HEADER DNA BINDING PROTEIN 05-FEB-19 6NVZ TITLE NMR STRUCTURE OF THE DNA BINDING DOMAIN OF EHMYBS3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYB FAMILY DNA-BINDING PROTEIN SHAQKYF FAMILY; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 47-101; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTAMOEBA HISTOLYTICA; SOURCE 3 ORGANISM_TAXID: 5759; SOURCE 4 GENE: CL6EHI_136420; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.A.TITAUX-DELGADO,F.DEL RIO-PORTILLA REVDAT 3 14-JUN-23 6NVZ 1 REMARK REVDAT 2 10-FEB-21 6NVZ 1 JRNL REVDAT 1 12-FEB-20 6NVZ 0 JRNL AUTH H.CARDENAS-HERNANDEZ,G.A.TITAUX-DELGADO,E.J.CASTANEDA-ORTIZ, JRNL AUTH 2 A.TORRES-LARIOS,L.G.BRIEBA,F.DEL RIO-PORTILLA, JRNL AUTH 3 E.AZUARA-LICEAGA JRNL TITL GENOME-WIDE AND STRUCTURAL ANALYSIS OF THE MYB-SHAQKYF JRNL TITL 2 FAMILY IN ENTAMOEBA HISTOLYTICA. JRNL REF BIOCHIM BIOPHYS ACTA V.1869 40601 2021 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1878-1454 JRNL PMID 33422669 JRNL DOI 10.1016/J.BBAPAP.2021.140601 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6NVZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239479. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM EHMYBS3, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, CARA 1.8, CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 10 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 18 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 18 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 19 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 20 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES 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 HIS A 27 82.67 55.58 REMARK 500 1 ASP A 29 79.40 -153.60 REMARK 500 1 LYS A 31 5.47 -63.54 REMARK 500 1 LYS A 58 43.52 -90.50 REMARK 500 1 THR A 59 45.53 -142.12 REMARK 500 2 HIS A 27 100.71 60.05 REMARK 500 2 ASP A 29 79.63 -157.53 REMARK 500 2 LYS A 31 0.59 -59.35 REMARK 500 2 THR A 39 29.54 -143.15 REMARK 500 2 VAL A 42 -38.62 59.26 REMARK 500 3 GLU A 9 46.55 -85.03 REMARK 500 3 HIS A 27 84.49 56.23 REMARK 500 3 LYS A 28 48.24 70.06 REMARK 500 4 LYS A 7 -19.40 -141.34 REMARK 500 4 HIS A 27 103.26 50.87 REMARK 500 4 ASP A 29 80.23 -153.83 REMARK 500 4 LYS A 31 -5.47 -56.88 REMARK 500 5 ALA A 17 -9.87 -58.02 REMARK 500 5 HIS A 27 85.56 59.74 REMARK 500 5 ASP A 29 85.28 -155.72 REMARK 500 5 LYS A 31 -2.85 -57.24 REMARK 500 6 HIS A 27 86.48 55.30 REMARK 500 6 LYS A 28 70.98 60.10 REMARK 500 6 ASP A 29 80.76 -161.47 REMARK 500 6 LYS A 31 -1.93 -58.70 REMARK 500 7 ARG A 8 24.36 -75.20 REMARK 500 7 ASP A 13 23.20 -72.46 REMARK 500 7 ALA A 14 -17.27 -140.26 REMARK 500 7 HIS A 27 82.50 56.89 REMARK 500 7 ASP A 29 79.47 -155.37 REMARK 500 7 LYS A 31 5.22 -58.36 REMARK 500 8 LEU A 3 12.76 58.24 REMARK 500 8 HIS A 27 -56.62 67.69 REMARK 500 8 LYS A 28 64.61 -163.83 REMARK 500 8 LYS A 31 -5.30 -59.16 REMARK 500 8 LYS A 40 -4.57 65.10 REMARK 500 9 HIS A 27 98.71 51.11 REMARK 500 9 ASP A 29 81.72 -152.89 REMARK 500 9 LYS A 31 3.30 -61.16 REMARK 500 9 THR A 39 17.14 -148.52 REMARK 500 10 HIS A 27 -61.52 68.32 REMARK 500 10 LYS A 28 58.43 -158.76 REMARK 500 10 ASP A 29 89.77 -156.19 REMARK 500 10 LYS A 40 -47.21 66.29 REMARK 500 10 LYS A 58 -7.97 60.91 REMARK 500 11 HIS A 27 88.51 57.17 REMARK 500 11 ASP A 29 86.84 -152.38 REMARK 500 11 LYS A 31 -5.31 -57.66 REMARK 500 12 HIS A 27 95.69 64.07 REMARK 500 12 ASP A 29 86.54 -159.81 REMARK 500 REMARK 500 THIS ENTRY HAS 88 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 HIS A 16 0.20 SIDE CHAIN REMARK 500 1 PHE A 19 0.12 SIDE CHAIN REMARK 500 2 TYR A 52 0.07 SIDE CHAIN REMARK 500 8 TYR A 52 0.07 SIDE CHAIN REMARK 500 9 TYR A 52 0.08 SIDE CHAIN REMARK 500 10 TYR A 52 0.07 SIDE CHAIN REMARK 500 11 TYR A 52 0.07 SIDE CHAIN REMARK 500 12 TYR A 52 0.10 SIDE CHAIN REMARK 500 13 TYR A 52 0.09 SIDE CHAIN REMARK 500 14 ARG A 46 0.08 SIDE CHAIN REMARK 500 14 TYR A 52 0.10 SIDE CHAIN REMARK 500 15 TYR A 52 0.07 SIDE CHAIN REMARK 500 16 TYR A 52 0.08 SIDE CHAIN REMARK 500 17 ARG A 8 0.08 SIDE CHAIN REMARK 500 17 TYR A 52 0.14 SIDE CHAIN REMARK 500 18 TYR A 52 0.08 SIDE CHAIN REMARK 500 19 TYR A 52 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30567 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE DNA BINDING DOMAIN OF EHMYBS3 DBREF1 6NVZ A 6 60 UNP A0A175JNU7_ENTHI DBREF2 6NVZ A A0A175JNU7 47 101 SEQADV 6NVZ GLY A 1 UNP A0A175JNU EXPRESSION TAG SEQADV 6NVZ PRO A 2 UNP A0A175JNU EXPRESSION TAG SEQADV 6NVZ LEU A 3 UNP A0A175JNU EXPRESSION TAG SEQADV 6NVZ GLY A 4 UNP A0A175JNU EXPRESSION TAG SEQADV 6NVZ SER A 5 UNP A0A175JNU EXPRESSION TAG SEQRES 1 A 60 GLY PRO LEU GLY SER LYS LYS ARG GLU VAL TRP THR ASP SEQRES 2 A 60 ALA GLU HIS ALA LYS PHE VAL GLU GLY LEU ALA LEU PHE SEQRES 3 A 60 HIS LYS ASP TRP LYS LYS ILE LYS GLU TYR ILE GLY THR SEQRES 4 A 60 LYS THR VAL VAL GLN ILE ARG SER HIS ALA GLN LYS TYR SEQRES 5 A 60 PHE LEU LYS LEU ASN LYS THR ALA HELIX 1 AA1 THR A 12 PHE A 26 1 15 HELIX 2 AA2 ASP A 29 GLY A 38 1 10 HELIX 3 AA3 VAL A 42 LEU A 56 1 15 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 MODEL 1