HEADER PROTEIN BINDING 14-JAN-02 1KSQ
TITLE NMR STUDY OF THE THIRD TB DOMAIN FROM LATENT TRANSFORMING GROWTH
TITLE 2 FACTOR-BETA BINDING PROTEIN-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LATENT TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: THIRD TB DOMAIN;
COMPND 5 SYNONYM: TRANSFORMING GROWTH FACTOR BETA-1 BINDING PROTEIN 1,TGF-
COMPND 6 BETA1-BP-1;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: LTBP1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30;
SOURCE 11 EXPRESSION_SYSTEM_GENE: LTBP1
KEYWDS LATENT TRANSFORMING GROWTH FACTOR-BETA BINDING PROTEIN-1, LTBP-1,
KEYWDS 2 TGF-BETA, TB DOMAIN, LATENCY ASSOCIATED PROPEPTIDE, LAP, PROTEIN
KEYWDS 3 BINDING
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.LACK,J.M.O'LEARY,V.KNOTT,X.YUAN,D.B.RIFKIN,P.A.HANDFORD,A.K.DOWNING
REVDAT 4 03-NOV-21 1KSQ 1 REMARK SEQADV
REVDAT 3 24-FEB-09 1KSQ 1 VERSN
REVDAT 2 25-NOV-03 1KSQ 1 AUTHOR JRNL
REVDAT 1 26-AUG-03 1KSQ 0
JRNL AUTH J.LACK,J.M.O'LEARY,V.KNOTT,X.YUAN,D.B.RIFKIN,P.A.HANDFORD,
JRNL AUTH 2 A.K.DOWNING
JRNL TITL SOLUTION STRUCTURE OF THE THIRD TB DOMAIN FROM LTBP1
JRNL TITL 2 PROVIDES INSIGHT INTO ASSEMBLY OF THE LARGE LATENT COMPLEX
JRNL TITL 3 THAT SEQUESTERS LATENT TGF-BETA.
JRNL REF J.MOL.BIOL. V. 334 281 2003
JRNL REFN ISSN 0022-2836
JRNL PMID 14607119
JRNL DOI 10.1016/J.JMB.2003.09.053
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.10
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 1676 RESTRAINTS, 1610 NOE-DERIVED DISTANCE CONSTRAINTS, 36
REMARK 3 DISTANCE RESTRAINTS FOR 18 HYDROGEN BONDS, AND 30 DIHEDRAL ANGLE
REMARK 3 PHI RESTRAINTS.
REMARK 4
REMARK 4 1KSQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-02.
REMARK 100 THE DEPOSITION ID IS D_1000015303.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 5.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.7 MM [U-15N] TB3-LTBP-1, 90%
REMARK 210 H2O/10% D2O; 1.2 MM [U-15N] TB3-
REMARK 210 LTBP-1, 99.9% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D
REMARK 210 NOESY; HMQC-J
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : OMEGA
REMARK 210 SPECTROMETER MANUFACTURER : GE
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR 3.851, NMRVIEW 3.1.2,
REMARK 210 FELIX 2.30
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: 3D NOESY MIXING TIME 150MS
REMARK 210 2D NOESY MIXING TIME 90MS
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 O CYS A 36 H SER A 39 1.57
REMARK 500 O VAL A 30 HE1 TRP A 43 1.60
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 ASP A 3 47.60 -91.77
REMARK 500 1 GLN A 4 141.06 172.11
REMARK 500 1 PRO A 5 97.76 -55.04
REMARK 500 1 GLU A 7 71.24 33.03
REMARK 500 1 GLU A 8 95.36 -168.24
REMARK 500 1 ASN A 15 -109.64 -67.89
REMARK 500 1 ASN A 17 -35.17 -169.12
REMARK 500 1 ASP A 18 19.10 56.27
REMARK 500 1 SER A 20 -25.85 173.31
REMARK 500 1 CYS A 22 109.33 48.87
REMARK 500 1 ASN A 24 -94.24 -79.73
REMARK 500 1 VAL A 25 75.87 70.13
REMARK 500 1 LEU A 26 83.26 87.66
REMARK 500 1 LYS A 32 -37.59 -31.10
REMARK 500 1 SER A 39 58.23 94.39
REMARK 500 1 ALA A 41 -33.01 -151.88
REMARK 500 1 ASN A 46 104.42 25.37
REMARK 500 1 CYS A 47 -20.37 86.65
