PDB Short entry for 2LD5 HEADER TRANSCRIPTION/DNA 14-MAY-11 2LD5 TITLE SOLUTION NMR-DERIVED COMPLEX STRUCTURE OF HOXA13 DNA BINDING DOMAIN TITLE 2 BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN HOX-A13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HOMEOBOX DNA BINDING RESIDUES 320-386; COMPND 5 SYNONYM: HOMEOBOX PROTEIN HOX-1.10; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: HOX-1.10, HOXA13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.ZHANG REVDAT 3 27-APR-16 2LD5 1 ATOM REMARK SEQRES REVDAT 2 28-MAR-12 2LD5 1 JRNL REVDAT 1 10-AUG-11 2LD5 0 JRNL AUTH Y.ZHANG,C.A.LARSEN,H.S.STADLER,J.B.AMES JRNL TITL STRUCTURAL BASIS FOR SEQUENCE SPECIFIC DNA BINDING AND JRNL TITL 2 PROTEIN DIMERIZATION OF HOXA13. JRNL REF PLOS ONE V. 6 23069 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21829694 JRNL DOI 10.1371/JOURNAL.PONE.0023069 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-11. REMARK 100 THE RCSB ID CODE IS RCSB102251. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.025 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 SODIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 LEU A 5 REMARK 465 GLU A 6 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 O2 DC B 1 H22 DG C 22 1.41 REMARK 500 O2 DC B 11 H22 DG C 12 1.43 REMARK 500 O2 DC B 11 N2 DG C 12 2.18 REMARK 500 O2 DC B 1 N2 DG C 22 2.19 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 10 -99.38 -101.67 REMARK 500 1 TYR A 14 -125.26 -80.65 REMARK 500 1 ASN A 29 -71.75 -163.87 REMARK 500 1 LYS A 30 -47.49 174.57 REMARK 500 1 GLU A 48 -53.32 71.10 REMARK 500 1 LYS A 70 -39.32 -142.36 REMARK 500 2 LYS A 10 -97.76 -90.97 REMARK 500 2 TYR A 14 -92.94 -72.55 REMARK 500 2 ASN A 29 -73.85 -160.14 REMARK 500 2 LYS A 30 -55.56 170.71 REMARK 500 2 GLU A 48 -43.29 69.59 REMARK 500 3 ARG A 8 -54.13 71.41 REMARK 500 3 LYS A 10 -86.59 -93.46 REMARK 500 3 TYR A 14 -81.00 -76.48 REMARK 500 3 ASN A 29 -74.44 -177.57 REMARK 500 3 LYS A 30 -57.07 -177.24 REMARK 500 3 SER A 47 43.21 -78.81 REMARK 500 3 GLU A 48 -53.72 67.23 REMARK 500 4 LYS A 10 -91.02 -77.78 REMARK 500 4 ASN A 29 -67.54 -172.49 REMARK 500 4 LYS A 30 -55.72 173.50 REMARK 500 4 ASN A 45 80.55 64.73 REMARK 500 4 SER A 47 39.16 -81.15 REMARK 500 4 GLU A 48 -66.54 67.15 REMARK 500 4 THR A 71 84.26 46.23 REMARK 500 5 ARG A 8 -56.78 71.54 REMARK 500 5 LYS A 10 -87.93 -77.86 REMARK 500 5 TYR A 14 -81.07 -64.59 REMARK 500 5 ASN A 29 -81.49 -144.37 REMARK 500 5 LYS A 30 -61.42 179.38 REMARK 500 5 GLU A 48 -43.91 70.87 REMARK 500 5 THR A 71 85.76 59.36 REMARK 500 6 LYS A 10 -89.69 -81.63 REMARK 500 6 TYR A 14 -71.74 -64.51 REMARK 500 6 ASN A 29 -72.20 -176.67 REMARK 500 6 LYS A 30 -58.55 178.30 REMARK 500 6 SER A 47 40.34 -80.35 REMARK 500 6 GLU A 48 -67.05 69.17 REMARK 500 7 LYS A 10 -92.56 -84.13 REMARK 500 7 ASN A 29 -66.60 -164.94 REMARK 500 7 LYS A 30 -55.55 177.57 REMARK 500 7 ASN A 45 82.66 56.20 REMARK 500 7 GLU A 48 -50.49 74.12 REMARK 500 8 ARG A 8 -51.17 70.53 REMARK 500 8 LYS A 10 -89.49 -93.81 REMARK 500 8 ASN A 29 -83.67 -156.91 REMARK 500 8 LYS A 30 -51.00 -175.30 REMARK 500 8 ASN A 45 98.74 61.99 REMARK 500 8 SER A 47 32.86 -85.02 REMARK 500 8 GLU A 48 -57.73 68.30 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16577 RELATED DB: BMRB DBREF 2LD5 A 7 73 UNP Q62424 HXA13_MOUSE 320 386 DBREF 2LD5 B 1 11 PDB 2LD5 2LD5 1 11 DBREF 2LD5 C 12 22 PDB 2LD5 2LD5 12 22 SEQADV 2LD5 HIS A 3 UNP Q62424 EXPRESSION TAG SEQADV 2LD5 MET A 4 UNP Q62424 EXPRESSION TAG SEQADV 2LD5 LEU A 5 UNP Q62424 EXPRESSION TAG SEQADV 2LD5 GLU A 6 UNP Q62424 EXPRESSION TAG SEQRES 1 A 71 HIS MET LEU GLU GLY ARG LYS LYS ARG VAL PRO TYR THR SEQRES 2 A 71 LYS VAL GLN LEU LYS GLU LEU GLU ARG GLU TYR ALA THR SEQRES 3 A 71 ASN LYS PHE ILE THR LYS ASP LYS ARG ARG ARG ILE SER SEQRES 4 A 71 ALA THR THR ASN LEU SER GLU ARG GLN VAL THR ILE TRP SEQRES 5 A 71 PHE GLN ASN ARG ARG VAL LYS GLU LYS LYS VAL ILE ASN SEQRES 6 A 71 LYS LEU LYS THR THR SER SEQRES 1 B 11 DC DA DA DA DT DA DA DA DA DT DC SEQRES 1 C 11 DG DA DT DT DT DT DA DT DT DT DG HELIX 1 1 THR A 15 ASN A 29 1 15 HELIX 2 2 THR A 33 ASN A 45 1 13 HELIX 3 3 GLU A 48 LEU A 69 1 22 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