10 20 30 40 50 60 70 80 2KDZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION/DNA 21-JAN-09 2KDZ
TITLE STRUCTURE OF THE R2R3 DNA BINDING DOMAIN OF MYB1 PROTEIN TITLE 2 FROM PROTOZOAN PARASITE TRICHOMONAS VAGINALIS IN COMPLEX TITLE 3 WITH MRE-1/MRE-2R 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'- COMPND 8 D(*AP*AP*GP*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*TP*A)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'- COMPND 13 D(*TP*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*TP*CP*TP*T)-3'; COMPND 14 CHAIN: C; COMPND 15 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 KEYWDS 2 COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR Y.C.LOU,S.Y.WEI,M.RAJASEKARAN,C.C.CHOU,H.M.HSU,J.H.TAI, AUTHOR 2 C.CHEN
REVDAT 1 17-MAR-09 2KDZ 0
JRNL AUTH Y.C.LOU,S.Y.WEI,M.RAJASEKARAN,C.C.CHOU,H.M.HSU, JRNL AUTH 2 J.H.TAI,C.CHEN JRNL TITL NMR STRUCTURAL ANALYSIS OF DNA RECOGNITION BY A JRNL TITL 2 NOVEL MYB1 DNA-BINDING DOMAIN IN THE PROTOZOAN JRNL TITL 3 PARASITE TRICHOMONAS VAGINALIS. JRNL REF NUCLEIC ACIDS RES. 2009 JRNL REFN ESSN 1362-4962 JRNL PMID 19246540 JRNL DOI 10.1093/NAR/GKP097
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KDZ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB101002.
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% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 3D HNCO, 3D REMARK 210 CBCA(CO)NH, 3D HNCACB, 3D 1H- REMARK 210 15N NOESY, 3D 1H-13C NOESY, 3D REMARK 210 HN(CA)CO, 3D HCCH-TOCSY, 3D REMARK 210 C(CO)NH, 3D HBHA(CO)NH, 2D 1H- REMARK 210 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, REMARK 210 SPARKY, TALOS, X-PLOR_NIH, REMARK 210 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 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 3 LYS A 106 -74.99 -158.31 REMARK 500 4 LYS A 3 161.32 66.92 REMARK 500 4 PHE A 4 175.12 65.85 REMARK 500 4 THR A 5 178.67 172.83 REMARK 500 4 LYS A 22 -48.39 -131.55 REMARK 500 4 TYR A 46 -52.41 -126.86 REMARK 500 4 ALA A 50 59.88 -117.04 REMARK 500 4 LEU A 51 70.85 -64.18 REMARK 500 4 ARG A 52 -148.10 -147.56 REMARK 500 4 THR A 53 55.39 38.92 REMARK 500 4 ASP A 54 169.78 65.04 REMARK 500 4 PRO A 55 -157.69 -74.49 REMARK 500 4 LEU A 82 76.50 -119.83 REMARK 500 4 LYS A 83 89.83 -58.69 REMARK 500 4 ASN A 84 -44.10 172.36 REMARK 500 4 ASP A 87 -75.17 -51.98 REMARK 500 4 LYS A 103 -145.93 51.42 REMARK 500 4 LYS A 106 -64.30 -148.24 REMARK 500 5 LYS A 3 -178.67 61.49 REMARK 500 5 PHE A 4 173.18 63.60 REMARK 500 5 THR A 5 174.93 173.36 REMARK 500 5 ALA A 21 26.26 -159.65 REMARK 500 5 LYS A 22 -43.40 -136.03 REMARK 500 5 TYR A 46 -49.14 -155.65 REMARK 500 5 ARG A 52 -147.62 -151.38 REMARK 500 5 THR A 53 46.85 38.87 REMARK 500 5 ASP A 54 165.42 69.94 REMARK 500 5 PRO A 55 -155.64 -68.14 REMARK 500 5 PRO A 73 39.28 -76.31 REMARK 500 5 ASN A 84 -43.42 -177.81 REMARK 500 5 ASP A 87 -78.40 -45.36 REMARK 