PDB Short entry for 2NLU HEADER HORMONE/GROWTH FACTOR 20-OCT-06 2NLU TITLE DOMAIN-SWAPPED DIMER OF THE PWWP MODULE OF HUMAN HEPATOMA-DERIVED TITLE 2 GROWTH FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOMA-DERIVED GROWTH FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HATH DOMAIN; COMPND 5 SYNONYM: HDGF, HIGH-MOBILITY GROUP PROTEIN 1-LIKE 2, HMG-1L2; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS HDGF, HHDGF, HRP, HATH, PWWP, HEPARIN, DOMAIN-SWAPPING, HORMONE- KEYWDS 2 GROWTH FACTOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR S.C.SUE,W.T.LEE,T.H.HUANG REVDAT 4 27-DEC-23 2NLU 1 REMARK REVDAT 3 16-MAR-22 2NLU 1 REMARK REVDAT 2 24-FEB-09 2NLU 1 VERSN REVDAT 1 04-SEP-07 2NLU 0 JRNL AUTH S.C.SUE,W.T.LEE,S.C.TIEN,S.C.LEE,J.G.YU,W.J.WU,W.G.WU, JRNL AUTH 2 T.H.HUANG JRNL TITL PWWP MODULE OF HUMAN HEPATOMA-DERIVED GROWTH FACTOR FORMS A JRNL TITL 2 DOMAIN-SWAPPED DIMER WITH MUCH HIGHER AFFINITY FOR HEPARIN JRNL REF J.MOL.BIOL. V. 367 456 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17270212 JRNL DOI 10.1016/J.JMB.2007.01.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, ARIA 1.2 REMARK 3 AUTHORS : BRUKER (XWINNMR), M.NILGES, A.M.GRONENBORN, REMARK 3 G.M.CLORE (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NLU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040020. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 150MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM U-15N, 13C, 2H AND UNLABELED REMARK 210 HATH DIMER; 10MM PHOSPHATE REMARK 210 BUFFER, 150MM NACL; 90% H2O, 10% REMARK 210 D2O; 1MM U-15N, 2H AND U-2H HATH REMARK 210 DIMER; 10MM PHOSPHATE BUFFER, REMARK 210 150MM NACL ;90% H2O, 10% D2O; REMARK 210 1MM U-15N, 13C HATH DIMER; 10MM REMARK 210 PHOSPHATE BUFFER, 150MM NACL; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C, 15N FILTERED, 15N EDITED REMARK 210 NOESY-HSQC; 13C, 15N FILTERED, REMARK 210 13C EDITED NOESY-HSQC; 3D_15N- REMARK 210 SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, SPARKY 3.113, ARIA REMARK 210 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED STRUCTURES ARE THE REMARK 210 16 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 OE2 GLU A 35 HZ2 LYS A 39 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 4 TYR A 66 CE1 TYR A 66 CZ 0.122 REMARK 500 4 TYR A 66 CZ TYR A 66 CE2 -0.126 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 CYS A 12 -46.55 66.30 REMARK 500 1 ASP A 14 -149.76 58.02 REMARK 500 1 HIS A 25 81.32 69.49 REMARK 500 1 GLU A 32 172.48 75.02 REMARK 500 1 MET A 33 94.80 -166.41 REMARK 500 1 PRO A 34 87.01 -69.74 REMARK 500 1 GLU A 35 -21.61 -140.79 REMARK 500 1 ALA A 37 -81.75 63.23 REMARK 500 1 ASN A 43 7.98 57.36 REMARK 500 1 ALA A 97 139.86 65.85 REMARK 500 1 ARG B 103 -74.19 69.59 REMARK 500 1 GLU B 135 85.90 67.14 REMARK 500 1 ALA B 136 74.47 -167.13 REMARK 500 1 ALA B 137 -43.75 72.21 REMARK 500 1 LYS B 139 -37.63 -178.64 REMARK 500 1 THR B 141 98.13 65.32 REMARK 500 1 ALA B 142 -72.13 -66.43 REMARK 500 1 PRO B 176 -159.30 -95.66 REMARK 500 1 ASN B 177 153.92 76.36 REMARK 500 1 LYS B 178 -40.23 73.72 REMARK 500 1 ASN B 192 71.18 -164.42 REMARK 500 1 VAL B 195 100.66 63.46 REMARK 500 1 SER B 198 -56.42 -126.29 REMARK 500 2 GLU A 9 -55.60 71.84 