HEADER TRANSCRIPTION 13-SEP-10 2L3D TITLE THE SOLUTION STRUCTURE OF THE SHORT FORM SWIRM DOMAIN OF LSD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SWIRM DOMAIN; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-4T KEYWDS LSD1, SWIRM, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.LIU,K.LO,G.ZHU,K.SZE REVDAT 2 01-MAY-24 2L3D 1 REMARK SEQADV REVDAT 1 21-SEP-11 2L3D 0 JRNL AUTH C.LIU,R.LUO,K.SZE JRNL TITL THE CHEMICAL SHIFT ASSIGNMENT OF THE SWIRM DOMAIN OF LSD1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, AMBER REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL, REMARK 3 SINGH,WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AMBER REMARK 4 REMARK 4 2L3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000101905. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM [U-100% 13C; U-100% 15N] REMARK 210 SWIRM-1, 50MM SODIUM PHOSPHATE-2, REMARK 210 50MM SODIUM CHLORIDE-3, 2MM DTT- REMARK 210 4, 1MM EDTA-5, 90% H2O/10% D2O; REMARK 210 0.8MM SWIRM-6, 50MM SODIUM REMARK 210 PHOSPHATE-7, 50MM SODIUM REMARK 210 CHLORIDE-8, 2MM DTT-9, 1MM EDTA- REMARK 210 10, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HBHA(CO)NH; 3D H(CCO)NH; REMARK 210 3D C(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, CYANA REMARK 210 METHOD USED : 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 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: 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 4 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ASN A 53 75.84 56.59 REMARK 500 1 LYS A 55 -87.31 -161.81 REMARK 500 1 ILE A 56 -57.12 -125.24 REMARK 500 1 GLU A 68 63.76 -109.31 REMARK 500 1 TYR A 96 98.02 -58.19 REMARK 500 2 LYS A 55 -73.99 -71.27 REMARK 500 2 GLU A 68 74.90 -108.44 REMARK 500 3 ASP A 15 19.14 58.47 REMARK 500 3 GLU A 68 57.74 -103.99 REMARK 500 4 ALA A 6 44.46 -74.81 REMARK 500 4 GLN A 57 91.10 -69.31 REMARK 500 4 PHE A 93 66.67 -110.66 REMARK 500 4 TYR A 96 9.35 52.25 REMARK 500 5 ALA A 6 11.05 53.46 REMARK 500 5 GLN A 9 -76.44 -65.83 REMARK 500 5 ASP A 15 14.61 -144.01 REMARK 500 5 GLU A 68 48.79 -73.20 REMARK 500 5 HIS A 88 -7.77 -58.84 REMARK 500 5 ILE A 99 -39.85 -133.99 REMARK 500 6 ALA A 6 -79.30 -114.80 REMARK 500 6 ASP A 52 0.23 -69.79 REMARK 500 6 ASN A 53 89.59 61.60 REMARK 500 6 ASN A 92 67.18 36.47 REMARK 500 7 TYR A 96 75.03 -109.11 REMARK 500 7 LYS A 100 75.58 46.55 REMARK 500 8 LEU A 90 18.43 56.84 REMARK 500 9 ASN A 53 59.48 -140.68 REMARK 500 9 GLU A 68 66.11 -69.90 REMARK 500 9 ASP A 74 94.74 -69.69 REMARK 500 9 LEU A 90 47.14 -72.13 REMARK 500 9 ILE A 91 29.62 44.52 REMARK 500 10 ARG A 11 -71.91 -122.33 REMARK 500 10 LEU A 12 158.37 63.01 REMARK 500 10 LEU A 58 96.55 -64.29 REMARK 500 10 GLU A 68 53.69 -103.89 REMARK 500 10 ILE A 99 -73.14 -122.56 REMARK 500 10 LYS A 100 -57.15 -157.02 REMARK 500 11 VAL A 3 63.55 -103.51 REMARK 500 11 SER A 10 95.87 -67.75 REMARK 500 11 LEU A 12 162.45 64.28 REMARK 500 11 ASN A 53 77.36 -119.47 REMARK 500 11 LYS A 55 -75.71 -77.99 REMARK 500 11 GLU A 68 60.80 -101.08 REMARK 500 11 ILE A 91 103.26 -46.93 REMARK 500 12 ALA A 6 44.62 -71.52 REMARK 500 12 HIS A 14 78.28 59.12 REMARK 500 12 PHE A 25 67.98 -119.61 REMARK 500 12 GLU A 68 65.44 -113.95 REMARK 500 13 ASN A 53 72.05 -119.16 REMARK 500 14 PHE A 8 -72.78 -135.72 REMARK 500 REMARK 500 THIS ENTRY HAS 72 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2L3D A 3 102 UNP O60341 KDM1A_HUMAN 174 273 SEQADV 2L3D GLY A 1 UNP O60341 EXPRESSION TAG SEQADV 2L3D SER A 2 UNP O60341 EXPRESSION TAG SEQRES 1 A 102 GLY SER VAL GLU GLY ALA ALA PHE GLN SER ARG LEU PRO SEQRES 2 A 102 HIS ASP ARG MET THR SER GLN GLU ALA ALA CYS PHE PRO SEQRES 3 A 102 ASP ILE ILE SER GLY PRO GLN GLN THR GLN LYS VAL PHE SEQRES 4 A 102 LEU PHE ILE ARG ASN ARG THR LEU GLN LEU TRP LEU ASP SEQRES 5 A 102 ASN PRO LYS ILE GLN LEU THR PHE GLU ALA THR LEU GLN SEQRES 6 A 102 GLN LEU GLU ALA PRO TYR ASN SER ASP THR VAL LEU VAL SEQRES 7 A 102 HIS ARG VAL HIS SER TYR LEU GLU ARG HIS GLY LEU ILE SEQRES 8 A 102 ASN PHE GLY ILE TYR LYS ARG ILE LYS PRO LEU HELIX 1 1 THR A 18 ALA A 23 1 6 HELIX 2 2 PHE A 25 SER A 30 1 6 HELIX 3 3 PRO A 32 ASP A 52 1 21 HELIX 4 4 THR A 59 LEU A 67 1 9 HELIX 5 5 ALA A 69 SER A 73 5 5 HELIX 6 6 ASP A 74 GLY A 89 1 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 MODEL 1