HEADER TRANSCRIPTION 10-SEP-07 2JV0 TITLE SET DOMAIN OF RIZ1 TUMOR SUPPRESSOR (PRDM2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PR DOMAIN ZINC FINGER PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SET DOMAIN RESIDUES 1-161; COMPND 5 SYNONYM: PR DOMAIN-CONTAINING PROTEIN 2, RETINOBLASTOMA PROTEIN- COMPND 6 INTERACTING ZINC FINGER PROTEIN, ZINC FINGER PROTEIN RIZ, MTE-BINDING COMPND 7 PROTEIN, MTB-ZF, GATA-3-BINDING PROTEIN G3B; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRDM2, RIZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PKG-PBR KEYWDS SET DOMAIN, PR DOMAIN, RIZ1, PRDM2, PROTEIN LYSINE METHYLTRANSFERASE, KEYWDS 2 HISTONE LYSINE METHYLTRANSFERASE, HKMT, ACTIVATOR, ALTERNATIVE KEYWDS 3 INITIATION, DNA-BINDING, METAL-BINDING, NUCLEUS, PHOSPHORYLATION, KEYWDS 4 TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR K.BRIKNAROVA REVDAT 6 20-OCT-21 2JV0 1 REMARK SEQADV LINK REVDAT 5 27-JUL-11 2JV0 1 HETNAM HETSYN REMARK REVDAT 4 13-JUL-11 2JV0 1 VERSN REVDAT 3 29-DEC-09 2JV0 1 HET REVDAT 2 24-FEB-09 2JV0 1 VERSN REVDAT 1 22-JAN-08 2JV0 0 JRNL AUTH K.BRIKNAROVA,X.ZHOU,A.SATTERTHWAIT,D.W.HOYT,K.R.ELY,S.HUANG JRNL TITL STRUCTURAL STUDIES OF THE SET DOMAIN FROM RIZ1 TUMOR JRNL TITL 2 SUPPRESSOR JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 366 807 2008 JRNL REFN ISSN 0006-291X JRNL PMID 18082620 JRNL DOI 10.1016/J.BBRC.2007.12.034 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX, X-PLOR NIH 2.13 REMARK 3 AUTHORS : ACCELRYS SOFTWARE INC. (FELIX), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JV0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000100324. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.082 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4-1 MM [U-99% 15N] ENTITY_1, REMARK 210 20 MM POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2.5 MM DTT, REMARK 210 0-2 MM EDTA, 0-4.5 MM S-ADENOSYL- REMARK 210 L-HOMOCYSTEINE, 90% H2O/10% D2O; REMARK 210 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 ENTITY_1, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 2.5 MM DTT, 0-2 MM REMARK 210 EDTA, 0-4.5 MM S-ADENOSYL-L- REMARK 210 HOMOCYSTEINE, 90% H2O/10% D2O; REMARK 210 0.5-1 MM [U-99% 13C; U-99% 15N; REMARK 210 80% 2H] ENTITY_1, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2.5 MM DTT, REMARK 210 1-2 MM EDTA, 0-4.5 MM S-ADENOSYL- REMARK 210 L-HOMOCYSTEINE, 90% H2O/10% D2O; REMARK 210 0.9 MM [U-99% 15N; 80% 2H] REMARK 210 ENTITY_1, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 2.5 MM DTT, 1-2 MM REMARK 210 EDTA, 4.5 MM S-ADENOSYL-L- REMARK 210 HOMOCYSTEINE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D 1H-13C AROMATIC NOESY; REMARK 210 4D 15N,15N NOESY; 3D CBCA(CO)NH; REMARK 210 3D C(CO)NH; 3D HNCACB; 3D H(CCO) REMARK 210 NH; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, ARIA 1.