PDB Short entry for 2KYU HEADER TRANSFERASE 08-JUN-10 2KYU TITLE THE SOLUTION STRUCTURE OF THE PHD3 FINGER OF MLL COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE MLL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD3 FINGER (UNP RESIDUES 1564-1628); COMPND 5 SYNONYM: ZINC FINGER PROTEIN HRX, ALL-1, TRITHORAX-LIKE PROTEIN, COMPND 6 LYSINE N-METHYLTRANSFERASE 2A, KMT2A, CXXC-TYPE ZINC FINGER PROTEIN COMPND 7 7; 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: MLL, ALL1, CXXC7, HRX, HTRX, KMT2A, MLL1, TRX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: GE HEALTHCARE KEYWDS PHD, CHROMATIN REGULATION, TRANSCRIPTION, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.PARK,J.H.BUSHWELLER REVDAT 2 05-FEB-20 2KYU 1 REMARK SEQADV REVDAT 1 25-AUG-10 2KYU 0 JRNL AUTH S.PARK,U.OSMERS,G.RAMAN,R.H.SCHWANTES,M.O.DIAZ, JRNL AUTH 2 J.H.BUSHWELLER JRNL TITL THE PHD3 DOMAIN OF MLL ACTS AS A CYP33-REGULATED SWITCH JRNL TITL 2 BETWEEN MLL-MEDIATED ACTIVATION AND REPRESSION. JRNL REF BIOCHEMISTRY V. 49 6576 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20677832 JRNL DOI 10.1021/BI1009387 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000101744. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1 MM [U-98% 13C; U-98% 15N] REMARK 210 PHD3, 100 UM ZINC ION, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 3 MM DTT, REMARK 210 50 MM SODIUM CHLORIDE, 1 MM REMARK 210 SODIUM AZIDE, 95% H2O/5% 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 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HCCH-TOCSY; 3D HNHA; REMARK 210 3D C(CO)NH; 3D TROSY-HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN 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 : 10 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 H MET A 25 O VAL A 34 1.58 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 6 176.97 54.50 REMARK 500 1 CYS A 11 -48.54 -155.64 REMARK 500 1 LYS A 13 -102.04 60.65 REMARK 500 1 CYS A 14 100.23 -175.40 REMARK 500 1 TYR A 15 -42.10 79.13 REMARK 500 1 ASP A 16 85.12 59.69 REMARK 500 1 LYS A 23 90.30 -54.81 REMARK 500 1 GLU A 54 10.60 83.79 REMARK 500 1 GLU A 65 -167.45 43.21 REMARK 500 1 ARG A 66 76.72 62.29 REMARK 500 2 ALA A 3 110.39 61.33 REMARK 500 2 CYS A 11 -43.70 -156.17 REMARK 500 2 ASP A 12 22.18 49.80 REMARK 500 2 LYS A 13 144.86 59.00 REMARK 500 2 CYS A 14 90.68 -67.06 REMARK 500 2 TYR A 15 -38.87 78.63 REMARK 500 2 ASP A 16 95.20 43.13 REMARK 500 2 LYS A 23 86.10 -58.41 REMARK 500 2 ASP A 31 18.33 59.40 REMARK 500 2 GLU A 54 17.28 85.84 REMARK 500 2 GLU A 65 -170.76 46.96 REMARK 500 3 LYS A 4 -172.59 62.34 REMARK 500 3 ASN A 6 106.72 -162.72 REMARK 500 3 CYS A 8 179.74 -59.73 REMARK 500 3 LEU A 10 -57.91 -136.71 REMARK 500 3 CYS A 11 -67.87 -136.04 REMARK 500 3 LYS A 13 18.88 46.49 REMARK 500 3 CYS A 14 