HEADER HORMONE/GROWTH FACTOR 22-OCT-02 1N27 TITLE SOLUTION STRUCTURE OF THE PWWP DOMAIN OF MOUSE HEPATOMA- TITLE 2 DERIVED GROWTH FACTOR, RELATED PROTEIN 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOMA-DERIVED GROWTH FACTOR, RELATED PROTEIN COMPND 3 3; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PWWP DOMAIN; COMPND 6 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 GENE: 4632410H03; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P020408-01; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS SYSTEM KEYWDS NUCLEAR TRANSLOCATION, HDGF FAMILY, HATH, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, KEYWDS 3 HORMONE/GROWTH FACTOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.NAMEKI,T.KIGAWA,S.KOSHIBA,N.KOBAYASHI,N.TOCHIO,M.INOUE, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI) REVDAT 2 24-FEB-09 1N27 1 VERSN REVDAT 1 23-DEC-03 1N27 0 JRNL AUTH N.NAMEKI,N.TOCHIO,S.KOSHIBA,M.INOUE,T.YABUKI, JRNL AUTH 2 M.AOKI,E.SEKI,T.MATSUDA,Y.FUJIKURA,M.SAITO,M.IKARI, JRNL AUTH 3 M.WATANABE,T.TERADA,M.SHIROUZU,M.YOSHIDA,H.HIROTA, JRNL AUTH 4 A.TANAKA,Y.HAYASHIZAKI,P.GUNTERT,T.KIGAWA, JRNL AUTH 5 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE PWWP DOMAIN OF THE JRNL TITL 2 HEPATOMA-DERIVED GROWTH FACTOR FAMILY. JRNL REF PROTEIN SCI. V. 14 756 2005 JRNL REFN ISSN 0961-8368 JRNL PMID 15689505 JRNL DOI 10.1110/PS.04975305 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP REMARK 3 AUTHORS : KORADI, R., BILLETER, M., GUENTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1N27 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-02. REMARK 100 THE RCSB ID CODE IS RCSB017426. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7MM PWWP DOMAIN U-15N,13C; REMARK 210 20MM PHOSPHATE BUFFER NA; REMARK 210 100MM NACL; 1MM D-DTT; 0.02% REMARK 210 NAN3; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 20020425, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.613, CYANA 1.0.6 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 : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY,TARGET FUNCTION 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 18 ARG A 28 NE - CZ - NH2 ANGL. DEV. = -3.3 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 8 109.22 -169.58 REMARK 500 1 LYS A 20 93.46 -64.50 REMARK 500 1 HIS A 24 92.33 -64.96 REMARK 500 1 ALA A 36 -159.74 -97.90 REMARK 500 1 ASN A 42 -26.56 97.92 REMARK 500 1 LYS A 79 143.35 61.98 REMARK 500 1 SER A 95 2.26 57.65 REMARK 500 2 SER A 2 -51.79 -140.95 REMARK 500 2 ASP A 30 -164.08 -78.21 REMARK 500 2 GLU A 31 -167.75 -125.74 REMARK 500 2 SER A 75 99.03 -58.04 REMARK 500 3 SER A 2 43.96 37.60 REMARK 500 3 GLU A 8 94.71 56.00 REMARK 500 3 GLU A 34 103.77 -54.65 REMARK 500 3 ALA A 36 -168.79 -68.50 REMARK 500 3 ASN A 42 21.35 -153.79 REMARK 500 3 HIS A 52 11.91 58.72 REMARK 500 3 GLU A 67 -77.73 -72.86 REMARK 500 3 SER A 75 107.45 -57.52 REMARK 500 4 SER A 2 -52.49 -150.84 REMARK 500 4 SER A 3 107.54 -58.17 REMARK 500 4 SER A 5 114.57 -169.85 REMARK 500 4 HIS A 24 96.93 -60.25 REMARK 500 4 ASN A 42 9.83 -160.33 REMARK 500 4 PRO A 45 95.31 -67.26 REMARK 500 4 PHE A 49 150.25 -47.58 REMARK 500 4 HIS A 52 16.53 53.11 REMARK 500 4 GLU A 67 -72.25 -70.39 REMARK 500 4 SER A 94 126.97 80.97 REMARK 500 5 SER A 5 -51.50 -140.81 REMARK 500 5 SER A 6 170.20 63.36 REMARK 500 5 GLU A 8 -149.05 -142.25 REMARK 500 5 HIS A 24 107.16 -55.19 REMARK 500 5 GLU A 31 -161.65 -126.68 REMARK 500 5 HIS A 52 11.56 55.27 REMARK 500 5 ASN A 76 -96.99 -135.27 REMARK 500 5 LYS A 77 -20.93 -160.36 REMARK 500 5 ASN A 90 -71.34 -103.96 REMARK 500 6 TYR A 9 155.86 -48.34 REMARK 500 6 ALA A 11 103.25 -58.30 REMARK 500 6 HIS A 24 103.31 -59.57 REMARK 500 6 ASN A 42 0.97 -174.92 REMARK 500 6 HIS A 52 14.59 58.12 REMARK 500 7 SER A 2 109.66 -170.99 REMARK 500 7 SER A 3 48.40 -76.59 REMARK 500 7 SER A 5 92.75 59.59 REMARK 500 7 SER A 6 166.57 59.22 REMARK 500 7 ALA A 41 91.96 -43.74 REMARK 500 7 ASN A 42 58.19 33.64 REMARK 500 7 SER A 75 97.77 -56.90 REMARK 500 7 SER A 95 -53.57 -155.01 REMARK 500 8 SER A 2 157.91 57.19 REMARK 500 8 SER A 3 -154.81 50.48 REMARK 500 8 SER A 6 -87.40 -160.83 REMARK 500 8 GLU A 34 21.87 -69.97 REMARK 500 8 PRO A 45 91.63 -68.45 REMARK 500 8 SER A 75 105.35 -59.58 REMARK 500 8 PRO A 93 25.84 -76.98 REMARK 500 9 SER A 2 164.16 62.50 REMARK 500 9 SER A 3 -53.00 -169.06 REMARK 500 9 GLU A 8 88.07 74.14 REMARK 500 9 HIS A 24 97.04 -64.02 REMARK 500 9 ASN A 42 1.19 83.55 REMARK 500 9 ASN A 90 43.17 -81.69 REMARK 500 9 SER A 95 -21.26 -146.00 REMARK 500 10 SER A 2 107.15 -162.33 REMARK 500 10 HIS A 24 89.75 -62.53 REMARK 500 10 ASP A 30 -156.42 -83.91 REMARK 500 10 SER A 94 -41.53 67.90 REMARK 500 11 GLU A 8 165.65 68.25 REMARK 500 11 HIS A 24 97.61 -63.07 REMARK 500 11 VAL A 37 -173.11 -68.27 REMARK 500 11 PRO A 45 94.57 -66.18 REMARK 500 11 ASN A 76 -6.01 -142.12 REMARK 500 11 LYS A 77 -40.00 121.64 REMARK 500 11 SER A 91 74.60 -68.92 REMARK 500 11 SER A 94 -25.83 65.81 REMARK 500 11 SER A 95 29.06 45.79 REMARK 500 12 SER A 2 -175.55 63.87 REMARK 500 12 SER A 3 -174.04 57.59 REMARK 500 12 HIS A 24 98.42 -67.09 REMARK 500 12 GLU A 31 -169.71 -104.04 REMARK 500 12 PRO A 59 5.71 -66.81 REMARK 500 12 SER A 94 -78.06 -171.75 REMARK 500 13 SER A 5 -70.93 63.72 REMARK 500 13 HIS A 24 88.09 -62.59 REMARK 500 13 GLU A 34 24.13 -69.75 REMARK 500 13 VAL A 37 131.16 -35.19 REMARK 500 13 HIS A 52 3.15 58.09 REMARK 500 13 GLU A 67 -71.21 -74.02 REMARK 500 14 SER A 5 -62.50 -169.34 REMARK 500 14 LYS A 71 -62.48 -97.76 REMARK 500 14 SER A 95 -79.30 -137.85 REMARK 500 15 SER A 3 50.68 -160.99 REMARK 500 15 GLU A 31 -163.91 -101.74 REMARK 500 15 GLU A 67 -64.49 -92.90 REMARK 500 15 SER A 75 103.54 -54.40 REMARK 500 15 ASN A 90 39.18 -96.04 REMARK 500 16 SER A 2 -91.79 55.00 REMARK 500 16 SER A 6 -174.57 -171.65 REMARK 500 16 GLU A 8 98.02 10.19 REMARK 500 16 HIS A 24 92.66 -67.18 REMARK 500 16 SER A 75 79.79 -61.62 REMARK 500 16 LYS A 77 41.96 -91.97 REMARK 500 17 SER A 2 82.22 50.08 REMARK 500 17 SER A 5 -83.20 -77.06 REMARK 500 17 ASN A 42 6.42 -175.08 REMARK 500 18 SER A 2 -161.75 -75.11 REMARK 500 18 GLU A 8 141.32 109.48 REMARK 500 18 LYS A 20 44.28 -80.74 REMARK 500 18 PRO A 23 -178.20 -68.57 REMARK 500 18 LYS A 38 108.94 -28.22 REMARK 500 18 ASN A 42 -4.48 131.67 REMARK 500 18 HIS A 52 18.01 55.56 REMARK 500 18 ARG A 78 -126.10 44.50 REMARK 500 19 HIS A 24 94.12 -69.86 REMARK 