PDB Short entry for 2COM HEADER OXIDOREDUCTASE 18-MAY-05 2COM TITLE THE SOLUTION STRUCTURE OF THE SWIRM DOMAIN OF HUMAN LSD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SWIRM DOMAIN; COMPND 5 SYNONYM: AMINE OXIDASE FLAVIN CONTAINING DOMAIN PROTEIN 2, AOF2 COMPND 6 PROTEIN, BRAF35-HDAC COMPLEX PROTEIN BHC110; COMPND 7 EC: 1.-.-.-; COMPND 8 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: LSD1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040401-21; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS SWIRM DOMAIN, LSD1, AOF2, KIAA0601, HISTONE MODULATION, STRUCTURAL KEYWDS 2 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.TOCHIO,T.UMEHARA,S.KOSHIBA,M.INOUE,A.TANAKA,T.KIGAWA,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 09-MAR-22 2COM 1 REMARK SEQADV REVDAT 4 24-FEB-09 2COM 1 VERSN REVDAT 3 18-APR-06 2COM 1 JRNL REVDAT 2 10-JAN-06 2COM 1 JRNL TITLE REVDAT 1 18-NOV-05 2COM 0 JRNL AUTH N.TOCHIO,T.UMEHARA,S.KOSHIBA,M.INOUE,T.YABUKI,M.AOKI,E.SEKI, JRNL AUTH 2 S.WATANABE,Y.TOMO,M.HANADA,M.IKARI,M.SATO,T.TERADA,T.NAGASE, JRNL AUTH 3 O.OHARA,M.SHIROUZU,A.TANAKA,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE SWIRM DOMAIN OF HUMAN HISTONE JRNL TITL 2 DEMETHYLASE LSD1 JRNL REF STRUCTURE V. 14 457 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16531230 JRNL DOI 10.1016/J.STR.2005.12.004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2COM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024454. 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 : 1.2MM SWIRM DOMAIN U-15N,13C; REMARK 210 20MM D-TRIS HCL; 100MM NACL; 1MM REMARK 210 D-DTT; 0.02% NAN3; 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -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 : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.8994, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION,STRUCTURES WITH REMARK 210 THE LEAST 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 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: 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 PRO A 10 -177.74 -69.71 REMARK 500 1 ARG A 21 78.16 -69.44 REMARK 500 1 SER A 40 35.47 -99.09 REMARK 500 1 GLN A 43 -36.25 -37.33 REMARK 500 1 ALA A 79 165.12 -47.37 REMARK 500 1 TYR A 94 -36.06 -38.46 REMARK 500 1 ILE A 105 -36.80 -132.46 REMARK 500 1 ILE A 109 112.75 -33.78 REMARK 500 1 LYS A 110 140.32 -171.41 REMARK 500 1 PRO A 113 94.97 -69.82 REMARK 500 1 LYS A 115 75.67 -60.86 REMARK 500 1 SER A 123 46.99 34.34 REMARK 500 2 GLU A 9 74.75 -115.40 REMARK 500 2 PRO A 10 4.38 -69.76 REMARK 500 2 ARG A 21 44.03 31.50 REMARK 500 2 SER A 40 33.28 -94.62 REMARK 500 2 ALA A 79 161.69 -44.83 REMARK 500 2 TYR A 94 -38.00 -39.54 REMARK 500 2 ILE A 105 -33.15 -39.18 REMARK 500 2 ARG A 108 151.99 -44.71 REMARK 500 2 SER A 119 95.21 -63.28 REMARK 500 3 SER A 3 108.66 -172.91 REMARK 500 3 PRO A 10 91.32 -69.80 REMARK 500 3 ALA A 17 -36.60 -33.90 REMARK 500 3 ARG A 21 41.20 -82.91 REMARK 500 3 ALA A 79 156.66 -41.33 REMARK 500 3 ILE A 105 -37.80 -33.54 REMARK 500 3 ILE A 109 111.40 -38.74 REMARK 500 3 PRO A 111 -173.82 -69.79 REMARK 500 3 PRO A 113 97.12 -69.76 REMARK 500 3 LYS A 115 43.64 34.25 REMARK 500 3 LYS A 116 46.91 -77.62 