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 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 OD1 ASN A 112 H LEU A 137 1.26 REMARK 500 H GLY A 53 O THR A 126 1.30 REMARK 500 O PRO A 34 H ALA A 36 1.37 REMARK 500 OD1 ASN A 72 H VAL A 73 1.44 REMARK 500 O VAL A 73 H MET A 75 1.47 REMARK 500 H TYR A 80 O GLY A 84 1.47 REMARK 500 OD1 ASN A 145 H ILE A 148 1.49 REMARK 500 H SER A 35 O ARG A 41 1.52 REMARK 500 O PHE A 33 H GLY A 43 1.53 REMARK 500 H PHE A 33 O GLY A 43 1.57 REMARK 500 O GLU A 153 H ALA A 157 1.57 REMARK 500 H VAL A 78 O MET A 86 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 8 TYR A 124 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 12 TYR A 124 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 13 TYR A 80 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES 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 SER A 0 -46.42 75.39 REMARK 500 1 ASP A 2 -6.48 -150.08 REMARK 500 1 GLN A 3 179.74 -52.80 REMARK 500 1 ALA A 10 106.46 67.73 REMARK 500 1 ALA A 11 -76.54 -129.86 REMARK 500 1 THR A 12 -46.92 151.52 REMARK 500 1 PRO A 27 -112.08 -36.25 REMARK 500 1 GLU A 29 37.20 -172.89 REMARK 500 1 VAL A 30 171.39 -45.69 REMARK 500 1 SER A 35 52.43 -61.69 REMARK 500 1 ALA A 36 -5.36 -56.84 REMARK 500 1 ASP A 38 -66.72 -156.04 REMARK 500 1 LYS A 39 3.60 -58.72 REMARK 500 1 THR A 40 14.64 35.73 REMARK 500 1 ARG A 41 -116.46 -107.30 REMARK 500 1 VAL A 60 -63.46 -21.68 REMARK 500 1 SER A 67 -27.40 -38.08 REMARK 500 1 GLN A 68 -150.35 -91.29 REMARK 500 1 VAL A 69 153.47 58.72 REMARK 500 1 LYS A 70 89.83 -179.16 REMARK 500 1 ASN A 71 64.11 66.56 REMARK 500 1 VAL A 73 -48.50 -134.30 REMARK 500 1 TYR A 74 34.69 -62.09 REMARK 500 1 LEU A 83 -1.16 -166.69 REMARK 500 1 ASN A 97 -151.59 -71.88 REMARK 500 1 ASN A 103 -143.75 -87.42 REMARK 500 1 ALA A 105 -134.62 -101.78 REMARK 500 1 CYS A 106 -51.81 -154.21 REMARK 500 1 SER A 107 65.40 -165.26 REMARK 500 1 PRO A 132 105.48 -41.30 REMARK 500 1 TRP A 139 -164.70 171.87 REMARK 500 1 TYR A 140 48.23 108.08 REMARK 500 1 GLU A 143 -89.32 -33.74 REMARK 500 1 ASP A 144 56.55 -108.93 REMARK 500 1 ALA A 159 8.91 -67.81 REMARK 500 1 ARG A 160 -82.96 -124.65 REMARK 500 2 SER A 0 -63.71 -146.57 REMARK 500 2 MET A 1 -178.39 -55.53 REMARK 500 2 GLU A 7 79.22 41.02 REMARK 500 2 VAL A 9 -174.75 -61.11 REMARK 500 2 ALA A 10 96.14 48.33 REMARK 500 2 ALA A 11 -62.68 -106.80 REMARK 500 2 PRO A 27 -109.41 -34.00 REMARK 500 2 GLU A 29 47.36 -170.24 REMARK 500 2 SER A 35 -60.33 102.72 REMARK 500 2 LYS A 39 -32.19 -32.38 REMARK 500 2 THR A 40 55.38 -143.28 REMARK 500 2 VAL A 60 -67.34 -16.38 REMARK 500 2 GLN