10 20 30 40 50 60 70 80 1X57 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA BINDING PROTEIN 15-MAY-05 1X57
TITLE SOLUTION STRUCTURES OF THE HTH DOMAIN OF HUMAN EDF-1 PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOTHELIAL DIFFERENTIATION-RELATED FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HTH DOMAIN; COMPND 5 SYNONYM: EDF-1, MULTIPROTEIN BRIDGING FACTOR 1, MBF1; COMPND 6 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: EDF-1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P041012-15; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS EDF1, HMBF1ALPHA, HELIX-TURN-HELIX, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR N.NAMEKI,M.SATO,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI)
REVDAT 2 24-FEB-09 1X57 1 VERSN REVDAT 1 15-NOV-05 1X57 0
JRNL AUTH N.NAMEKI,M.SATO,N.TOCHIO,S.KOSHIBA,M.INOUE, JRNL AUTH 2 T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURES OF THE HTH DOMAIN OF HUMAN JRNL TITL 2 EDF-1 PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP 1.2 REMARK 3 AUTHORS : KORADI, R.,BILLETER, M.,GUNTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1X57 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAY-05. REMARK 100 THE RCSB ID CODE IS RCSB024393.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM HTH DOMAIN U-15N,13C; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, NMRPIPE REMARK 210 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, CYANA 1.0.7 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY, REMARK 210 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 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 6 ASP A 45 CB - CG - OD1 ANGL. DEV. = -7.3 DEGREES REMARK 500 14 ARG A 70 CD - NE - CZ ANGL. DEV. = 10.1 DEGREES REMARK 500 14 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 4.6 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 SER A 5 72.68 76.60 REMARK 500 1 ASP A 8 93.12 50.28 REMARK 500 1 GLU A 79 -72.15 70.48 REMARK 500 1 SER A 89 -165.14 -123.91 REMARK 500 2 SER A 2 -52.34 -135.67 REMARK 500 2 SER A 5 -12.77 76.87 REMARK 500 2 ASN A 37 6.78 55.12 REMARK 500 2 GLU A 79 80.17 44.36 REMARK 500 2 LYS A 80 84.56 -62.93 REMARK 500 2 ARG A 83 53.37 37.59 REMARK 500 2 SER A 86 -63.72 -146.90 REMARK 500 2 SER A 90 -179.08 52.48 REMARK 500 3 ASN A 37 71.50 44.92 REMARK 500 3 GLU A 79 23.16 49.12 REMARK 500 3 LYS A 80 85.46 -22.82 REMARK 500 3 PRO A 82 95.06 -62.02 REMARK 500 3 ALA A 84 75.55 41.01 REMARK 500 3 LYS A 85 -46.89 -152.21 REMARK 500 3 SER A 86 72.51 48.00 REMARK 500 3 SER A 89 -69.75 -136.45 REMARK 500 3 SER A 90 -67.61 -154.68 REMARK 500 4 SER A 3 -53.10 -135.60 REMARK 500 4 SER A 6 -160.53 48.06 