PDB Short entry for 1RI0 HEADER HORMONE/GROWTH FACTOR 16-NOV-03 1RI0 TITLE NMR STRUCTURE OF THE N-TERMINAL HATH DOMAIN OF HUMAN HDGF COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOMA-DERIVED GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL 100 RESIDUES; COMPND 5 SYNONYM: THE HATH DOMAIN OF HHDGF, HDGF, HIGH-MOBILITY GROUP PROTEIN COMPND 6 1-LIKE 2, HMG-1L2; 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: HDGF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS HDGF, HATH DOMAIN, PWWP DOMAIN, HEPARIN-BINDING, GROWTH FACTOR, KEYWDS 2 HORMONE-GROWTH FACTOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.-C.SUE,J.-Y.CHEN,T.-H.HUANG REVDAT 3 02-MAR-22 1RI0 1 REMARK SEQADV REVDAT 2 24-FEB-09 1RI0 1 VERSN REVDAT 1 16-NOV-04 1RI0 0 JRNL AUTH S.-C.SUE,J.-Y.CHEN,S.-C.LEE,W.-G.WU,T.-H.HUANG JRNL TITL SOLUTION STRUCTURE AND HEPARIN INTERACTION OF HUMAN JRNL TITL 2 HEPATOMA-DERIVED GROWTH FACTOR JRNL REF J.MOL.BIOL. V. 343 1365 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15491618 JRNL DOI 10.1016/J.JMB.2004.09.014 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1, CYANA 1.0.5 REMARK 3 AUTHORS : BRUKER (XWINNMR), PETER GUNTERT, TORSTEN HERRMANN REMARK 3 (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1507 RESTRAINTS, INCLUDING 1245 NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 196 DIHEDRAL ANGLE RESTRAINTS, 66 DISTANCE RESTRAINTS OF REMARK 3 HYDROGEN BONDS. REMARK 4 REMARK 4 1RI0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000020759. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 TO 3MM 15N AND 13C UNIFORM REMARK 210 LABELED PROTEIN, 100MM PHOSPHATE REMARK 210 BUFFER, 150MM NACL, 1MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA 2.8.13, CYANA 1.0.5 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS 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: THE STRUCTURE WAS DETERMINED BY USING STANDARD TRIPLE REMARK 210 -RESONANCE NMR SPECTROSCOPY. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 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 TYR A 66 H LYS A 70 1.51 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 2 140.57 -179.65 REMARK 500 1 ARG A 6 -178.50 -69.93 REMARK 500 1 GLN A 7 -82.98 -102.17 REMARK 500 1 GLU A 35 41.92 -144.57 REMARK 500 1 ALA A 36 -70.16 -106.14 REMARK 500 1 LYS A 44 147.26 -173.20 REMARK 500 1 HIS A 53 39.35 74.29 REMARK 500 1 LYS A 72 -65.77 -103.60 REMARK 500 1 PHE A 73 -72.32 -131.44 REMARK 500 1 LYS A 96 -38.65 -178.99 REMARK 500 2 ASN A 5 -171.23 -54.06 REMARK 500 2 ARG A 6 -178.38 -66.69 REMARK 500 2 LYS A 8 -40.80 -141.22 REMARK 500 2 GLU A 9 98.38 -59.43 REMARK 500 2 GLU A 35 33.46 -142.48 REMARK 500 2 ALA A 36 -70.07 -99.66 REMARK 500 2 ASN A 43 -43.58 -163.01 REMARK 500 2 HIS A 53 37.84 74.54 REMARK 500 2 LYS A 72 -69.05 -104.30 REMARK 500 2 PHE A 73 -83.52 -133.05 REMARK 500 2 LYS A 96 -43.66 -171.53 REMARK 500 2 SER A 98 160.36 62.64 REMARK 500 3 LYS A 8 -40.90 -141.12 REMARK 500 3 GLU A 9 97.68 -58.34 REMARK 500 3 CYS A 12 136.20 -39.19 REMARK 500 3 GLU A 35 36.08 -145.59 REMARK 500 3 ALA A 36 -65.79 -104.58 REMARK 500 3 LYS A 44 147.26 -172.48 REMARK 500 3 HIS A 53 39.14 74.61 REMARK 500 3 LYS A 72 -67.67 -101.28 REMARK 500 3 PHE A 73 -85.35 -132.55 REMARK 500 3 LYS A 96 -36.76 179.70 REMARK 500 4 LYS A 8 -38.38 -140.60 REMARK 500 4 ASN A 43 -32.39 168.93 REMARK 500 4 HIS A 53 40.71 70.69 REMARK 500 4 LYS A 72 -67.60 -104.00 REMARK 500 4 PHE A 73 -75.64 -132.83 REMARK 500 4 VAL A 95 98.49 -56.53 REMARK 500 5 ARG A 6 -177.35 -64.43 REMARK 500 5 GLN A 7 -71.30 -115.14 REMARK 500 5 GLU A 35 31.41 -144.04 REMARK 500 5 ALA A 36 -62.89 -106.35 REMARK 500 5 ASN A 43 -33.86 171.22 REMARK 500 5 HIS A 53 40.21 72.19 REMARK 500 5 LYS A 72 -66.70 -93.44 REMARK 500 5 PHE A 73 -52.48 -133.09 REMARK 500 5 LYS A 96 -43.02 -163.94 REMARK 500 5 ALA A 97 102.82 -42.04 REMARK 500 6 GLN A 7 -126.30 -60.62 REMARK 500 6 ASN A 43 82.30 40.54 REMARK 500 REMARK 500 THIS ENTRY HAS 172 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KHC RELATED DB: PDB REMARK 900 DNA METHYLTRANSFERASE, DNMT3B REMARK 900 RELATED ID: 1H3Z RELATED DB: PDB REMARK 900 S. POMBE PROTEIN SPBC215.07C REMARK 900 RELATED ID: 6541 RELATED DB: BMRB REMARK 900 S. POMBE PROTEIN SPBC215.07C DBREF 1RI0 A 1 100 UNP P51858 HDGF_HUMAN 1 100 SEQADV 1RI0 MET A -9 UNP P51858 EXPRESSION TAG SEQADV 1RI0 HIS A -8 UNP P51858 EXPRESSION TAG SEQADV 1RI0 HIS A -7 UNP P51858 EXPRESSION TAG SEQADV 1RI0 HIS A -6 UNP P51858 EXPRESSION TAG SEQADV 1RI0 HIS A -5 UNP P51858 EXPRESSION TAG SEQADV 1RI0 HIS A -4 UNP P51858 EXPRESSION TAG SEQADV 1RI0 HIS A -3 UNP P51858 EXPRESSION TAG SEQADV 1RI0 ALA A -2 UNP P51858 EXPRESSION TAG SEQADV 1RI0 MET A -1 UNP P51858 EXPRESSION TAG SEQADV 1RI0 ALA A 0 UNP P51858 EXPRESSION TAG SEQRES 1 A 110 MET HIS HIS HIS HIS HIS HIS ALA MET ALA MET SER ARG SEQRES 2 A 110 SER ASN ARG GLN LYS GLU TYR LYS CYS GLY ASP LEU VAL SEQRES 3 A 110 PHE ALA LYS MET LYS GLY TYR PRO HIS TRP PRO ALA ARG SEQRES 4 A 110 ILE ASP GLU MET PRO GLU ALA ALA VAL LYS SER THR ALA SEQRES 5 A 110 ASN LYS TYR GLN VAL PHE PHE PHE GLY THR HIS GLU THR SEQRES 6 A 110 ALA PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR GLU GLU SEQRES 7 A 110 SER LYS GLU LYS PHE GLY LYS PRO ASN LYS ARG LYS GLY SEQRES 8 A 110 PHE SER GLU GLY LEU TRP GLU ILE GLU ASN ASN PRO THR SEQRES 9 A 110 VAL LYS ALA SER GLY TYR HELIX 1 1 TYR A 66 LYS A 72 1 7 HELIX 2 2 LYS A 80 GLU A 90 1 11 SHEET 1 A 5 GLU A 54 LEU A 58 0 SHEET 2 A 5 TYR A 45 PHE A 49 -1 N PHE A 49 O GLU A 54 SHEET 3 A 5 TYR A 23 ASP A 31 -1 N ARG A 29 O PHE A 48 SHEET 4 A 5 LEU A 15 MET A 20 -1 N ALA A 18 O TRP A 26 SHEET 5 A 5 LEU A 63 PHE A 64 -1 O PHE A 64 N PHE A 17 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