PDB Short entry for 2ODD HEADER METAL BINDING PROTEIN 22-DEC-06 2ODD TITLE SOLUTION STRUCTURE OF THE MYND DOMAIN FROM AML1-ETO COMPLEXED WITH TITLE 2 SMRT, A COREPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMRT; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: SMRT (RESIDUES 1101-1113); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN CBFA2T1; COMPND 8 CHAIN: A; COMPND 9 FRAGMENT: MYND DOMAIN (AML1-ETO, RESIDUES 658-707); COMPND 10 SYNONYM: PROTEIN MTG8, PROTEIN ETO, EIGHT TWENTY ONE PROTEIN, CYCLIN- COMPND 11 D-RELATED PROTEIN, ZINC FINGER MYND DOMAIN- CONTAINING PROTEIN 2; COMPND 12 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: SMRT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T3; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: AML1-ETO; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL-21; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX4T3 KEYWDS MYND ZINC FINGER, CROSS-BRACED TOPOLOGY, POLY-PROLINE, PROLINE- KEYWDS 2 TRYPTOPHAN INTERACTION, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR Y.Z.LIU,W.CHEN,J.GAUDET,M.D.CHENEY,L.ROUDAIA,T.CIERPICKI,R.C.KLET, AUTHOR 2 K.HARTMAN,T.M.LAUE,N.A.SPECK,J.H.BUSHWELLER REVDAT 5 27-DEC-23 2ODD 1 REMARK REVDAT 4 16-MAR-22 2ODD 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2ODD 1 VERSN REVDAT 2 17-JUL-07 2ODD 1 JRNL REVDAT 1 19-JUN-07 2ODD 0 JRNL AUTH Y.LIU,W.CHEN,J.GAUDET,M.D.CHENEY,L.ROUDAIA,T.CIERPICKI, JRNL AUTH 2 R.C.KLET,K.HARTMAN,T.M.LAUE,N.A.SPECK,J.H.BUSHWELLER JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF SMRT/N-COR BY THE MYND JRNL TITL 2 DOMAIN AND ITS CONTRIBUTION TO AML1/ETO'S ACTIVITY. JRNL REF CANCER CELL V. 11 483 2007 JRNL REFN ISSN 1535-6108 JRNL PMID 17560331 JRNL DOI 10.1016/J.CCR.2007.04.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, CNS REMARK 3 AUTHORS : BRUNGER, A.T. ET AL. (CNS), BRUNGER, A.T. ET AL. REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ODD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040993. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM SMRT-MYND, 25MM BIS-TRIS, PH REMARK 210 6.8, 50UM ZNCL2, 1MM DTT, 95%H2O, REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-25 REMARK 465 RES C SSSEQI REMARK 465 GLY B 1097 REMARK 465 SER B 1098 REMARK 465 GLY B 1099 REMARK 465 SER B 1100 REMARK 465 GLU A 644 REMARK 465 ASN A 645 REMARK 465 LEU A 646 REMARK 465 TYR A 647 REMARK 465 PHE A 648 REMARK 465 GLN A 649 REMARK 465 GLY A 650 REMARK 465 GLU A 651 REMARK 465 ASN A 652 REMARK 465 LEU A 653 REMARK 465 TYR A 654 REMARK 465 PHE A 655 REMARK 465 GLN A 656 REMARK 465 GLY A 657 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 B1103 -173.27 -55.42 REMARK 500 1 ALA B1112 132.47 -175.89 REMARK 500 1 SER A 659 -43.06 -171.49 REMARK 500 1 SER A 662 133.84 -174.19 REMARK 500 1 ASN A 665 -63.60 -101.35 REMARK 500 1 ARG A 668 -65.79 -127.22 REMARK 500 1 CYS A 699 149.69 -37.52 REMARK 500 1 GLN A 701 167.54 61.78 REMARK 500 1 THR A 702 97.05 60.11 REMARK 500 1 ALA A 705 -62.29 -136.74 REMARK 500 2 SER B1103 -172.39 -69.88 REMARK 500 2 ALA B1112 90.39 -162.15 REMARK 500 2 SER A 659 82.76 -67.41 REMARK 500 2 ASN A 665 -62.50 -102.37 REMARK 500 2 ARG A 668 -66.44 -121.39 REMARK 500 2 CYS A 699 156.07 -36.95 REMARK 500 3 SER B1103 -176.93 -55.71 REMARK 500 3 SER A 659 33.21 -98.44 REMARK 500 3 GLU A 661 80.73 61.79 REMARK 500 3 SER A 662 135.17 -176.97 REMARK 500 3 ASN A 665 -62.68 -96.97 REMARK 500 3 ARG A 668 -72.36 -126.46 REMARK 500 3 GLN A 701 101.22 -55.07 REMARK 500 3 GLN A 706 -67.44 -107.87 REMARK 500 4 SER A 662 138.28 -175.95 REMARK 500 4 ASN A 665 -62.62 -96.46 REMARK 500 4 ARG A 668 -70.57 -129.22 REMARK 500 4 GLN A 701 89.52 -167.30 REMARK 500 4 LEU A 703 -45.51 -160.04 REMARK 500 5 SER A 659 36.31 -98.66 REMARK 500 5 GLU A 661 111.75 61.24 REMARK 500 5 SER A 662 128.56 -173.56 REMARK 500 5 ASN A 665 -62.67 -103.22 REMARK 500 5 ARG A 668 -62.01 -125.42 REMARK 500 5 CYS A 699 155.08 -36.17 REMARK 500 5 GLN A 701 85.64 -159.97 REMARK 500 5 GLN A 704 171.01 60.60 REMARK 500 5 ALA A 705 -48.64 -136.09 REMARK 500 5 GLN A 706 75.23 -153.66 REMARK 500 6 ALA B1112 65.75 -158.58 REMARK 500 6 SER A 662 130.50 -171.88 REMARK 500 6 ASN A 665 -61.99 -103.92 REMARK 500 6 ARG A 668 -62.84 -127.24 REMARK 500 6 GLN A 701 116.99 65.42 REMARK 500 6 THR A 702 160.30 59.77 REMARK 500 6 GLN A 704 163.45 63.87 REMARK 500 7 ILE B1102 -82.23 60.24 REMARK 500 7 PRO B1106 173.18 -55.89 REMARK 500 7 ALA B1112 92.07 -160.71 REMARK 500 7 SER A 659 79.87 -150.65 REMARK 500 REMARK 500 THIS ENTRY HAS 179 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 663 SG REMARK 620 2 CYS A 666 SG 116.8 REMARK 620 3 CYS A 683 SG 119.6 112.6 REMARK 620 4 CYS A 687 SG 114.4 94.9 93.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 674 SG REMARK 620 2 CYS A 677 SG 104.2 REMARK 620 3 HIS A 695 NE2 116.6 98.7 REMARK 620 4 CYS A 699 SG 101.9 108.5 125.0 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OD1 RELATED DB: PDB DBREF 2ODD A 658 707 UNP Q06455 MTG8_HUMAN 510 559 DBREF 2ODD B 1097 1113 PDB 2ODD 2ODD 1097 1113 SEQADV 2ODD GLU A 644 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD ASN A 645 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD LEU A 646 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD TYR A 647 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD PHE A 648 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD GLN A 649 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD GLY A 650 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD GLU A 651 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD ASN A 652 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD LEU A 653 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD TYR A 654 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD PHE A 655 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD GLN A 656 UNP Q06455 CLONING ARTIFACT SEQADV 2ODD GLY A 657 UNP Q06455 CLONING ARTIFACT SEQRES 1 B 17 GLY SER GLY SER THR ILE SER ASN PRO PRO PRO LEU ILE SEQRES 2 B 17 SER SER ALA LYS SEQRES 1 A 64 GLU ASN LEU TYR PHE GLN GLY GLU ASN LEU TYR PHE GLN SEQRES 2 A 64 GLY ASP SER SER GLU SER CYS TRP ASN CYS GLY ARG LYS SEQRES 3 A 64 ALA SER GLU THR CYS SER GLY CYS ASN THR ALA ARG TYR SEQRES 4 A 64 CYS GLY SER PHE CYS GLN HIS LYS ASP TRP GLU LYS HIS SEQRES 5 A 64 HIS HIS ILE CYS GLY GLN THR LEU GLN ALA GLN GLN HET ZN A 1 1 HET ZN A 2 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 GLY A 684 HIS A 696 1 13 SHEET 1 A 3 LEU B1108 SER B1110 0 SHEET 2 A 3 GLU A 672 CYS A 674 -1 O THR A 673 N ILE B1109 SHEET 3 A 3 ARG A 681 TYR A 682 -1 O TYR A 682 N GLU A 672 LINK ZN ZN A 1 SG CYS A 663 1555 1555 2.30 LINK ZN ZN A 1 SG CYS A 666 1555 1555 2.34 LINK ZN ZN A 1 SG CYS A 683 1555 1555 2.32 LINK ZN ZN A 1 SG CYS A 687 1555 1555 2.34 LINK ZN ZN A 2 SG CYS A 674 1555 1555 2.30 LINK ZN ZN A 2 SG CYS A 677 1555 1555 2.34 LINK ZN ZN A 2 NE2 HIS A 695 1555 1555 2.03 LINK ZN ZN A 2 SG CYS A 699 1555 1555 2.33 SITE 1 AC1 4 CYS A 663 CYS A 666 CYS A 683 CYS A 687 SITE 1 AC2 4 CYS A 674 CYS A 677 HIS A 695 CYS A 699 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