REMARK 500 4 ASN A 37 68.85 37.09 REMARK 500 4 ASP A 73 8.23 -64.93 REMARK 500 4 GLU A 79 -171.15 61.59 REMARK 500 5 SER A 5 -67.56 60.25 REMARK 500 5 SER A 6 177.00 55.21 REMARK 500 5 ASN A 37 74.21 45.02 REMARK 500 5 ASP A 73 11.69 -66.62 REMARK 500 5 GLU A 79 -77.27 63.50 REMARK 500 5 LYS A 80 94.04 -65.58 REMARK 500 5 SER A 89 79.96 36.67 REMARK 500 6 SER A 2 -172.07 57.13 REMARK 500 6 SER A 5 84.24 -161.81 REMARK 500 6 ASP A 8 111.74 -166.71 REMARK 500 6 ASN A 37 76.31 42.27 REMARK 500 6 LYS A 85 -35.86 71.03 REMARK 500 6 SER A 86 -177.66 -66.12 REMARK 500 7 SER A 2 75.60 53.32 REMARK 500 7 SER A 6 -4.78 -148.67 REMARK 500 7 LEU A 12 155.12 62.06 REMARK 500 7 LYS A 85 -160.07 53.12 REMARK 500 7 SER A 86 -66.08 -153.77 REMARK 500 7 SER A 89 164.04 176.53 REMARK 500 8 SER A 3 166.84 52.55 REMARK 500 8 SER A 6 48.82 -153.74 REMARK 500 8 ARG A 9 162.60 59.20 REMARK 500 8 ARG A 83 121.63 95.08 REMARK 500 8 ALA A 84 -61.49 -144.60 REMARK 500 8 LYS A 85 163.21 61.26 REMARK 500 8 SER A 86 77.29 30.80 REMARK 500 9 SER A 2 -37.85 -145.95 REMARK 500 9 SER A 3 49.38 33.96 REMARK 500 9 SER A 5 74.88 -162.87 REMARK 500 9 LEU A 12 -177.12 66.30 REMARK 500 9 ASN A 37 72.15 36.74 REMARK 500 9 LYS A 80 66.95 -116.65 REMARK 500 9 SER A 90 170.20 63.44 REMARK 500 10 SER A 5 26.56 -156.20 REMARK 500 10 ASP A 73 16.73 -69.91 REMARK 500 10 GLU A 79 -178.33 59.43 REMARK 500 10 ARG A 83 -48.91 -152.45 REMARK 500 10 ALA A 84 -176.46 53.39 REMARK 500 10 LYS A 85 83.55 29.10 REMARK 500 11 SER A 2 -64.09 -144.48 REMARK 500 11 SER A 3 -165.48 51.99 REMARK 500 11 LEU A 12 172.18 64.94 REMARK 500 11 ASP A 73 21.33 -73.52 REMARK 500 11 ARG A 83 88.51 -163.30 REMARK 500 11 SER A 90 20.70 -148.15 REMARK 500 12 SER A 2 -66.79 64.06 REMARK 500 12 SER A 5 94.01 52.80 REMARK 500 12 ASP A 8 48.44 -81.66 REMARK 500 12 ASP A 73 6.94 -67.53 REMARK 500 12 GLU A 79 58.97 23.83 REMARK 500 12 ARG A 83 -119.03 47.43 REMARK 500 12 ALA A 84 76.76 21.30 REMARK 500 12 SER A 89 -66.68 -156.39 REMARK 500 13 SER A 2 53.72 93.78 REMARK 500 13 ARG A 9 -172.29 56.76 REMARK 500 13 GLU A 79 61.25 25.02 REMARK 500 13 LYS A 80 -30.48 -171.00 REMARK 500 14 SER A 5 -40.42 -159.26 REMARK 500 14 SER A 6 75.26 38.05 REMARK 500 14 ASN A 37 13.14 57.53 REMARK 500 14 GLU A 79 68.86 35.42 REMARK 500 14 ARG A 83 6.03 -153.11 REMARK 500 14 ALA A 84 -177.76 -171.66 REMARK 500 14 SER A 86 178.69 61.37 REMARK 500 14 SER A 89 166.89 57.74 REMARK 500 14 SER A 90 -25.72 -162.24 REMARK 500 16 SER A 2 -37.75 -164.97 REMARK 500 16 SER A 3 -26.17 -152.78 REMARK 500 16 GLU A 79 -23.78 38.32 REMARK 500 16 ARG A 83 29.75 -162.82 REMARK 500 16 SER A 86 155.76 176.20 REMARK 500 17 SER A 2 169.58 