PDB Short entry for 2KDZ HEADER TRANSCRIPTION/DNA 21-JAN-09 2KDZ TITLE STRUCTURE OF THE R2R3 DNA BINDING DOMAIN OF MYB1 PROTEIN FROM TITLE 2 PROTOZOAN PARASITE TRICHOMONAS VAGINALIS IN COMPLEX WITH MRE-1/MRE-2R TITLE 3 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYB24; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MYB1 R2R3 DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*TP*A)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*TP*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*TP*CP*TP*T)-3'; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHOMONAS VAGINALIS; SOURCE 3 ORGANISM_TAXID: 5722; SOURCE 4 STRAIN: T1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET29B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS MYB1, R2R3 DOMAIN, DNA-BINDING, NUCLEUS, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.C.LOU,S.Y.WEI,M.RAJASEKARAN,C.C.CHOU,H.M.HSU,J.H.TAI,C.CHEN REVDAT 2 16-MAR-22 2KDZ 1 REMARK REVDAT 1 17-MAR-09 2KDZ 0 JRNL AUTH Y.C.LOU,S.Y.WEI,M.RAJASEKARAN,C.C.CHOU,H.M.HSU,J.H.TAI, JRNL AUTH 2 C.CHEN JRNL TITL NMR STRUCTURAL ANALYSIS OF DNA RECOGNITION BY A NOVEL MYB1 JRNL TITL 2 DNA-BINDING DOMAIN IN THE PROTOZOAN PARASITE TRICHOMONAS JRNL TITL 3 VAGINALIS. JRNL REF NUCLEIC ACIDS RES. 2009 JRNL REFN ESSN 1362-4962 JRNL PMID 19246540 JRNL DOI 10.1093/NAR/GKP097 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRVIEWJ 8.0, X-PLOR NIH REMARK 3 AUTHORS : JOHNSON, ONE MOON SCIENTIFIC (NMRVIEWJ), REMARK 3 SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000101002. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.32 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM CHLORIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 5 MM SODIUM REMARK 210 AZIDE, 10 MM DTT, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D HN(CA) REMARK 210 CO; 3D HCCH-TOCSY; 3D C(CO)NH; REMARK 210 3D HBHA(CO)NH; 2D 1H-15N HXNOE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEWJ 8.0, NMRPIPE, SPARKY, REMARK 210 TALOS, X-PLOR NIH, HADDOCK 2.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, WATER REMARK 210 REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 HE2 PHE A 4 HG3 ARG A 42 1.14 REMARK 500 O4 DT B 11 H62 DA C 22 1.52 REMARK 500 OE2 GLU A 8 HZ2 LYS A 11 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 LYS A 3 175.32 63.43 REMARK 500 1 PHE A 4 176.79 60.39 REMARK 500 1 THR A 5 171.97 170.27 REMARK 500 1 LYS A 22 -32.87 -144.76 REMARK 500 1 TYR A 46 -50.13 -141.78 REMARK 500 1 PRO A 49 -165.00 -100.77 REMARK 500 1 ARG A 52 -156.17 -145.58 REMARK 500 1 THR A 53 57.40 37.34 REMARK 500 1 ASP A 54 162.79 71.12 REMARK 500 1 PRO A 55 -148.52 -72.13 