500 5 LYS A 103 -168.17 63.13 REMARK 500 5 LYS A 106 -49.40 -155.90 REMARK 500 6 LYS A 3 172.11 62.39 REMARK 500 6 PHE A 4 -171.80 61.67 REMARK 500 6 THR A 5 179.64 172.96 REMARK 500 6 TYR A 46 -52.83 -122.50 REMARK 500 6 ARG A 52 -153.58 -148.25 REMARK 500 6 THR A 53 54.54 37.02 REMARK 500 6 ASP A 54 163.76 67.93 REMARK 500 6 PRO A 55 -152.08 -71.98 REMARK 500 6 PRO A 73 35.20 -79.70 REMARK 500 6 ASN A 84 -49.89 177.17 REMARK 500 6 ASP A 87 -72.38 -49.16 REMARK 500 6 LYS A 103 -150.76 51.77 REMARK 500 6 HIS A 104 101.98 -162.10 REMARK 500 6 LYS A 106 -52.77 -154.76 REMARK 500 7 LYS A 3 -176.35 60.38 REMARK 500 7 PHE A 4 168.30 62.87 REMARK 500 7 THR A 5 170.88 169.01 REMARK 500 7 LYS A 22 -31.41 -141.30 REMARK 500 7 ASP A 23 49.25 -80.38 REMARK 500 7 TYR A 46 -52.19 -140.40 REMARK 500 7 ARG A 52 -154.12 -140.01 REMARK 500 7 THR A 53 52.67 33.03 REMARK 500 7 ASP A 54 153.40 72.84 REMARK 500 7 PRO A 55 -144.45 -74.77 REMARK 500 7 PRO A 73 37.88 -77.46 REMARK 500 7 LYS A 83 92.55 -64.48 REMARK 500 7 ASN A 84 -72.65 -161.72 REMARK 500 7 ASP A 87 -84.13 -46.36 REMARK 500 7 LYS A 103 -143.36 53.29 REMARK 500 7 LYS A 106 -45.50 -164.64 REMARK 500 8 LYS A 3 139.12 71.98 REMARK 500 8 PHE A 4 -170.61 63.62 REMARK 500 8 THR A 5 176.04 176.37 REMARK 500 8 LYS A 22 -43.30 -130.78 REMARK 500 8 TYR A 46 -42.29 -142.93 REMARK 500 8 THR A 53 47.65 -70.32 REMARK 500 8 ASP A 54 174.86 60.04 REMARK 500 8 GLU A 70 -122.49 -89.79 REMARK 500 8 TYR A 71 -60.44 -10.98 REMARK 500 8 PRO A 73 37.04 -77.25 REMARK 500 8 LYS A 83 86.07 -64.79 REMARK 500 8 ASN A 84 -37.61 154.94 REMARK 500 8 ASP A 87 -70.54 -49.06 REMARK 500 8 LYS A 103 -163.32 59.92 REMARK 500 8 LYS A 106 -54.76 -163.40 REMARK 500 9 LYS A 3 172.45 65.73 REMARK 500 9 PHE A 4 178.47 63.19 REMARK 500 9 THR A 5 171.77 167.73 REMARK 500 9 LYS A 22 -34.51 -136.49 REMARK 500 9 TYR A 46 -45.38 -156.47 REMARK 500 9 LEU A 51 75.27 -67.30 REMARK 500 9 ARG A 52 -145.88 -147.07 REMARK 500 9 ASP A 54 171.83 64.35 REMARK 500 9 PRO A 55 -159.19 -72.18 REMARK 500 9 PRO A 73 32.89 -77.96 REMARK 500 9 LYS A 83 83.71 -67.51 REMARK 500 9 ASN A 84 -39.16 166.64 REMARK 500 9 ASP A 87 -76.64 -48.52 REMARK 500 9 LYS A 103 -147.38 49.66 REMARK 500 9 HIS A 104 110.11 -174.32 REMARK 500 9 LYS A 106 -64.43 -152.34 REMARK 500 10 LYS A 3 -178.67 61.49 REMARK 500 10 PHE A 4 173.18 63.60 REMARK 500 10 THR A 5 174.93 173.36 REMARK 500 10 ALA A 21 26.26 -159.65 REMARK 500 10 LYS A 22 -43.40 -136.03 REMARK 500 10 TYR A 46 -49.14 -155.65 REMARK 500 10 ARG A 52 -147.62 -151.38 REMARK 500 10 THR A 53 46.85 38.87 REMARK 500 10 ASP A 54 165.42 69.94 REMARK 500 10 PRO A 55 -155.64 -68.14 REMARK 500 10 PRO A 73 39.28 -76.31 REMARK 500 10 ASN A 84 -43.42 -177.81 REMARK 500 10 ASP A 87 -78.40 -45.36 REMARK 500 10 LYS A 103 -168.17 63.13 REMARK 500 10 LYS A 106 -49.40 -155.90 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