500 19 PRO A 33 -152.94 -81.22 REMARK 500 19 GLU A 34 -138.45 -66.78 REMARK 500 19 ALA A 36 -179.83 -61.35 REMARK 500 19 ASN A 42 -8.80 -173.82 REMARK 500 19 PHE A 49 151.01 -49.18 REMARK 500 19 SER A 95 -151.90 53.25 REMARK 500 20 SER A 3 -37.57 -135.45 REMARK 500 20 GLU A 8 159.26 62.52 REMARK 500 20 HIS A 24 96.31 -66.70 REMARK 500 20 ALA A 36 -167.50 -75.05 REMARK 500 20 ASN A 42 7.52 -163.47 REMARK 500 20 ASN A 90 -74.28 -76.03 REMARK 500 20 SER A 91 73.20 48.36 REMARK 500 20 SER A 95 135.72 103.76 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 SER A 95 GLY A 96 7 135.96 REMARK 500 ASP A 30 GLU A 31 10 147.44 REMARK 500 LYS A 79 GLY A 80 15 -143.77 REMARK 500 ASN A 76 LYS A 77 16 -149.48 REMARK 500 GLY A 7 GLU A 8 19 143.24 REMARK 500 SER A 95 GLY A 96 20 -146.66 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 ARG A 78 0.08 SIDE_CHAIN REMARK 500 4 ARG A 28 0.13 SIDE_CHAIN REMARK 500 7 ARG A 28 0.08 SIDE_CHAIN REMARK 500 8 TYR A 9 0.07 SIDE_CHAIN REMARK 500 8 ARG A 78 0.12 SIDE_CHAIN REMARK 500 10 ARG A 78 0.11 SIDE_CHAIN REMARK 500 11 ARG A 78 0.08 SIDE_CHAIN REMARK 500 13 ARG A 28 0.08 SIDE_CHAIN REMARK 500 13 TYR A 44 0.09 SIDE_CHAIN REMARK 500 14 ARG A 78 0.08 SIDE_CHAIN REMARK 500 16 TYR A 68 0.07 SIDE_CHAIN REMARK 500 19 ARG A 28 0.10 SIDE_CHAIN REMARK 500 19 TYR A 68 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MMT007017903.1 RELATED DB: TARGETDB DBREF 1N27 A 8 90 UNP Q9JMG7 HDGR3_MOUSE 8 90 SEQADV 1N27 GLY A 1 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 SER A 2 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 SER A 3 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 GLY A 4 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 SER A 5 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 SER A 6 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 GLY A 7 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 SER A 91 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 GLY A 92 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 PRO A 93 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 SER A 94 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 SER A 95 UNP Q9JMG7 CLONING ARTIFACT SEQADV 1N27 GLY A 96 UNP Q9JMG7 CLONING ARTIFACT SEQRES 1 A 96 GLY SER SER GLY SER SER GLY GLU TYR LYS ALA GLY ASP SEQRES 2 A 96 LEU VAL PHE ALA LYS MET LYS GLY TYR PRO HIS TRP PRO SEQRES 3 A 96 ALA ARG ILE ASP GLU LEU PRO GLU GLY ALA VAL LYS PRO SEQRES 4 A 96 PRO ALA ASN LYS TYR PRO ILE PHE PHE PHE GLY THR HIS SEQRES 5 A 96 GLU THR ALA PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR SEQRES 6 A 96 LYS GLU TYR LYS ASP LYS PHE GLY LYS SER ASN LYS ARG SEQRES 7 A 96 LYS GLY PHE ASN GLU GLY LEU TRP GLU ILE GLU ASN SER SEQRES 8 A 96 GLY PRO SER SER GLY HELIX 1 1 PRO A 59 ASP A 61 5 3 HELIX 2 2 TYR A 65 TYR A 68 1 4 HELIX 3 3 PHE A 81 ASN A 90 1 10 SHEET 1 A 5 GLU A 53 LEU A 57 0 SHEET 2 A 5 TYR A 44 PHE A 48 -1 N ILE A 46 O ALA A 55 SHEET 3 A 5 HIS A 24 ILE A 29 -1 O ARG A 28 N PHE A 47 SHEET 4 A 5 LEU A 14 LYS A 18 -1 N VAL A 15 O ALA A 27 SHEET 5 A 5 LEU A 62 PRO A 64 -1 O PHE A 63 N PHE A 16 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 269 0 0 3 5 0 0 6 0 0 0 8 END