PDB Short entry for 2ME6 HEADER TRANSCRIPTION/DNA 23-SEP-13 2ME6 TITLE NMR STRUCTURE OF THE HOMEODOMAIN TRANSCRIPTION FACTOR GBX1 FROM HOMO TITLE 2 SAPIENS IN COMPLEX WITH THE DNA SEQUENCE CGACTAATTAGTCG COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN GBX-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HOMEOBOX DNA BINDING REGION, RESIDUES 256-325; COMPND 5 SYNONYM: GASTRULATION AND BRAIN-SPECIFIC HOMEOBOX PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*CP*G)-3'); COMPND 9 CHAIN: B, C; COMPND 10 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: GBX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET46; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS DNA BINDING, TRANSCRIPTION, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR A.PROUDFOOT,P.SERRANO,M.GERALT,K.WUTHRICH,JOINT CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (JCSG),PARTNERSHIP FOR STEM CELL BIOLOGY (STEMCELL) REVDAT 1 30-OCT-13 2ME6 0 JRNL AUTH A.PROUDFOOT,K.WUTHRICH,P.SERRANO,M.GERALT JRNL TITL NMR STRUCTURE OF THE HOMEODOMAIN TRANSCRIPTION FACTOR GBX1 JRNL TITL 2 FROM HOMO SAPIENS IN COMPLEX WITH THE DNA SEQUENCE JRNL TITL 3 CGACTAATTAGTCG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, HADDOCK REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), ALEXANDRE REMARK 3 BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ME6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-13. REMARK 100 THE RCSB ID CODE IS RCSB103528. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.220 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN, 50 MM SODIUM CHLORIDE, REMARK 210 20 MM SODIUM PHOSPHATE, 5 MM REMARK 210 SODIUM AZIDE, 0.8 MM DNA, 95% REMARK 210 H2O/5% D2O; 0.8 MM [U-98% 13C; U- REMARK 210 98% 15N] PROTEIN, 50 MM SODIUM REMARK 210 CHLORIDE, 20 MM SODIUM PHOSPHATE, REMARK 210 5 MM SODIUM AZIDE, 0.8 MM DNA, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; APSY REMARK 210 4D-HACANH; APSY 5D-CBCACONH; APSY REMARK 210 5D-HACACONH; 2D 13C/15N DOUBLE- REMARK 210 FILTERED 1H-1H NOESY; 2D 1H-1H REMARK 210 TOCSY; 3D F2-EDITED, F3-FILTERED REMARK 210 1H-13C NOESY 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 : CNS, UNIO, TOPSPIN, XEASY, 3D_ REMARK 210 DART REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 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: 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 O2 DC B 1 H22 DG C 28 1.42 REMARK 500 OE1 GLU A 25 HZ1 LYS A 29 1.57 REMARK 500 O2 DC B 1 N2 DG C 28 2.18 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 ARG A 11 93.78 167.17 REMARK 500 1 THR A 12 120.62 -39.90 REMARK 500 2 GLU A 21 60.64 -107.48 REMARK 500 2 LEU A 22 -33.07 -157.40 REMARK 500 2 LYS A 45 35.91 -82.61 REMARK 500 3 LEU A 34 -89.36 52.25 REMARK 500 3 LEU A 44 -166.78 -120.72 REMARK 500 3 ILE A 65 -59.79 -121.72 REMARK 500 3 ALA A 67 -153.69 -162.60 REMARK 500 4 ARG A 11 95.40 -169.91 REMARK 500 4 LEU A 34 69.27 -67.33 REMARK 500 4 THR A 35 -22.59 158.78 REMARK 500 4 LYS A 66 42.13 -84.08 REMARK 500 4 ASN A 69 -164.08 -110.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19511 RELATED DB: BMRB REMARK 900 RELATED ID: JCSG-424577 RELATED DB: TARGETTRACK DBREF 2ME6 A 2 71 UNP Q14549 GBX1_HUMAN 256 325 DBREF 2ME6 B 1 14 PDB 2ME6 2ME6 1 14 DBREF 2ME6 C 15 28 PDB 2ME6 2ME6 15 28 SEQADV 2ME6 SER A 1 UNP Q14549 EXPRESSION TAG SEQRES 1 A 71 SER ALA PRO GLY GLY LYS SER ARG ARG ARG ARG THR ALA SEQRES 2 A 71 PHE THR SER GLU GLN LEU LEU GLU LEU GLU LYS GLU PHE SEQRES 3 A 71 HIS CYS LYS LYS TYR LEU SER LEU THR GLU ARG SER GLN SEQRES 4 A 71 ILE ALA HIS ALA LEU LYS LEU SER GLU VAL GLN VAL LYS SEQRES 5 A 71 ILE TRP PHE GLN ASN ARG ARG ALA LYS TRP LYS ARG ILE SEQRES 6 A 71 LYS ALA GLY ASN VAL SER SEQRES 1 B 14 DC DG DA DC DT DA DA DT DT DA DG DT DC SEQRES 2 B 14 DG SEQRES 1 C 14 DC DG DA DC DT DA DA DT DT DA DG DT DC SEQRES 2 C 14 DG HELIX 1 1 THR A 15 HIS A 27 1 13 HELIX 2 2 SER A 33 LEU A 44 1 12 HELIX 3 3 SER A 47 ARG A 64 1 18 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