PDB Short entry for 2MA5 HEADER OXIDOREDUCTASE 28-JUN-13 2MA5 TITLE SOLUTION NMR STRUCTURE OF PHD TYPE ZINC FINGER DOMAIN OF LYSINE- TITLE 2 SPECIFIC DEMETHYLASE 5B (PLU-1/JARID1B) FROM HOMO SAPIENS, NORTHEAST TITLE 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET HR7375C COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1487-1544; COMPND 5 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, COMPND 6 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA- COMPND 7 BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1; COMPND 8 EC: 1.14.11.-; COMPND 9 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: JARID1B, KDM5B, PLU1, RBBP2H1; 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_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15AVI6HT_NESG; SOURCE 11 OTHER_DETAILS: AVI TAG CUT WITH TEV PROTEASE KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 2 PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, ZINC BINDING PROTEIN, KEYWDS 3 PHD, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.HASSAN,T.A.RAMELOT,Y.YANG,J.R.CORT,H.JANJUA,E.KOHAN,D.LEE,R.XIAO, AUTHOR 2 T.B.ACTON,J.K.EVERETT,G.T.MONTELIONE,M.A.KENNEDY,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 14-JUN-23 2MA5 1 REMARK SEQADV LINK REVDAT 1 14-AUG-13 2MA5 0 JRNL AUTH F.HASSAN,T.A.RAMELOT,Y.YANG,J.R.CORT,H.JANJUA,E.KOHAN,D.LEE, JRNL AUTH 2 R.XIAO,T.B.ACTON,J.K.EVERETT,G.T.MONTELIONE,M.A.KENNEDY JRNL TITL SOLUTION NMR STRUCTURE OF PHD TYPE ZINC FINGER DOMAIN OF JRNL TITL 2 LYSINE-SPECIFIC DEMETHYLASE 5B (PLU-1/JARID1B) FROM HOMO JRNL TITL 3 SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) JRNL TITL 4 TARGET HR7375C JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3, FMCGUI FMCGUI2.1_LINUX, CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), ALEX LEMAK, CHERYL ARROWMITH (FMCGUI), BRUNGER,ADAMS, REMARK 3 CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS WATER REFINEMENT OF CYANA REMARK 3 STRUCTURES, NULL REMARK 4 REMARK 4 2MA5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000103401. 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 : 1.04 MM [U-100% 13C; U-100% 15N] REMARK 210 HR7375C.005, 0.02 % NAN3, 10 MM REMARK 210 DTT, 5 MM CACL2, 100 MM NACL, 1 REMARK 210 X PROTEINASE INHIBITORS, 20 MM REMARK 210 MES PH 6.5, 10 % D2O, 50 UM DSS, REMARK 210 90% H2O/10% D2O; 1.04 MM [U-100% REMARK 210 13C; U-100% 15N] HR7375C.006, REMARK 210 0.02 % NAN3, 10 MM DTT, 5 MM REMARK 210 CACL2, 100 MM NACL, 1 X REMARK 210 PROTEINASE INHIBITORS, 20 MM MES REMARK 210 PH 6.5, 10 % D2O, 50 UM DSS, 90% REMARK 210 H2O/10% D2O; 0.33 MM [U-100% 15N] REMARK 210 5% 13C FRACTIONALLY LABELED REMARK 210 HR7375C.007, 0.02 % NAN3, 10 MM REMARK 210 DTT, 5 MM CACL2, 100 MM NACL, 1 REMARK 210 X PROTEINASE INHIBITORS, 20 MM REMARK 210 MES PH 6.5, 10 % D2O, 50 UM DSS, REMARK 210 90% H2O/10% D2O; 1.04 MM [U-100% REMARK 210 13C; U-100% 15N] HR7375C.005, REMARK 210 0.02 % NAN3, 10 MM DTT, 5 MM REMARK 210 CACL2, 100 MM NACL, 1 X REMARK 210 PROTEINASE INHIBITORS, 20 MM MES REMARK 210 PH 6.5, 100 % D2O, 50 UM DSS, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-15N NOESY NUS; REMARK 210 3D 1H-13C NOESY ALIPHATIC NUS; REMARK 210 3D 1H-13C NOESY AROMATIC NUS; 2D REMARK 210 1H-15N HSQC HIS; 1D 1H-15N HSQC REMARK 210 T1 ARRAY; 1D 1H-15N HSQC T2 REMARK 210 ARRAY; 2D 1H-15N HSQC NH2 ONLY; REMARK 210 2D 1H-13C HSQC AROMATIC CT; 2D REMARK 210 1H-13C HSQC AROMATIC NOCT; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HN(CO) REMARK 210 CA; 3D HNCO; 3D HBHA(CO)NH; 3D REMARK 210 C(CO)NH; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, AUTOSTRUCTURE 2.1, REMARK 210 NMRPIPE NMRPIPE-2008// REMARK 210 NMRBIN.LINUX9, TOPSPIN 2.4, REMARK 210 VNMRJ, PINE, SPARKY 3.113, TALOS+ REMARK 210 VERSION 1.2009.0721.18, PSVS 1.4 REMARK 210 METHOD