HEADER OXIDOREDUCTASE 17-DEC-13 2MIQ TITLE SOLUTION NMR STRUCTURE OF PHD TYPE 1 ZINC FINGER DOMAIN 1 OF LYSINE- TITLE 2 SPECIFIC DEMETHYLASE LID FROM DROSOPHILA MELANOGASTER, NORTHEAST TITLE 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET FR824J COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE LID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD-TYPE 1 ZINC FINGER RESIDUES 414-504; COMPND 5 SYNONYM: HISTONE DEMETHYLASE LID, JUMONJI/ARID DOMAIN-CONTAINING COMPND 6 PROTEIN LID, PROTEIN LITTLE IMAGINAL DISKS, RETINOBLASTOMA-BINDING COMPND 7 PROTEIN 2 HOMOLOG; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CG9088, LID; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15AVI6HT_NESG KEYWDS ZINC FINGER, PSI-BIOLOGY, OXIDOREDUCTASE, STRUCTURAL GENOMICS, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, CHAPERONE-ENABLED KEYWDS 3 STUDIES OF EPIGENETIC REGULATION ENZYMES, CEBS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.XU,A.ELETSKY,R.SHASTRY,M.MAGLAQUI,H.JANJUA,R.XIAO,J.K.EVERETT, AUTHOR 2 D.K.SUKUMARAN,G.T.MONTELIONE,T.SZYPERSKI,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG),CHAPERONE-ENABLED STUDIES OF EPIGENETIC AUTHOR 4 REGULATION ENZYMES (CEBS) REVDAT 4 14-JUN-23 2MIQ 1 REMARK SEQADV LINK REVDAT 3 23-APR-14 2MIQ 1 AUTHOR JRNL REVDAT 2 19-FEB-14 2MIQ 1 AUTHOR KEYWDS REVDAT 1 29-JAN-14 2MIQ 0 JRNL AUTH X.XU,A.ELETSKY,R.SHASTRY,M.MAGLAQUI,H.JANJUA,R.XIAO, JRNL AUTH 2 J.K.EVERETT,D.SUKUMARAN,G.T.MONTELIONE,T.SZYPERSKI JRNL TITL SOLUTION NMR STRUCTURE OF PHD TYPE 1 ZINC FINGER DOMAIN 1 JRNL TITL 2 FROM LYSINE-SPECIFIC DEMETHYLASE LID FROM DROSOPHILA JRNL TITL 3 MELANOGASTER, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM JRNL TITL 4 (NESG) TARGET FR824J JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, PROSA, CARA, CSI, CYANA 3.0, AUTOSTRUCTURE REMARK 3 2.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT (PROSA), KELLER AND WUTHRICH (CARA), REMARK 3 DAVID WISHART,LEIGH WILLARD,TIM JELLARD,BRIAN REMARK 3 SYKES (CSI), GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 (CYANA), HUANG, TEJERO, POWERS AND MONTELIONE REMARK 3 (AUTOSTRUCTURE) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED REMARK 3 CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM REMARK 3 TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN REMARK 3 ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 REMARK 3 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY REMARK 3 SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS REMARK 3 WITH PARAM19 FORCE FIELD NMR ENSEMBLE INFORMATION REMARK 4 REMARK 4 2MIQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103660. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.321 MM 10% 13C AND 100% 15N REMARK 210 LABELED PROTEIN, 90% H2O/10% D2O; REMARK 210 0.321 MM 13C AND 15N LABELED REMARK 210 PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D SIMUTANEOUS 13C- REMARK 210 AROMATIC,13C-ALIPHATIC,15N REMARK 210 EDITED 1H-1H NOESY; 2D 1H-13C CT REMARK 210 HSQC ALIPHATIC; 2D 1H-13C CT REMARK 210 HSQC AROMATIC; 3D HN(CA)CO; 3D REMARK 210 (H)CCH-COSY-ALI; 3D (H)CCH-COSY REMARK 210 ARO; 3D (H)CCH-TOCSY ALI; 2D REMARK 210 GNFHSQC_HIS; 2D 1H-13C CT- REMARK 210 HSQC(28MS); 2D 1H-13C CT- REMARK 210 HSQC(42MS); 2D 1H-13C CT- REMARK 210 HSQC(56MS); 2D J-MODULATION 1H- REMARK 210 15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS, PROSA, CARA, CSI, CYANA REMARK 210 3.0, AUTOSTRUCTURE 2.1, REMARK 210 AUTOASSIGN 2.1, XEASY, VNMRJ, REMARK 210 TALOS+, PSVS, MOLMOL REMARK 210 METHOD USED : SIMULATED ANNEALING 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: 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 HIS A 2 73.58 -112.54 REMARK 500 1 LEU A 9 54.49 -100.70 REMARK 500 1 SER A 21 74.89 -116.36 REMARK 500 1 LEU A 36 -78.39 -99.71 REMARK 500 1 TYR A 39 95.40 -69.74 REMARK 500 1 ASN A 45 9.51 55.49 REMARK 500 1 ASP A 48 -76.28 -42.83 REMARK 500 1 CYS A 59 -155.88 177.09 REMARK 500 1 ASP A 60 104.96 -161.28 REMARK 500 1 ASP A 61 146.25 -175.68 REMARK 500 1 PRO A 93 45.48 -74.56 REMARK 500 2 PRO A 8 84.63 -65.35 REMARK 500 2 THR A 11 91.84 -69.64 REMARK 500 2 ALA A 15 97.09 -67.70 REMARK 500 2 THR A 17 93.17 -67.93 REMARK 500 2 LYS A 24 39.28 -146.97 REMARK 500 2 PRO A 29 -74.35 -41.10 REMARK 500 2 ALA A 30 124.67 -176.59 REMARK 500 2 ILE A 32 76.45 61.60 REMARK 500 2 ASN A 45 -8.68 74.55 REMARK 500 2 ASP A 57 85.17 -61.90 REMARK 500 2 ASP A 60 76.40 61.15 REMARK 500 2 LYS A 77 -28.77 73.03 REMARK 500 2 GLU A 88 124.17 71.66 REMARK 500 2 SER A 91 46.43 -83.78 REMARK 500 2 LYS A 92 95.85 59.84 REMARK 500 3 ALA A 10 94.95 -67.70 REMARK 500 3 LEU A 36 -93.21 -152.47 REMARK 500 3 TYR A 39 99.53 -59.55 REMARK 500 3 ASN A 45 -56.50 75.60 REMARK 500 3 ASP A 57 99.52 -63.02 REMARK 500 3 CYS A 59 10.64 -147.04 REMARK 500 3 ASP A 61 99.35 -66.56 REMARK 500 3 PRO A 76 -179.90 -66.08 REMARK 500 3 LYS A 77 35.90 -83.08 REMARK 500 3 GLU A 79 99.69 -68.16 REMARK 500 3 GLU A 89 -71.22 59.38 REMARK 500 3 VAL A 90 82.33 57.96 REMARK 500 4 THR A 13 86.73 -66.03 REMARK 500 4 ALA A 20 92.79 -67.99 REMARK 500 4 GLN A 22 99.92 -161.76 REMARK 500 4 PRO A 28 -175.14 -67.44 REMARK 500 4 ILE A 32 109.96 -57.16 REMARK 500 4 PRO A 35 32.22 -86.00 REMARK 500 4 ASP A 48 -89.15 62.61 REMARK 500 4 CYS A 59 -153.82 -171.40 REMARK 500 4 LYS A 77 105.67 -58.93 REMARK 500 4 GLU A 79 176.57 67.59 REMARK 500 4 VAL A 87 -53.45 75.39 REMARK 500 4 GLU A 88 -164.48 -77.27 REMARK 500 REMARK 500 THIS ENTRY HAS 247 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 41 SG REMARK 620 2 CYS A 44 SG 101.9 REMARK 620 3 HIS A 64 ND1 111.0 111.5 REMARK 620 4 CYS A 67 SG 95.0 114.8 119.