HEADER TRANSCRIPTION REGULATOR/DNA 30-DEC-14 2MXF TITLE STRUCTURE OF THE DNA COMPLEX OF THE C-TERMINAL DOMAIN OF MVAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MVAT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 77-124); COMPND 5 SYNONYM: TRANSCRIPTIONAL REGULATOR MVAT, P16 SUBUNIT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'; COMPND 9 CHAIN: B, C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 GENE: MVAT, PA4315; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS TRANSCRIPTION REGULATOR-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.DING,B.XIA REVDAT 1 01-JUL-15 2MXF 0 JRNL AUTH P.DING,K.A.MCFARLAND,S.JIN,G.TONG,B.DUAN,A.YANG,T.R.HUGHES, JRNL AUTH 2 J.LIU,S.L.DOVE,W.W.NAVARRE,B.XIA JRNL TITL A NOVEL AT-RICH DNA RECOGNITION MECHANISM FOR BACTERIAL JRNL TITL 2 XENOGENEIC SILENCER MVAT. JRNL REF PLOS PATHOG. V. 11 04967 2015 JRNL REFN ISSN 1553-7366 JRNL PMID 26068099 JRNL DOI 10.1371/JOURNAL.PPAT.1004967 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 2MXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-15. REMARK 100 THE RCSB ID CODE IS RCSB104164. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 MVAT, 50 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 1 MM DNA (5' REMARK 210 -D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HCCH-TOCSY; REMARK 210 3D HCCH-COSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 2D 1H-1H NOESY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2848 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6575 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.2 KCAL/MOL 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 76 REMARK 465 LYS A 77 REMARK 465 ARG A 78 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 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 DC B 1 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC B 3 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA B 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 4 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 4 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT B 5 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DA B 6 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 6 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 6 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 8 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 8 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT B 9 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 11 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC C 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC C 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC C 15 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DA C 16 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA C 16 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA C 16 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT C 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT C 17 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA C 18 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA C 18 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA C 18 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT C 19 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA C 20 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA C 20 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA C 20 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG C 22 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC C 23 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG C 24 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC B 1 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC B 3 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DA B 4 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA B 4 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DA B 4 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT B 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA B 6 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA B 6 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA B 6 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA B 8 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DA B 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA B 8 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 DT B 9 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 721 ANGLE DEVIATIONS. 