REMARK 500 4 ALA A 16 -34.24 -38.28 REMARK 500 4 GLN A 19 -35.51 -39.22 REMARK 500 4 ARG A 21 72.44 -69.76 REMARK 500 4 ALA A 79 163.80 -46.08 REMARK 500 4 TYR A 94 -37.47 -39.91 REMARK 500 4 ILE A 105 -33.38 -133.97 REMARK 500 4 ARG A 108 -55.53 -123.74 REMARK 500 4 PRO A 121 3.74 -69.74 REMARK 500 4 SER A 122 162.53 -41.87 REMARK 500 5 SER A 11 132.12 -170.45 REMARK 500 5 ALA A 17 -32.56 -35.49 REMARK 500 5 GLN A 30 -70.87 -59.59 REMARK 500 5 GLU A 31 -38.51 -37.77 REMARK 500 5 SER A 40 36.67 -95.27 REMARK 500 5 PRO A 64 4.46 -69.76 REMARK 500 5 ALA A 79 160.10 -43.77 REMARK 500 5 ILE A 105 -37.26 -134.11 REMARK 500 5 PRO A 111 -176.78 -69.78 REMARK 500 REMARK 500 THIS ENTRY HAS 206 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002000585.1 RELATED DB: TARGETDB DBREF 2COM A 8 118 UNP O60341 LSD1_HUMAN 169 279 SEQADV 2COM GLY A 1 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 2 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 3 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 4 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 5 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 6 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 7 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 119 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 120 UNP O60341 CLONING ARTIFACT SEQADV 2COM PRO A 121 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 122 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 123 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 124 UNP O60341 CLONING ARTIFACT SEQRES 1 A 124 GLY SER SER GLY SER SER GLY GLU GLU PRO SER GLY VAL SEQRES 2 A 124 GLU GLY ALA ALA PHE GLN SER ARG LEU PRO HIS ASP ARG SEQRES 3 A 124 MET THR SER GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE SEQRES 4 A 124 SER GLY PRO GLN GLN THR GLN LYS VAL PHE LEU PHE ILE SEQRES 5 A 124 ARG ASN ARG THR LEU GLN LEU TRP LEU ASP ASN PRO LYS SEQRES 6 A 124 ILE GLN LEU THR PHE GLU ALA THR LEU GLN GLN LEU GLU SEQRES 7 A 124 ALA PRO TYR ASN SER ASP THR VAL LEU VAL HIS ARG VAL SEQRES 8 A 124 HIS SER TYR LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY SEQRES 9 A 124 ILE TYR LYS ARG ILE LYS PRO LEU PRO THR LYS LYS THR SEQRES 10 A 124 GLY SER GLY PRO SER SER GLY HELIX 1 1 GLY A 12 GLN A 19 1 8 HELIX 2 2 THR A 28 PHE A 35 1 8 HELIX 3 3 PHE A 35 SER A 40 1 6 HELIX 4 4 PRO A 42 ASN A 63 1 22 HELIX 5 5 THR A 69 LEU A 77 1 9 HELIX 6 6 ASP A 84 HIS A 98 1 15 CISPEP 1 ALA A 79 PRO A 80 1 -0.04 CISPEP 2 ALA A 79 PRO A 80 2 -0.02 CISPEP 3 ALA A 79 PRO A 80 3 0.06 CISPEP 4 ALA A 79 PRO A 80 4 -0.01 CISPEP 5 ALA A 79 PRO A 80 5 -0.01 CISPEP 6 ALA A 79 PRO A 80 6 0.02 CISPEP 7 ALA A 79 PRO A 80 7 -0.03 CISPEP 8 ALA A 79 PRO A 80 8 0.03 CISPEP 9 ALA A 79 PRO A 80 9 -0.01 CISPEP 10 ALA A 79 PRO A 80 10 0.01 CISPEP 11 ALA A 79 PRO A 80 11 0.03 CISPEP 12 ALA A 79 PRO A 80 12 0.05 CISPEP 13 ALA A 79 PRO A 80 13 0.05 CISPEP 14 ALA A 79 PRO A 80 14 0.02 CISPEP 15 ALA A 79 PRO A 80 15 -0.03 CISPEP 16 ALA A 79 PRO A 80 16 0.08 CISPEP 17 ALA A 79 PRO A 80 17 0.05 CISPEP 18 ALA A 79 PRO A 80 18 0.03 CISPEP 19 ALA A 79 PRO A 80 19 -0.05 CISPEP 20 ALA A 79 PRO A 80 20 0.04 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