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 56 SG REMARK 620 2 GLY A 58 O 86.3 REMARK 620 3 CYS A 59 SG 113.4 92.9 REMARK 620 4 CYS A 82 SG 75.2 157.8 105.4 REMARK 620 5 CYS A 85 SG 135.7 93.8 110.8 91.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19682 RELATED DB: BMRB REMARK 900 RELATED ID: NESG-FR824J RELATED DB: TARGETTRACK DBREF 2MIQ A 4 94 UNP Q9VMJ7 KDM5_DROME 414 504 SEQADV 2MIQ SER A 1 UNP Q9VMJ7 EXPRESSION TAG SEQADV 2MIQ HIS A 2 UNP Q9VMJ7 EXPRESSION TAG SEQADV 2MIQ MET A 3 UNP Q9VMJ7 EXPRESSION TAG SEQRES 1 A 94 SER HIS MET SER GLY GLY SER PRO LEU ALA THR GLY THR SEQRES 2 A 94 THR ALA ASN THR ARG GLY ALA SER GLN LYS LYS GLY GLY SEQRES 3 A 94 GLU PRO PRO ALA LEU ILE VAL ASP PRO LEU MET LYS TYR SEQRES 4 A 94 ILE CYS HIS ILE CYS ASN ARG GLY ASP VAL GLU GLU SER SEQRES 5 A 94 MET LEU LEU CYS ASP GLY CYS ASP ASP SER TYR HIS THR SEQRES 6 A 94 PHE CYS LEU LEU PRO PRO LEU THR SER ILE PRO LYS GLY SEQRES 7 A 94 GLU TRP LEU CYS PRO ARG CYS VAL VAL GLU GLU VAL SER SEQRES 8 A 94 LYS PRO GLN HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 VAL A 49 GLU A 51 5 3 HELIX 2 2 CYS A 82 VAL A 87 1 6 SHEET 1 A 2 MET A 53 LEU A 55 0 SHEET 2 A 2 SER A 62 HIS A 64 -1 O TYR A 63 N LEU A 54 SSBOND 1 CYS A 41 CYS A 67 1555 1555 2.92 SSBOND 2 CYS A 56 CYS A 82 1555 1555 2.89 SSBOND 3 CYS A 82 CYS A 85 1555 1555 2.82 LINK SG CYS A 41 ZN ZN A 101 1555 1555 2.05 LINK SG CYS A 44 ZN ZN A 101 1555 1555 1.84 LINK SG CYS A 56 ZN ZN A 102 1555 1555 2.62 LINK O GLY A 58 ZN ZN A 102 1555 1555 1.89 LINK SG CYS A 59 ZN ZN A 102 1555 1555 1.90 LINK ND1 HIS A 64 ZN ZN A 101 1555 1555 1.90 LINK SG CYS A 67 ZN ZN A 101 1555 1555 1.90 LINK SG CYS A 82 ZN ZN A 102 1555 1555 2.07 LINK SG CYS A 85 ZN ZN A 102 1555 1555 1.87 CISPEP 1 LEU A 69 PRO A 70 1 -4.18 CISPEP 2 LEU A 69 PRO A 70 2 -0.56 CISPEP 3 LEU A 69 PRO A 70 3 4.05 CISPEP 4 LEU A 69 PRO A 70 4 -0.72 CISPEP 5 LEU A 69 PRO A 70 5 -3.99 CISPEP 6 LEU A 69 PRO A 70 6 -1.43 CISPEP 7 LEU A 69 PRO A 70 7 -3.98 CISPEP 8 LEU A 69 PRO A 70 8 2.62 CISPEP 9 LEU A 69 PRO A 70 9 -0.03 CISPEP 10 LEU A 69 PRO A 70 10 -3.16 CISPEP 11 LEU A 69 PRO A 70 11 -1.91 CISPEP 12 LEU A 69 PRO A 70 12 -2.10 CISPEP 13 LEU A 69 PRO A 70 13 -1.96 CISPEP 14 LEU A 69 PRO A 70 14 5.74 CISPEP 15 LEU A 69 PRO A 70 15 -5.81 CISPEP 16 LEU A 69 PRO A 70 16 -5.88 CISPEP 17 LEU A 69 PRO A 70 17 0.75 CISPEP 18 LEU A 69 PRO A 70 18 -1.82 CISPEP 19 LEU A 69 PRO A 70 19 5.99 CISPEP 20 LEU A 69 PRO A 70 20 -7.05 SITE 1 AC1 4 CYS A 41 CYS A 44 HIS A 64 CYS A 67 SITE 1 AC2 5 CYS A 56 GLY A 58 CYS A 59 CYS A 82 SITE 2 AC2 5 CYS A 85 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