HEADER LIGASE 12-JAN-12 2RSD TITLE SOLUTION STRUCTURE OF THE PLANT HOMEODOMAIN (PHD) OF THE E3 SUMO TITLE 2 LIGASE SIZ1 FROM RICE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 SUMO-PROTEIN LIGASE SIZ1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PLANT HOMEODOMAIN, UNP RESIDUES 107-172; COMPND 5 EC: 6.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA JAPONICA GROUP; SOURCE 3 ORGANISM_COMMON: JAPANESE RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: SIZ1, OS05G0125000, LOC_OS05G03430, OSJNBB0079L11.3; 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-4T-3 KEYWDS E3 SUMO LIGASE, PLANT HOMEODOMAIN (PHD), HISTONE BINDING, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.SHINDO,W.TSUCHIYA,R.SUZUKI,T.YAMAZAKI REVDAT 3 15-MAY-24 2RSD 1 REMARK REVDAT 2 14-JUN-23 2RSD 1 REMARK SEQADV LINK REVDAT 1 15-AUG-12 2RSD 0 JRNL AUTH H.SHINDO,R.SUZUKI,W.TSUCHIYA,M.TAICHI,Y.NISHIUCHI,T.YAMAZAKI JRNL TITL PHD FINGER OF THE SUMO LIGASE SIZ/PIAS FAMILY IN RICE JRNL TITL 2 REVEALS SPECIFIC BINDING FOR METHYLATED HISTONE H3 AT LYSINE JRNL TITL 3 4 AND ARGININE 2 JRNL REF FEBS LETT. V. 586 1783 2012 JRNL REFN ISSN 0014-5793 JRNL PMID 22626555 JRNL DOI 10.1016/J.FEBSLET.2012.04.063 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1, CYANA 2.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000150226. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1.0 MM [U-13C; U-15N] OSSIZ1 REMARK 210 -PHD-1, 1.0-2.0 MM ZINC ION-2, REMARK 210 100 MM SODIUM CHLORIDE-3, 10 MM REMARK 210 POTASSIUM PHOSPHATE-4, 5 MM DTT- REMARK 210 5, 100% D2O; 0.5-1.0 MM [U-13C; REMARK 210 U-15N] OSSIZ1-PHD-6, 1.0-2.0 MM REMARK 210 ZINC ION-7, 100 MM SODIUM REMARK 210 CHLORIDE-8, 10 MM POTASSIUM REMARK 210 PHOSPHATE-9, 5 MM DTT-10, 92% REMARK 210 H2O/8% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HCABGCO; 3D HCCH-COSY; 3D 15N- REMARK 210 SEPARATED NOESY-HSQC; 3D 13C/15N- REMARK 210 SEPARATED NOESY-HSQC; 4D 13C/13C- REMARK 210 SEPARATED NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE RELEASED AT FEB 10, REMARK 210 2006, SPARKY 3.113, CYANA 2.1, REMARK 210 TALOS+ 1.01F, AQUA 3.2, REMARK 210 PROCHECKNMR 3.5.4 REMARK 210 METHOD USED : TORSION ANGLE 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: 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 SER A 106 -57.37 -160.33 REMARK 500 1 THR A 122 31.39 -94.23 REMARK 500 1 ASN A 125 -169.25 -70.48 REMARK 500 1 CYS A 136 -59.66 -123.09 REMARK 500 1 CYS A 163 -178.69 -56.07 REMARK 500 2 SER A 106 -69.28 72.10 REMARK 500 2 ASP A 107 32.27 -96.50 REMARK 500 2 PHE A 109 92.22 -69.52 REMARK 500 2 THR A 122 31.18 -94.49 REMARK 500 2 ASN A 125 -169.02 -69.03 REMARK 500 2 CYS A 136 -60.83 -130.92 REMARK 500 2 CYS A 163 -175.89 -57.57 REMARK 500 3 THR A 122 31.41 -94.29 REMARK 500 3 ASN A 125 -169.97 -59.86 REMARK 500 3 CYS A 136 -61.30 -128.88 REMARK 500 3 CYS A 163 -176.07 -57.59 REMARK 500 4 SER A 106 -42.66 -173.07 REMARK 500 4 SER A 108 -35.62 -178.13 REMARK 500 4 PHE A 109 92.23 -67.63 REMARK 500 4 THR A 122 31.88 -94.36 REMARK 500 4 ASN A 125 -169.63 -60.14 REMARK 500 4 CYS A 136 -58.54 -125.84 REMARK 500 4 CYS A 163 -176.37 -57.21 REMARK 500 5 SER A 106 51.99 -95.58 REMARK 500 5 THR A 122 31.33 -93.99 REMARK 500 5 ASN A 125 -169.10 -69.46 REMARK 500 5 CYS A 136 -59.92 -127.75 REMARK 500 5 GLU A 153 -169.82 -75.68 REMARK 500 5 CYS A 163 -175.42 -57.63 REMARK 500 6 SER A 108 47.08 -166.43 REMARK 500 6 THR A 122 31.22 -94.54 REMARK 500 6 ASN A 125 -168.43 -70.06 REMARK 500 6 CYS A 136 -59.14 -124.49 REMARK 500 6 GLU A 153 -169.86 -69.19 REMARK 500 6 ALA A 155 165.27 -48.64 REMARK 500 6 CYS A 163 -177.28 -56.99 REMARK 500 7 SER A 106 -69.26 72.13 REMARK 500 7 SER A 108 46.80 -152.29 REMARK 500 7 VAL A 124 89.94 -65.37 REMARK 500 7 ASN A 125 -168.72 -60.59 REMARK 500 7 CYS A 136 -60.05 -128.12 REMARK 500 7 CYS A 163 -175.82 -57.45 REMARK 500 8 SER A 106 39.46 -169.70 REMARK 500 8 THR A 122 31.97 -94.55 REMARK 500 8 ASN A 125 -169.74 -60.08 REMARK 500 8 CYS A 136 -58.74 -125.53 REMARK 500 8 GLU A 153 -169.69 -76.04 REMARK 500 8 CYS A 163 -175.30 -57.64 REMARK 500 9 SER A 106 70.63 52.78 REMARK 500 9 THR A 122 31.11 -94.03 REMARK 500 REMARK 500 THIS ENTRY HAS 112 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 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 117 SG REMARK 620 2 CYS A 119 SG 101.0 REMARK 620 3 HIS A 141 ND1 112.1 96.7 REMARK 620 4 CYS A 144 SG 98.0 130.7 117.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 131 SG REMARK 620 2 CYS A 136 SG 126.3 REMARK 620 3 CYS A 163 SG 131.6 90.0 REMARK 620 4 CYS A 166 SG 95.5 93.8 114.6 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11469 RELATED DB: BMRB DBREF 2RSD A 107 172 UNP Q6L4L4 SIZ1_ORYSJ 107 172 SEQADV 2RSD GLY A 105 UNP Q6L4L4 EXPRESSION TAG SEQADV 2RSD SER A 106 UNP Q6L4L4 EXPRESSION TAG SEQRES 1 A 68 GLY SER ASP SER PHE GLN PRO GLU ALA LYS VAL ARG CYS SEQRES 2 A 68 ILE CYS SER SER THR MET VAL ASN ASP SER MET ILE GLN SEQRES 3 A 68 CYS GLU ASP GLN ARG CYS GLN VAL TRP GLN HIS LEU ASN SEQRES 4 A 68 CYS VAL LEU ILE PRO ASP LYS PRO GLY GLU SER ALA GLU SEQRES 5 A 68 VAL PRO PRO VAL PHE TYR CYS GLU LEU CYS ARG LEU SER SEQRES 6 A 68 ARG ALA ASP HET ZN A 901 1 HET ZN A 902 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 CYS A 163 ALA A 171 1 9 SHEET 1 A 3 LYS A 114 VAL A 115 0 SHEET 2 A 3 VAL A 138 HIS A 141 1 O TRP A 139 N LYS A 114 SHEET 3 A 3 MET A 128 GLN A 130 -1 N ILE A 129 O GLN A 140 LINK SG CYS A 117 ZN ZN A 901 1555 1555 2.42 LINK SG CYS A 119 ZN ZN A 901 1555 1555 2.32 LINK SG CYS A 131 ZN ZN A 902 1555 1555 2.42 LINK SG CYS A 136 ZN ZN A 902 1555 1555 2.54 LINK ND1 HIS A 141 ZN ZN A 901 1555 1555 2.07 LINK SG CYS A 144 ZN ZN A 901 1555 1555 2.41 LINK SG CYS A 163 ZN ZN A 902 1555 1555 2.45 LINK SG CYS A 166 ZN ZN A 902 1555 1555 2.41 SITE 1 AC1 4 CYS A 117 CYS A 119 HIS A 141 CYS A 144 SITE 1 AC2 5 CYS A 131 CYS A 136 VAL A 138 CYS A 163 SITE 2 AC2 5 CYS A 166 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