HEADER DNA BINDING PROTEIN 02-MAR-18 6FVC TITLE PROTEIN ENVIRONMENT AFFECTS THE WATER-TRYPTOPHAN BINDING MODE. TITLE 2 MOLECULAR DYNAMICS SIMULATIONS OF ENGRAILED HOMEODOMAIN MUTANTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEGMENTATION POLARITY HOMEOBOX PROTEIN ENGRAILED; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: EN, CG9015; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS ENGRAILED HOMEODOMAIN, K52E MUTATION, DNA, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 3 AUTHOR Z.TROSANOVA,M.ZACHRDLA,S.JANSEN,P.SRB,L.ZIDEK,J.KOZELKA REVDAT 4 19-JUN-24 6FVC 1 REMARK REVDAT 3 14-JUN-23 6FVC 1 REMARK REVDAT 2 08-MAY-19 6FVC 1 REMARK REVDAT 1 03-APR-19 6FVC 0 JRNL AUTH N.SPACKOVA,Z.TROSANOVA,F.SEBESTA,S.JANSEN,J.V.BURDA,P.SRB, JRNL AUTH 2 M.ZACHRDLA,L.ZIDEK,J.KOZELKA JRNL TITL PROTEIN ENVIRONMENT AFFECTS THE WATER-TRYPTOPHAN BINDING JRNL TITL 2 MODE. MD, QM/MM, AND NMR STUDIES OF ENGRAILED HOMEODOMAIN JRNL TITL 3 MUTANTS. JRNL REF PHYS CHEM CHEM PHYS V. 20 12664 2018 JRNL REFN ESSN 1463-9084 JRNL DOI 10.1039/C7CP08623G 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 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200008753. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM ENHD_K52E, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 3 REMARK 210 CONFORMERS, SELECTION CRITERIA : THREE REPRESENTATIVE STRUCTURES REMARK 210 FOR THE CONFORMATIONAL REMARK 210 EQUILIBRIUM ALONG THE TORSION REMARK 210 ANGLE N-CA-CB-CG OF ASPARAGINE REMARK 210 N51 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 ARG A 18 CZ ARG A 18 NH1 -0.111 REMARK 500 3 ARG A 34 CZ ARG A 34 NH1 -0.091 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 6 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 1 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 ARG A 27 NH1 - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 ARG A 27 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 TYR A 28 CB - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 11.9 DEGREES REMARK 500 1 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 ARG A 33 CG - CD - NE ANGL. DEV. = -13.0 DEGREES REMARK 500 1 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 PHE A 52 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 56 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 ARG A 6 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 ARG A 8 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 2 ARG A 18 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 2 PHE A 23 CB - CG - CD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 2 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 TRP A 51 CG - CD2 - CE3 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 3 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 ARG A 21 CD - NE - CZ ANGL. DEV. = 10.0 DEGREES REMARK 500 3 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 3 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 TYR A 28 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 3 TRP A 51 NE1 - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 3 ARG A 56 NH1 - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 3 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 5.8 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 ALA A 2 26.04 -72.51 REMARK 500 1 ALA A 10 56.66 -69.88 REMARK 500 1 SER A 62 -36.47 -139.01 REMARK 500 2 SER A 62 -25.22 -141.75 REMARK 500 3 SER A 62 -22.04 -170.20 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 ARG A 21 0.10 SIDE CHAIN REMARK 500 1 PHE A 52 0.08 SIDE CHAIN REMARK 500 2 ARG A 21 0.08 SIDE CHAIN REMARK 500 2 TYR A 28 0.08 SIDE CHAIN REMARK 500 3 ARG A 6 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 2 GLN A 36 -10.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34240 RELATED DB: BMRB REMARK 900 PROTEIN ENVIRONMENT AFFECTS THE WATER-TRYPTOPHAN BINDING MODE. REMARK 900 MOLECULAR DYNAMICS SIMULATIONS OF ENGRAILED HOMEODOMAIN MUTANTS DBREF 6FVC A 4 62 UNP P02836 HMEN_DROME 454 512 SEQADV 6FVC GLY A 1 UNP P02836 EXPRESSION TAG SEQADV 6FVC ALA A 2 UNP P02836 EXPRESSION TAG SEQADV 6FVC MET A 3 UNP P02836 EXPRESSION TAG SEQADV 6FVC GLU A 55 UNP P02836 LYS 505 ENGINEERED MUTATION SEQADV 6FVC GLY A 63 UNP P02836 EXPRESSION TAG SEQADV 6FVC SER A 64 UNP P02836 EXPRESSION TAG SEQRES 1 A 64 GLY ALA MET GLU LYS ARG PRO ARG THR ALA PHE SER SER SEQRES 2 A 64 GLU GLN LEU ALA ARG LEU LYS ARG GLU PHE ASN GLU ASN SEQRES 3 A 64 ARG TYR LEU THR GLU ARG ARG ARG GLN GLN LEU SER SER SEQRES 4 A 64 GLU LEU GLY LEU ASN GLU ALA GLN ILE LYS ILE TRP PHE SEQRES 5 A 64 GLN ASN GLU ARG ALA LYS ILE LYS LYS SER GLY SER FORMUL 2 HOH *(H2 O) HELIX 1 AA1 SER A 12 ASN A 24 1 13 HELIX 2 AA2 THR A 30 GLY A 42 1 13 HELIX 3 AA3 ASN A 44 ALA A 57 1 14 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