104.66 56.79 REMARK 500 3 TYR A 15 -39.25 80.08 REMARK 500 3 ASP A 16 96.96 47.22 REMARK 500 3 ASN A 40 31.96 70.65 REMARK 500 3 GLU A 54 8.19 87.01 REMARK 500 3 ARG A 66 -72.72 -79.05 REMARK 500 4 SER A -1 36.90 -153.17 REMARK 500 4 ASN A 6 92.51 -160.20 REMARK 500 4 CYS A 11 -54.83 -156.64 REMARK 500 4 LYS A 13 -93.65 54.79 REMARK 500 4 CYS A 14 69.69 -176.24 REMARK 500 4 TYR A 15 -44.98 78.46 REMARK 500 4 ASP A 16 167.79 58.23 REMARK 500 4 ASP A 18 64.05 -160.43 REMARK 500 4 SER A 22 26.53 -70.48 REMARK 500 4 LYS A 23 72.92 59.59 REMARK 500 4 ASP A 31 14.07 58.22 REMARK 500 4 GLU A 54 6.59 86.08 REMARK 500 4 GLU A 65 97.60 47.21 REMARK 500 4 ARG A 66 168.51 61.74 REMARK 500 5 SER A -1 82.63 61.32 REMARK 500 5 ALA A 3 -170.18 61.91 REMARK 500 5 ASN A 6 83.64 62.24 REMARK 500 REMARK 500 THIS ENTRY HAS 128 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 81 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 ND1 REMARK 620 2 CYS A 8 SG 112.2 REMARK 620 3 CYS A 11 SG 119.9 122.4 REMARK 620 4 CYS A 38 SG 111.5 90.5 91.9 REMARK 620 5 ASP A 12 N 91.4 79.2 77.0 157.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 82 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 30 SG REMARK 620 2 CYS A 63 SG 100.2 REMARK 620 3 CYS A 27 SG 112.7 119.5 REMARK 620 4 CYS A 60 SG 103.4 106.3 112.9 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 81 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 82 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16983 RELATED DB: BMRB DBREF 2KYU A 3 67 UNP Q03164 MLL1_HUMAN 1564 1628 SEQADV 2KYU GLY A -2 UNP Q03164 EXPRESSION TAG SEQADV 2KYU SER A -1 UNP Q03164 EXPRESSION TAG SEQRES 1 A 67 GLY SER ALA LYS GLY ASN PHE CYS PRO LEU CYS ASP LYS SEQRES 2 A 67 CYS TYR ASP ASP ASP ASP TYR GLU SER LYS MET MET GLN SEQRES 3 A 67 CYS GLY LYS CYS ASP ARG TRP VAL HIS SER LYS CYS GLU SEQRES 4 A 67 ASN LEU SER ASP GLU MET TYR GLU ILE LEU SER ASN LEU SEQRES 5 A 67 PRO GLU SER VAL ALA TYR THR CYS VAL ASN CYS THR GLU SEQRES 6 A 67 ARG HIS HET ZN A 81 1 HET ZN A 82 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 SER A 42 LEU A 52 1 11 HELIX 2 2 CYS A 60 GLU A 65 1 6 SHEET 1 A 2 MET A 24 GLN A 26 0 SHEET 2 A 2 TRP A 33 HIS A 35 -1 O VAL A 34 N MET A 25 LINK ND1 HIS A 35 ZN ZN A 81 1555 1555 2.07 LINK SG CYS A 30 ZN ZN A 82 1555 1555 2.25 LINK SG CYS A 63 ZN ZN A 82 1555 1555 2.28 LINK SG CYS A 27 ZN ZN A 82 1555 1555 2.29 LINK SG CYS A 8 ZN ZN A 81 1555 1555 2.31 LINK SG CYS A 60 ZN ZN A 82 1555 1555 2.32 LINK SG CYS A 11 ZN ZN A 81 1555 1555 2.32 LINK SG CYS A 38 ZN ZN A 81 1555 1555 2.42 LINK N ASP A 12 ZN ZN A 81 1555 1555 2.57 SITE 1 AC1 5 CYS A 8 CYS A 11 ASP A 12 HIS A 35 SITE 2 AC1 5 CYS A 38 SITE 1 AC2 5 CYS A 27 LYS A 29 CYS A 30 CYS A 60 SITE 2 AC2 5 CYS A 63 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