REMARK 500 1 TYR A 68 -47.29 -171.72 REMARK 500 1 PRO A 73 36.46 -93.02 REMARK 500 1 LYS A 83 87.44 -60.35 REMARK 500 1 ASN A 84 -37.35 177.33 REMARK 500 1 ASP A 87 -78.55 -47.25 REMARK 500 1 LYS A 103 -168.49 63.64 REMARK 500 1 LYS A 106 -60.32 -158.20 REMARK 500 2 LYS A 3 -176.04 60.53 REMARK 500 2 PHE A 4 175.54 61.88 REMARK 500 2 THR A 5 178.76 171.17 REMARK 500 2 ALA A 21 30.40 -97.49 REMARK 500 2 LYS A 22 -37.24 -138.79 REMARK 500 2 TYR A 46 -53.28 -135.13 REMARK 500 2 ARG A 52 -157.93 -137.40 REMARK 500 2 THR A 53 57.05 38.08 REMARK 500 2 ASP A 54 164.62 67.20 REMARK 500 2 PRO A 55 -158.50 -70.77 REMARK 500 2 PRO A 73 34.29 -76.10 REMARK 500 2 LYS A 83 80.70 -68.78 REMARK 500 2 ASN A 84 -50.68 167.52 REMARK 500 2 ASP A 87 -71.58 -52.61 REMARK 500 2 LYS A 103 -157.78 55.72 REMARK 500 2 HIS A 104 102.88 -161.50 REMARK 500 2 LYS A 106 -57.78 -150.45 REMARK 500 3 LYS A 3 173.98 64.93 REMARK 500 3 PHE A 4 173.34 65.43 REMARK 500 3 THR A 5 165.17 176.89 REMARK 500 3 LYS A 22 -50.21 -134.76 REMARK 500 3 ALA A 50 72.72 -119.88 REMARK 500 3 LEU A 51 91.42 -67.17 REMARK 500 3 ARG A 52 -149.92 -160.28 REMARK 500 3 THR A 53 47.39 37.92 REMARK 500 3 ASP A 54 168.48 66.97 REMARK 500 3 PRO A 55 -149.39 -74.11 REMARK 500 3 LYS A 74 66.51 -118.17 REMARK 500 3 LYS A 83 82.42 -69.37 REMARK 500 3 ASN A 84 -40.88 -179.47 REMARK 500 3 ASP A 87 -87.25 -41.02 REMARK 500 3 LYS A 103 -159.95 59.92 REMARK 500 3 HIS A 104 115.89 -160.84 REMARK 500 REMARK 500 THIS ENTRY HAS 159 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KDZ A 1 107 UNP Q58HP2 Q58HP2_TRIVA 35 141 DBREF 2KDZ B 1 16 PDB 2KDZ 2KDZ 1 16 DBREF 2KDZ C 17 32 PDB 2KDZ 2KDZ 17 32 SEQRES 1 A 107 LYS VAL LYS PHE THR GLU GLU GLU ASP LEU LYS LEU GLN SEQRES 2 A 107 GLN LEU VAL MET ARG TYR GLY ALA LYS ASP TRP ILE ARG SEQRES 3 A 107 ILE SER GLN LEU MET ILE THR ARG ASN PRO ARG GLN CYS SEQRES 4 A 107 ARG GLU ARG TRP ASN ASN TYR ILE ASN PRO ALA LEU ARG SEQRES 5 A 107 THR ASP PRO TRP SER PRO GLU GLU ASP MET LEU LEU ASP SEQRES 6 A 107 GLN LYS TYR ALA GLU TYR GLY PRO LYS TRP ASN LYS ILE SEQRES 7 A 107 SER LYS PHE LEU LYS ASN ARG SER ASP ASN ASN ILE ARG SEQRES 8 A 107 ASN ARG TRP MET MET ILE ALA ARG HIS ARG ALA LYS HIS SEQRES 9 A 107 GLN LYS SER SEQRES 1 B 16 DA DA DG DA DT DA DA DC DG DA DT DA DT SEQRES 2 B 16 DT DT DA SEQRES 1 C 16 DT DA DA DA DT DA DT DC DG DT DT DA DT SEQRES 2 C 16 DC DT DT HELIX 1 1 THR A 5 GLY A 20 1 16 HELIX 2 2 ASP A 23 SER A 28 1 6 HELIX 3 3 ASN A 35 ILE A 47 1 13 HELIX 4 4 SER A 57 ASP A 65 1 9 HELIX 5 5 ASP A 65 GLU A 70 1 6 HELIX 6 6 LYS A 74 SER A 79 1 6 HELIX 7 7 SER A 86 ALA A 102 1 17 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