REMARK 500 1 GLU A 48 58.79 -112.95
REMARK 500 1 PRO A 51 98.05 -45.11
REMARK 500 1 LEU A 55 138.39 58.78
REMARK 500 1 GLU A 59 -87.61 -39.72
REMARK 500 1 THR A 61 -30.88 -34.80
REMARK 500 1 LYS A 66 -71.71 -90.04
REMARK 500 1 ALA A 73 -74.85 81.36
REMARK 500 2 PRO A 5 93.44 -52.77
REMARK 500 2 GLU A 7 36.30 35.53
REMARK 500 2 GLU A 8 76.93 -101.62
REMARK 500 2 ASN A 15 -116.73 -62.13
REMARK 500 2 LEU A 16 -150.21 -151.45
REMARK 500 2 ASN A 17 -28.75 172.93
REMARK 500 2 SER A 20 -81.52 176.50
REMARK 500 2 LEU A 21 -33.70 -33.20
REMARK 500 2 CYS A 22 100.98 71.13
REMARK 500 2 ASN A 24 -96.74 -79.58
REMARK 500 2 VAL A 25 52.77 83.81
REMARK 500 2 LEU A 26 133.15 87.10
REMARK 500 2 ALA A 27 122.54 161.20
REMARK 500 2 LYS A 32 -30.99 -37.18
REMARK 500 2 SER A 39 120.95 153.91
REMARK 500 2 ALA A 41 -32.12 -152.16
REMARK 500 2 ASN A 46 106.93 24.81
REMARK 500 2 CYS A 47 -42.15 81.16
REMARK 500 2 PRO A 51 93.74 -51.23
REMARK 500 2 LEU A 55 133.27 68.67
REMARK 500 2 GLU A 59 -81.30 -38.07
REMARK 500 2 PHE A 60 -81.06 -33.19
REMARK 500 2 LYS A 66 -81.67 -88.98
REMARK 500 2 PRO A 72 -79.30 -88.93
REMARK 500 2 ALA A 73 37.06 168.60
REMARK 500
REMARK 500 THIS ENTRY HAS 530 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1APJ RELATED DB: PDB
REMARK 900 NMR STUDY OF THE TRANSFORMING GROWTH FACTOR-BETA BINDING PROTEIN-
REMARK 900 LIKE DOMAIN (TB MODULE/8-CYS DOMAIN), NMR STRUCTURE, 21 STRUCTURES
DBREF 1KSQ A 3 75 UNP P22064 LTB1S_HUMAN 1013 1085
SEQADV 1KSQ SER A 1 UNP P22064 EXPRESSION TAG
SEQADV 1KSQ ALA A 2 UNP P22064 EXPRESSION TAG
SEQRES 1 A 75 SER ALA ASP GLN PRO LYS GLU GLU LYS LYS GLU CYS TYR
SEQRES 2 A 75 TYR ASN LEU ASN ASP ALA SER LEU CYS ASP ASN VAL LEU
SEQRES 3 A 75 ALA PRO ASN VAL THR LYS GLN GLU CYS CYS CYS THR SER
SEQRES 4 A 75 GLY ALA GLY TRP GLY ASP ASN CYS GLU ILE PHE PRO CYS
SEQRES 5 A 75 PRO VAL LEU GLY THR ALA GLU PHE THR GLU MET CYS PRO
SEQRES 6 A 75 LYS GLY LYS GLY PHE VAL PRO ALA GLY GLU
HELIX 1 1 LYS A 32 THR A 38 1 7
HELIX 2 2 THR A 57 CYS A 64 1 8
SHEET 1 A 4 ASN A 29 THR A 31 0
SHEET 2 A 4 LYS A 9 TYR A 13 -1 N LYS A 10 O VAL A 30
SHEET 3 A 4 GLY A 42 ASP A 45 -1 O GLY A 42 N TYR A 13
SHEET 4 A 4 GLU A 48 PRO A 51 -1 O GLU A 48 N ASP A 45
SSBOND 1 CYS A 12 CYS A 35 1555 1555 2.03
SSBOND 2 CYS A 22 CYS A 47 1555 1555 2.03
SSBOND 3 CYS A 36 CYS A 52 1555 1555 2.03
SSBOND 4 CYS A 37 CYS A 64 1555 1555 2.04
CISPEP 1 CYS A 52 PRO A 53 1 -0.44
CISPEP 2 CYS A 52 PRO A 53 2 -0.46
CISPEP 3 CYS A 52 PRO A 53 3 -0.70
CISPEP 4 CYS A 52 PRO A 53 4 -0.85
CISPEP 5 CYS A 52 PRO A 53 5 -0.62
CISPEP 6 CYS A 52 PRO A 53 6 -0.98
CISPEP 7 CYS A 52 PRO A 53 7 -1.24
CISPEP 8 CYS A 52 PRO A 53 8 -0.99
CISPEP 9 CYS A 52 PRO A 53 9 -0.45
CISPEP 10 CYS A 52 PRO A 53 10 -0.65
CISPEP 11 CYS A 52 PRO A 53 11 -0.94
CISPEP 12 CYS A 52 PRO A 53 12 -0.56
CISPEP 13 CYS A 52 PRO A 53 13 -0.14
CISPEP 14 CYS A 52 PRO A 53 14 -0.30
CISPEP 15 CYS A 52 PRO A 53 15 -0.63
CISPEP 16 CYS A 52 PRO A 53 16 -0.29
CISPEP 17 CYS A 52 PRO A 53 17 -0.20
CISPEP 18 CYS A 52 PRO A 53 18 0.12
CISPEP 19 CYS A 52 PRO A 53 19 -0.89
CISPEP 20 CYS A 52 PRO A 53 20 0.21
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
