE CHAIN
REMARK 500 6 ARG A 44 0.26 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 95 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: RGD
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: CELL ADHESION SITE.
REMARK 800
REMARK 800 SITE_IDENTIFIER: SGY
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: CELL ADHESION SYNERGETIC SITE.
DBREF 2MFN A 1 184 UNP P11276 FINC_MOUSE 1447 1630
SEQRES 1 A 184 GLY LEU ASP SER PRO THR GLY PHE ASP SER SER ASP ILE
SEQRES 2 A 184 THR ALA ASN SER PHE THR VAL HIS TRP VAL ALA PRO ARG
SEQRES 3 A 184 ALA PRO ILE THR GLY TYR ILE ILE ARG HIS HIS ALA GLU
SEQRES 4 A 184 HIS SER VAL GLY ARG PRO ARG GLN ASP ARG VAL PRO PRO
SEQRES 5 A 184 SER ARG ASN SER ILE THR LEU THR ASN LEU ASN PRO GLY
SEQRES 6 A 184 THR GLU TYR VAL VAL SER ILE ILE ALA VAL ASN GLY ARG
SEQRES 7 A 184 GLU GLU SER PRO PRO LEU ILE GLY GLN GLN ALA THR VAL
SEQRES 8 A 184 SER ASP ILE PRO ARG ASP LEU GLU VAL ILE ALA SER THR
SEQRES 9 A 184 PRO THR SER LEU LEU ILE SER TRP GLU PRO PRO ALA VAL
SEQRES 10 A 184 SER VAL ARG TYR TYR ARG ILE THR TYR GLY GLU THR GLY
SEQRES 11 A 184 GLY ASN SER PRO VAL GLN GLU PHE THR VAL PRO GLY SER
SEQRES 12 A 184 LYS SER THR ALA THR ILE ASN ASN ILE LYS PRO GLY ALA
SEQRES 13 A 184 ASP TYR THR ILE THR LEU TYR ALA VAL THR GLY ARG GLY
SEQRES 14 A 184 ASP SER PRO ALA SER SER LYS PRO VAL SER ILE ASN TYR
SEQRES 15 A 184 LYS THR
SHEET 1 A 3 SER A 56 LEU A 59 0
SHEET 2 A 3 PHE A 18 HIS A 21 -1 N VAL A 20 O ILE A 57
SHEET 3 A 3 ASP A 9 ILE A 13 -1 N ASP A 12 O THR A 19
SHEET 1 B 4 ARG A 46 VAL A 50 0
SHEET 2 B 4 GLY A 31 ALA A 38 -1 N HIS A 36 O ARG A 46
SHEET 3 B 4 THR A 66 VAL A 75 -1 N VAL A 75 O GLY A 31
SHEET 4 B 4 LEU A 84 THR A 90 -1 N THR A 90 O THR A 66
SHEET 1 C 3 THR A 146 ILE A 149 0
SHEET 2 C 3 SER A 107 SER A 111 -1 N ILE A 110 O ALA A 147
SHEET 3 C 3 GLU A 99 THR A 104 -1 N THR A 104 O SER A 107
SHEET 1 D 4 GLN A 136 VAL A 140 0
SHEET 2 D 4 TYR A 121 TYR A 126 -1 N TYR A 126 O GLN A 136
SHEET 3 D 4 ASP A 157 VAL A 165 -1 N VAL A 165 O TYR A 121
SHEET 4 D 4 VAL A 178 LYS A 183 -1 N TYR A 182 O TYR A 158
SITE 1 RGD 3 ARG A 168 GLY A 169 ASP A 170
SITE 1 SGY 5 PRO A 51 PRO A 52 SER A 53 ARG A 54
SITE 2 SGY 5 ASN A 55
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
(ATOM LINES ARE NOT SHOWN.)
END
