HEADER OXIDOREDUCTASE 16-APR-14 2MNY TITLE NMR STRUCTURE OF KDM5B PHD1 FINGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER DOMAIN PHD1, RESIDUES 306-360; 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: KDM5B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-1 KEYWDS PHD1, KDM5B, H3K4, DEMETHYLATION, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.ZHANG,H.R.YANG,X.GUO,N.Y.RONG,Y.J.SONG,Y.W.XU,W.X.LAN,Y.H.XU,C.CAO REVDAT 4 15-MAY-24 2MNY 1 REMARK REVDAT 3 14-JUN-23 2MNY 1 REMARK REVDAT 2 24-AUG-22 2MNY 1 JRNL REMARK LINK REVDAT 1 06-AUG-14 2MNY 0 JRNL AUTH Y.ZHANG,H.YANG,X.GUO,N.RONG,Y.SONG,Y.XU,W.LAN,X.ZHANG,M.LIU, JRNL AUTH 2 Y.XU,C.CAO JRNL TITL THE PHD1 FINGER OF KDM5B RECOGNIZES UNMODIFIED H3K4 DURING JRNL TITL 2 THE DEMETHYLATION OF HISTONE H3K4ME2/3 BY KDM5B. JRNL REF PROTEIN CELL V. 5 837 2014 JRNL REFN ESSN 1674-8018 JRNL PMID 24952722 JRNL DOI 10.1007/S13238-014-0078-4 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MNY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000103842. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-13C; U-15N] PHD1 REMARK 210 FINGER OF KDM5B-1, 90% H2O, 10% REMARK 210 D2O; 0.8 MM [U-13C; U-15N] PHD1 REMARK 210 FINGER OF KDM5B-2, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D REMARK 210 CBCA(CO)NH; 2D 1H-15N HSQC; 3D REMARK 210 HNCO; 3D 1H-15N TOCSY; 3D HNCA; REMARK 210 3D HNCACB; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D HCCH-TOCSY; 2D 1H- REMARK 210 13C HSQC AROMATIC; 2D 1H-13C REMARK 210 HSQC ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DD2 REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL 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 : 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: 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 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 315 -59.68 -128.51 REMARK 500 1 LEU A 339 -45.26 -174.34 REMARK 500 1 PRO A 342 162.87 -34.70 REMARK 500 1 LEU A 343 -129.49 -137.02 REMARK 500 2 CYS A 315 -66.02 -128.01 REMARK 500 2 ASP A 331 89.20 -68.16 REMARK 500 2 LEU A 339 -43.40 -175.05 REMARK 500 2 PRO A 342 164.03 -36.51 REMARK 500 2 LEU A 343 -95.83 -123.14 REMARK 500 3 ASP A 331 12.84 -60.41 REMARK 500 3 LEU A 339 -39.46 -175.34 REMARK 500 3 PRO A 342 162.29 -34.75 REMARK 500 3 LEU A 343 -138.56 -123.51 REMARK 500 4 CYS A 330 -145.41 -152.63 REMARK 500 4 LEU A 339 -36.75 -151.51 REMARK 500 4 PRO A 342 159.86 -34.67 REMARK 500 4 LYS A 348 -56.85 -163.43 REMARK 500 5 TYR A 310 108.24 58.22 REMARK 500 5 ASP A 331 14.03 -60.40 REMARK 500 5 LEU A 339 -45.47 -173.92 REMARK 500 5 PRO A 342 163.91 -36.29 REMARK 500 5 LEU A 343 -42.81 -172.07 REMARK 500 6 CYS A 315 28.95 -153.39 REMARK 500 6 CYS A 330 -140.20 -142.46 REMARK 500 6 LEU A 339 -31.42 -153.80 REMARK 500 6 PRO A 342 162.69 -35.41 REMARK 500 6 LEU A 343 -34.42 -131.58 REMARK 500 7 ASP A 331 86.83 -68.73 REMARK 500 7 LEU A 339 -46.25 -175.63 REMARK 500 7 PRO A 342 163.63 -34.79 REMARK 500 7 LYS A 348 -125.46 -173.24 REMARK 500 8 CYS A 315 -46.98 -151.63 REMARK 500 8 CYS A 330 -156.78 -142.55 REMARK 500 8 LEU A 339 -34.35 -150.15 REMARK 500 8 PRO A 342 163.72 -33.87 REMARK 500 8 LEU A 343 -60.73 179.87 REMARK 500 9 CYS A 315 -41.98 -147.45 REMARK 500 9 LEU A 339 -31.68 -164.76 REMARK 500 9 PRO A 342 161.32 -34.78 REMARK 500 9 LEU A 343 -121.97 -138.11 REMARK 500 10 CYS A 330 -153.60 -149.71 REMARK 500 10 LEU A 339 -46.77 -174.72 REMARK 500 10 PRO A 342 161.52 -33.93 REMARK 500 11 CYS A 315 -53.23 -125.34 REMARK 500 11 LEU A 339 -45.73 -175.00 REMARK 500 11 PRO A 342 161.80 -33.54 REMARK 500 11 LEU A 343 -129.08 -137.03 REMARK 500 12 SER A 317 -84.74 -83.42 REMARK 500 12 CYS A 330 -160.55 -127.78 REMARK 500 12 PRO A 342 159.86 -28.34 REMARK 500 REMARK 500 THIS ENTRY HAS 88 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 312 SG REMARK 620 2 CYS A 315 SG 108.3 REMARK 620 3 HIS A 335 ND1 108.5 112.8 REMARK 620 4 CYS A 338 SG 108.8 108.5 109.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 327 SG REMARK 620 2 CYS A 330 SG 108.2 REMARK 620 3 CYS A 353 SG 109.3 111.6 REMARK 620 4 CYS A 356 SG 112.6 112.3 102.7 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19913 RELATED DB: BMRB REMARK 900 RELATED ID: 2MNZ RELATED DB: PDB DBREF 2MNY A 306 360 UNP Q9UGL1 KDM5B_HUMAN 306 360 SEQRES 1 A 55 ALA VAL ASP LEU TYR VAL CYS LEU LEU CYS GLY SER GLY SEQRES 2 A 55 ASN ASP GLU ASP ARG LEU LEU LEU CYS ASP GLY CYS ASP SEQRES 3 A 55 ASP SER TYR HIS THR PHE CYS LEU ILE PRO PRO LEU HIS SEQRES 4 A 55 ASP VAL PRO LYS GLY ASP TRP ARG CYS PRO LYS CYS LEU SEQRES 5 A 55 ALA GLN GLU HET ZN A 401 1 HET ZN A 402 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 GLY A 318 ASP A 322 5 5 HELIX 2 2 CYS A 353 GLU A 360 1 8 SHEET 1 A 2 LEU A 324 LEU A 326 0 SHEET 2 A 2 SER A 333 HIS A 335 -1 O TYR A 334 N LEU A 325 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 315 ZN ZN A 401 1555 1555 2.31 LINK SG CYS A 327 ZN ZN A 402 1555 1555 2.29 LINK SG CYS A 330 ZN ZN A 402 1555 1555 2.30 LINK ND1 HIS A 335 ZN ZN A 401 1555 1555 2.01 LINK SG CYS A 338 ZN ZN A 401 1555 1555 2.31 LINK SG CYS A 353 ZN ZN A 402 1555 1555 2.31 LINK SG CYS A 356 ZN ZN A 402 1555 1555 2.29 SITE 1 AC1 4 CYS A 312 CYS A 315 HIS A 335 CYS A 338 SITE 1 AC2 4 CYS A 327 CYS A 330 CYS A 353 CYS A 356 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