52.21 REMARK 500 17 SER A 5 -51.25 -135.86 REMARK 500 17 ASP A 8 136.80 81.38 REMARK 500 17 VAL A 10 -153.68 55.40 REMARK 500 17 THR A 11 -157.02 52.57 REMARK 500 17 LEU A 12 157.98 74.52 REMARK 500 17 GLU A 13 -61.99 -98.21 REMARK 500 17 GLU A 79 72.38 37.26 REMARK 500 18 ASP A 8 -53.30 -147.17 REMARK 500 18 ARG A 9 154.50 58.04 REMARK 500 18 THR A 11 103.07 -57.67 REMARK 500 18 ASP A 73 9.31 -69.44 REMARK 500 18 GLU A 79 59.32 31.19 REMARK 500 18 ARG A 83 83.22 61.15 REMARK 500 18 SER A 89 -71.72 -114.01 REMARK 500 19 SER A 5 -52.81 67.17 REMARK 500 19 SER A 6 15.84 50.41 REMARK 500 19 ASP A 8 159.38 61.61 REMARK 500 19 GLU A 79 104.81 58.62 REMARK 500 19 LYS A 80 -167.85 70.53 REMARK 500 19 PRO A 88 48.99 -82.26 REMARK 500 20 ARG A 9 -165.45 56.74 REMARK 500 20 GLU A 79 161.29 67.04 REMARK 500 20 ALA A 84 92.47 8.39 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 ARG A 83 ALA A 84 9 149.33 REMARK 500 SER A 90 GLY A 91 11 -129.52 REMARK 500 SER A 89 SER A 90 13 149.62 REMARK 500 SER A 90 GLY A 91 16 149.88 REMARK 500 GLY A 1 SER A 2 17 -133.64 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 3 TYR A 46 0.07 SIDE_CHAIN REMARK 500 7 ARG A 50 0.12 SIDE_CHAIN REMARK 500 9 ARG A 70 0.08 SIDE_CHAIN REMARK 500 20 ARG A 50 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002010852.1 RELATED DB: TARGETDB
DBREF 1X57 A 8 85 UNP O60869 EDF1_HUMAN 71 148
SEQADV 1X57 GLY A 1 UNP O60869 CLONING ARTIFACT SEQADV 1X57 SER A 2 UNP O60869 CLONING ARTIFACT SEQADV 1X57 SER A 3 UNP O60869 CLONING ARTIFACT SEQADV 1X57 GLY A 4 UNP O60869 CLONING ARTIFACT SEQADV 1X57 SER A 5 UNP O60869 CLONING ARTIFACT SEQADV 1X57 SER A 6 UNP O60869 CLONING ARTIFACT SEQADV 1X57 GLY A 7 UNP O60869 CLONING ARTIFACT SEQADV 1X57 SER A 86 UNP O60869 CLONING ARTIFACT SEQADV 1X57 GLY A 87 UNP O60869 CLONING ARTIFACT SEQADV 1X57 PRO A 88 UNP O60869 CLONING ARTIFACT SEQADV 1X57 SER A 89 UNP O60869 CLONING ARTIFACT SEQADV 1X57 SER A 90 UNP O60869 CLONING ARTIFACT SEQADV 1X57 GLY A 91 UNP O60869 CLONING ARTIFACT
SEQRES 1 A 91 GLY SER SER GLY SER SER GLY ASP ARG VAL THR LEU GLU SEQRES 2 A 91 VAL GLY LYS VAL ILE GLN GLN GLY ARG GLN SER LYS GLY SEQRES 3 A 91 LEU THR GLN LYS ASP LEU ALA THR LYS ILE ASN GLU LYS SEQRES 4 A 91 PRO GLN VAL ILE ALA ASP TYR GLU SER GLY ARG ALA ILE SEQRES 5 A 91 PRO ASN ASN GLN VAL LEU GLY LYS ILE GLU ARG ALA ILE SEQRES 6 A 91 GLY LEU LYS LEU ARG GLY LYS ASP ILE GLY LYS PRO ILE SEQRES 7 A 91 GLU LYS GLY PRO ARG ALA LYS SER GLY PRO SER SER GLY
HELIX 1 1 LEU A 12 SER A 24 1 13 HELIX 2 2 THR A 28 ASN A 37 1 10 HELIX 3 3 LYS A 39 GLY A 49 1 11 HELIX 4 4 ASN A 54 GLY A 66 1 13
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