USED : SIMULATED ANNEALING, NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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: 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 5 80.96 -68.76 REMARK 500 1 PRO A 12 -145.48 -72.12 REMARK 500 1 ASP A 23 -80.34 -57.24 REMARK 500 1 SER A 25 26.96 -159.81 REMARK 500 1 CYS A 26 -41.29 -143.11 REMARK 500 1 ALA A 57 85.75 60.49 REMARK 500 2 PRO A 5 39.34 -80.53 REMARK 500 2 CYS A 9 86.11 -151.27 REMARK 500 2 GLU A 16 -71.96 -123.91 REMARK 500 2 SER A 25 32.54 -157.61 REMARK 500 2 CYS A 26 -48.38 -132.74 REMARK 500 2 ASN A 27 -6.65 74.37 REMARK 500 2 GLU A 45 118.88 -162.32 REMARK 500 2 ASP A 46 107.18 61.74 REMARK 500 2 ASP A 56 -35.34 73.63 REMARK 500 2 ARG A 60 120.77 69.76 REMARK 500 3 HIS A 2 35.62 -163.46 REMARK 500 3 MET A 3 169.11 66.65 REMARK 500 3 CYS A 4 81.23 64.36 REMARK 500 3 SER A 8 -35.79 -147.42 REMARK 500 3 CYS A 9 97.02 70.18 REMARK 500 3 SER A 25 60.32 -161.36 REMARK 500 3 CYS A 26 -45.67 -155.85 REMARK 500 3 LYS A 55 -73.17 -71.74 REMARK 500 3 ASP A 56 -76.43 -145.21 REMARK 500 3 ALA A 57 90.53 45.55 REMARK 500 3 ARG A 60 -179.28 67.86 REMARK 500 4 CYS A 4 157.14 68.22 REMARK 500 4 GLU A 16 61.07 64.86 REMARK 500 4 ASP A 23 -78.55 -94.40 REMARK 500 4 SER A 25 15.36 -157.33 REMARK 500 4 CYS A 26 57.37 -159.21 REMARK 500 4 ASN A 27 80.49 -49.87 REMARK 500 4 GLU A 45 127.68 -174.49 REMARK 500 4 ASP A 46 133.83 73.16 REMARK 500 4 TYR A 47 20.77 -151.25 REMARK 500 4 PRO A 58 95.21 -64.64 REMARK 500 4 ARG A 60 61.19 63.22 REMARK 500 5 CYS A 4 156.51 76.00 REMARK 500 5 ASP A 15 -80.73 -129.76 REMARK 500 5 GLU A 16 12.22 53.51 REMARK 500 5 CYS A 26 -26.34 -176.01 REMARK 500 5 ALA A 57 63.24 63.51 REMARK 500 5 ARG A 60 -174.28 61.86 REMARK 500 6 CYS A 4 67.26 -172.68 REMARK 500 6 VAL A 7 -71.15 62.62 REMARK 500 6 ASP A 15 -72.19 -69.24 REMARK 500 6 GLU A 16 25.83 -162.37 REMARK 500 6 ASP A 23 -84.71 62.41 REMARK 500 6 CYS A 26 -50.70 -146.28 REMARK 500 REMARK 500 THIS ENTRY HAS 164 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 6 HIS A 31 0.10 SIDE CHAIN 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 4 SG REMARK 620 2 CYS A 9 SG 112.4 REMARK 620 3 HIS A 31 NE2 107.0 111.0 REMARK 620 4 CYS A 34 SG 108.3 110.0 108.0 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 22 SG REMARK 620 2 CYS A 26 SG 109.4 REMARK 620 3 CYS A 49 SG 107.3 112.0 REMARK 620 4 CYS A 52 SG 111.1 107.8 109.3 REMARK 620 N 1 2 3 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: 19328 RELATED DB: BMRB REMARK 900 RELATED ID: NESG-HR7375C RELATED DB: TARGETTRACK DBREF 2MA5 A 4 61 UNP Q9UGL1 KDM5B_HUMAN 1487 1544 SEQADV 2MA5 SER A 1 UNP Q9UGL1 EXPRESSION TAG SEQADV 2MA5 HIS A 2 UNP Q9UGL1 EXPRESSION TAG SEQADV 2MA5 MET A 3 UNP Q9UGL1 EXPRESSION TAG SEQRES 1 A 61 SER HIS MET CYS PRO ALA VAL SER CYS LEU GLN PRO GLU SEQRES 2 A 61 GLY ASP GLU VAL ASP TRP VAL GLN CYS ASP GLY SER CYS SEQRES 3 A 61 ASN GLN TRP PHE HIS GLN VAL CYS VAL GLY VAL SER PRO SEQRES 4 A 61 GLU MET ALA GLU LYS GLU ASP TYR ILE CYS VAL ARG CYS SEQRES 5 A 61 THR VAL LYS ASP ALA PRO SER ARG LYS HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 GLN A 32 GLY A 36 1 5 HELIX 2 2 SER A 38 LYS A 44 1 7 HELIX 3 3 CYS A 49 LYS A 55 1 7 SHEET 1 A 2 TRP A 19 CYS A 22 0 SHEET 2 A 2 GLN A 28 HIS A 31 -1 O PHE A 30 N VAL A 20 LINK SG CYS A 4 ZN ZN A 101 1555 1555 2.34 LINK SG CYS A 9 ZN ZN A 101 1555 1555 2.35 LINK SG CYS A 22 ZN ZN A 102 1555 1555 2.35 LINK SG CYS A 26 ZN ZN A 102 1555 1555 2.35 LINK NE2 HIS A 31 ZN ZN A 101 1555 1555 2.12 LINK SG CYS A 34 ZN ZN A 101 1555 1555 2.36 LINK SG CYS A 49 ZN ZN A 102 1555 1555 2.33 LINK SG CYS A 52 ZN ZN A 102 1555 1555 2.34 SITE 1 AC1 4 CYS A 4 CYS A 9 HIS A 31 CYS A 34 SITE 1 AC2 4 CYS A 22 CYS A 26 CYS A 49 CYS A 52 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