A 68 -8.70 103.20 REMARK 500 2 LYS A 70 -131.22 -110.22 REMARK 500 REMARK 500 THIS ENTRY HAS 516 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QPW RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A SHORTHER CONSTRUCT DBREF 2JV0 A 1 161 UNP Q13029 PRDM2_HUMAN 1 161 SEQADV 2JV0 GLY A -1 UNP Q13029 EXPRESSION TAG SEQADV 2JV0 SER A 0 UNP Q13029 EXPRESSION TAG SEQADV 2JV0 ASP A 2 UNP Q13029 ASN 2 ENGINEERED MUTATION SEQADV 2JV0 IAS A 141 UNP Q13029 ASN 141 ENGINEERED MUTATION SEQRES 1 A 163 GLY SER MET ASP GLN ASN THR THR GLU PRO VAL ALA ALA SEQRES 2 A 163 THR GLU THR LEU ALA GLU VAL PRO GLU HIS VAL LEU ARG SEQRES 3 A 163 GLY LEU PRO GLU GLU VAL ARG LEU PHE PRO SER ALA VAL SEQRES 4 A 163 ASP LYS THR ARG ILE GLY VAL TRP ALA THR LYS PRO ILE SEQRES 5 A 163 LEU LYS GLY LYS LYS PHE GLY PRO PHE VAL GLY ASP LYS SEQRES 6 A 163 LYS LYS ARG SER GLN VAL LYS ASN ASN VAL TYR MET TRP SEQRES 7 A 163 GLU VAL TYR TYR PRO ASN LEU GLY TRP MET CYS ILE ASP SEQRES 8 A 163 ALA THR ASP PRO GLU LYS GLY ASN TRP LEU ARG TYR VAL SEQRES 9 A 163 ASN TRP ALA CYS SER GLY GLU GLU GLN ASN LEU PHE PRO SEQRES 10 A 163 LEU GLU ILE ASN ARG ALA ILE TYR TYR LYS THR LEU LYS SEQRES 11 A 163 PRO ILE ALA PRO GLY GLU GLU LEU LEU VAL TRP TYR IAS SEQRES 12 A 163 GLY GLU ASP ASN PRO GLU ILE ALA ALA ALA ILE GLU GLU SEQRES 13 A 163 GLU ARG ALA SER ALA ARG SER HET IAS A 141 12 HETNAM IAS BETA-L-ASPARTIC ACID HETSYN IAS L-ASPARTIC ACID FORMUL 1 IAS C4 H7 N O4 HELIX 1 1 PRO A 19 ARG A 24 1 6 HELIX 2 2 TRP A 98 VAL A 102 5 5 HELIX 3 3 ASN A 145 ALA A 159 1 15 SHEET 1 A 2 ARG A 31 PRO A 34 0 SHEET 2 A 2 ILE A 42 TRP A 45 -1 O GLY A 43 N PHE A 33 SHEET 1 B 3 LYS A 54 PHE A 59 0 SHEET 2 B 3 ALA A 121 THR A 126 -1 O TYR A 124 N PHE A 56 SHEET 3 B 3 PHE A 114 ILE A 118 -1 N ILE A 118 O ALA A 121 SHEET 1 C 3 LYS A 63 LYS A 64 0 SHEET 2 C 3 GLY A 84 ASP A 89 -1 O CYS A 87 N LYS A 64 SHEET 3 C 3 MET A 75 TYR A 80 -1 N TYR A 80 O GLY A 84 SHEET 1 D 2 ASN A 103 TRP A 104 0 SHEET 2 D 2 LEU A 137 VAL A 138 1 O VAL A 138 N ASN A 103 LINK C TYR A 140 N IAS A 141 1555 1555 1.34 LINK CG IAS A 141 N GLY A 142 1555 1555 1.35 CISPEP 1 GLY A 57 PRO A 58 1 0.43 CISPEP 2 GLY A 57 PRO A 58 2 0.74 CISPEP 3 GLY A 57 PRO A 58 3 -1.61 CISPEP 4 GLY A 57 PRO A 58 4 -0.61 CISPEP 5 GLY A 57 PRO A 58 5 -0.56 CISPEP 6 GLY A 57 PRO A 58 6 -0.44 CISPEP 7 GLY A 57 PRO A 58 7 0.23 CISPEP 8 GLY A 57 PRO A 58 8 0.04 CISPEP 9 GLY A 57 PRO A 58 9 -1.05 CISPEP 10 GLY A 57 PRO A 58 10 3.10 CISPEP 11 GLY A 57 PRO A 58 11 0.89 CISPEP 12 GLY A 57 PRO A 58 12 0.70 CISPEP 13 GLY A 57 PRO A 58 13 0.49 CISPEP 14 GLY A 57 PRO A 58 14 0.49 CISPEP 15 GLY A 57 PRO A 58 15 -0.57 CISPEP 16 GLY A 57 PRO A 58 16 0.68 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