REMARK 500 2 ASP A 14 -164.28 -113.45 REMARK 500 2 HIS A 25 85.46 72.37 REMARK 500 2 ASP A 31 -69.88 75.29 REMARK 500 2 GLU A 32 -71.42 67.43 REMARK 500 2 ALA A 36 80.57 62.21 REMARK 500 2 ALA A 37 -73.86 67.23 REMARK 500 2 THR A 41 59.32 -95.90 REMARK 500 2 ARG A 79 -177.20 67.85 REMARK 500 2 ASN A 92 97.46 58.83 REMARK 500 2 PRO A 93 -153.06 -77.07 REMARK 500 2 SER B 102 94.14 -161.76 REMARK 500 2 LYS B 108 87.43 52.03 REMARK 500 2 GLU B 135 111.14 -171.50 REMARK 500 2 ALA B 136 -114.97 -167.60 REMARK 500 2 LYS B 139 -69.48 66.23 REMARK 500 2 THR B 141 18.46 52.44 REMARK 500 2 ASN B 191 64.96 -104.22 REMARK 500 3 SER A 2 34.54 -77.17 REMARK 500 3 PRO A 24 -88.08 -56.25 REMARK 500 3 PRO A 27 101.95 -59.17 REMARK 500 3 GLU A 35 -47.16 73.95 REMARK 500 3 ALA A 37 -63.98 -126.22 REMARK 500 3 ASN A 43 -53.17 73.05 REMARK 500 3 PHE A 49 104.56 -59.56 REMARK 500 3 ASN A 77 -166.58 66.29 REMARK 500 3 LYS A 78 -40.48 72.66 REMARK 500 REMARK 500 THIS ENTRY HAS 289 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 10 TYR B 145 0.06 SIDE CHAIN REMARK 500 13 TYR A 66 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RI0 RELATED DB: PDB REMARK 900 MONOMER STRUCTURE REMARK 900 RELATED ID: 2B8A RELATED DB: PDB REMARK 900 MONOMER STRUCTURE REMARK 900 RELATED ID: 1N27 RELATED DB: PDB REMARK 900 HOMOLOGUE DBREF 2NLU A 1 100 UNP P51858 HDGF_HUMAN 1 100 DBREF 2NLU B 101 200 UNP P51858 HDGF_HUMAN 1 100 SEQRES 1 A 100 MET SER ARG SER ASN ARG GLN LYS GLU TYR LYS CYS GLY SEQRES 2 A 100 ASP LEU VAL PHE ALA LYS MET LYS GLY TYR PRO HIS TRP SEQRES 3 A 100 PRO ALA ARG ILE ASP GLU MET PRO GLU ALA ALA VAL LYS SEQRES 4 A 100 SER THR ALA ASN LYS TYR GLN VAL PHE PHE PHE GLY THR SEQRES 5 A 100 HIS GLU THR ALA PHE LEU GLY PRO LYS ASP LEU PHE PRO SEQRES 6 A 100 TYR GLU GLU SER LYS GLU LYS PHE GLY LYS PRO ASN LYS SEQRES 7 A 100 ARG LYS GLY PHE SER GLU GLY LEU TRP GLU ILE GLU ASN SEQRES 8 A 100 ASN PRO THR VAL LYS ALA SER GLY TYR SEQRES 1 B 100 MET SER ARG SER ASN ARG GLN LYS GLU TYR LYS CYS GLY SEQRES 2 B 100 ASP LEU VAL PHE ALA LYS MET LYS GLY TYR PRO HIS TRP SEQRES 3 B 100 PRO ALA ARG ILE ASP GLU MET PRO GLU ALA ALA VAL LYS SEQRES 4 B 100 SER THR ALA ASN LYS TYR GLN VAL PHE PHE PHE GLY THR SEQRES 5 B 100 HIS GLU THR ALA PHE LEU GLY PRO LYS ASP LEU PHE PRO SEQRES 6 B 100 TYR GLU GLU SER LYS GLU LYS PHE GLY LYS PRO ASN LYS SEQRES 7 B 100 ARG LYS GLY PHE SER GLU GLY LEU TRP GLU ILE GLU ASN SEQRES 8 B 100 ASN PRO THR VAL LYS ALA SER GLY TYR HELIX 1 1 GLY A 59 LYS A 61 5 3 HELIX 2 2 PRO A 65 GLY A 74 1 10 HELIX 3 3 ARG A 79 ASN A 91 1 13 HELIX 4 4 GLY B 159 LYS B 161 5 3 HELIX 5 5 PRO B 165 PHE B 173 1 9 HELIX 6 6 ARG B 179 ASN B 191 1 13 SHEET 1 A 5 GLU B 154 LEU B 158 0 SHEET 2 A 5 TYR B 145 PHE B 149 -1 N VAL B 147 O ALA B 156 SHEET 3 A 5 TYR A 23 ASP A 31 -1 N ARG A 29 O PHE B 148 SHEET 4 A 5 LEU A 15 MET A 20 -1 N ALA A 18 O TRP A 26 SHEET 5 A 5 LEU B 163 PHE B 164 -1 O PHE B 164 N PHE A 17 SHEET 1 B 5 GLU A 54 LEU A 58 0 SHEET 2 B 5 TYR A 45 PHE A 49 -1 N PHE A 49 O GLU A 54 SHEET 3 B 5 TYR B 123 ASP B 131 -1 O ARG B 129 N PHE A 48 SHEET 4 B 5 LEU B 115 MET B 120 -1 N ALA B 118 O TRP B 126 SHEET 5 B 5 LEU A 63 PHE A 64 -1 N PHE A 64 O PHE B 117 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