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 80 57.19 -68.57 REMARK 500 1 ASN A 100 101.73 -57.22 REMARK 500 1 TRP A 111 -55.82 -134.12 REMARK 500 2 ARG A 80 62.25 -65.32 REMARK 500 2 ASN A 100 102.56 -57.96 REMARK 500 2 TRP A 111 -47.99 -133.41 REMARK 500 3 ARG A 80 61.36 -66.47 REMARK 500 3 ASN A 100 100.45 -57.58 REMARK 500 3 TRP A 111 -46.92 -134.11 REMARK 500 4 ARG A 80 58.81 -67.41 REMARK 500 4 ASN A 100 101.25 -57.76 REMARK 500 4 TRP A 111 -47.50 -132.81 REMARK 500 5 ARG A 80 63.93 -60.00 REMARK 500 5 ASN A 100 100.42 -57.71 REMARK 500 5 TRP A 111 -48.06 -132.75 REMARK 500 6 ARG A 80 59.25 -63.45 REMARK 500 6 ASN A 100 100.02 -57.49 REMARK 500 6 LYS A 102 -70.92 -49.99 REMARK 500 6 TRP A 111 -48.15 -132.01 REMARK 500 7 ARG A 80 61.51 -67.47 REMARK 500 7 ASN A 100 100.91 -57.60 REMARK 500 7 TRP A 111 -46.11 -132.89 REMARK 500 8 ARG A 80 56.25 -69.03 REMARK 500 8 ASN A 100 99.30 -57.70 REMARK 500 8 LYS A 102 -71.24 -44.83 REMARK 500 8 TRP A 111 -48.26 -134.02 REMARK 500 9 ARG A 80 58.27 -69.46 REMARK 500 9 ASN A 100 100.49 -57.59 REMARK 500 9 TRP A 111 -48.43 -134.50 REMARK 500 10 ARG A 80 61.24 -69.68 REMARK 500 10 ASN A 100 102.57 -56.95 REMARK 500 10 TRP A 111 -54.55 -133.84 REMARK 500 11 ARG A 80 59.16 -67.56 REMARK 500 11 ASN A 100 102.97 -57.69 REMARK 500 11 TRP A 111 -47.16 -132.89 REMARK 500 12 ARG A 80 56.22 -69.65 REMARK 500 12 ASN A 100 102.05 -57.68 REMARK 500 12 TRP A 111 -48.16 -134.46 REMARK 500 13 ARG A 80 56.51 -68.84 REMARK 500 13 ASN A 100 103.15 -57.03 REMARK 500 13 TRP A 111 -47.84 -133.50 REMARK 500 14 ARG A 80 60.77 -66.28 REMARK 500 14 ASN A 100 101.36 -57.82 REMARK 500 14 TRP A 111 -48.83 -133.47 REMARK 500 15 ARG A 80 61.58 -65.41 REMARK 500 15 ASN A 100 100.99 -57.66 REMARK 500 15 TRP A 111 -46.50 -133.05 REMARK 500 16 ARG A 80 58.73 -67.81 REMARK 500 16 ASN A 100 101.42 -57.64 REMARK 500 16 TRP A 111 -47.01 -132.75 REMARK 500 REMARK 500 THIS ENTRY HAS 63 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 DA C 16 0.06 SIDE CHAIN REMARK 500 2 DA C 16 0.06 SIDE CHAIN REMARK 500 3 DA C 16 0.07 SIDE CHAIN REMARK 500 4 DA C 16 0.07 SIDE CHAIN REMARK 500 5 DA C 16 0.06 SIDE CHAIN REMARK 500 6 DA C 16 0.07 SIDE CHAIN REMARK 500 7 DA C 16 0.07 SIDE CHAIN REMARK 500 8 DA C 16 0.07 SIDE CHAIN REMARK 500 9 DA C 16 0.07 SIDE CHAIN REMARK 500 10 DA C 16 0.06 SIDE CHAIN REMARK 500 11 DA C 16 0.06 SIDE CHAIN REMARK 500 12 DA C 16 0.06 SIDE CHAIN REMARK 500 13 DA C 16 0.06 SIDE CHAIN REMARK 500 14 DA C 16 0.06 SIDE CHAIN REMARK 500 15 DA C 16 0.06 SIDE CHAIN REMARK 500 16 DA C 16 0.07 SIDE CHAIN REMARK 500 17 DA C 16 0.07 SIDE CHAIN REMARK 500 18 DA C 16 0.07 SIDE CHAIN REMARK 500 19 DA C 16 0.06 SIDE CHAIN REMARK 500 20 DA C 16 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25407 RELATED DB: BMRB REMARK 900 RELATED ID: 2MXE RELATED DB: PDB DBREF 2MXF A 77 124 UNP Q9HW86 Q9HW86_PSEAE 77 124 DBREF 2MXF B 1 12 PDB 2MXF 2MXF 1 12 DBREF 2MXF C 13 24 PDB 2MXF 2MXF 13 24 SEQADV 2MXF MET A 76 UNP Q9HW86 INITIATING METHIONINE SEQADV 2MXF HIS A 125 UNP Q9HW86 EXPRESSION TAG SEQADV 2MXF HIS A 126 UNP Q9HW86 EXPRESSION TAG SEQADV 2MXF HIS A 127 UNP Q9HW86 EXPRESSION TAG SEQADV 2MXF HIS A 128 UNP Q9HW86 EXPRESSION TAG SEQADV 2MXF HIS A 129 UNP Q9HW86 EXPRESSION TAG SEQADV 2MXF HIS A 130 UNP Q9HW86 EXPRESSION TAG SEQRES 1 A 55 MET LYS ARG ALA ARG LYS VAL LYS GLN TYR LYS ASN PRO SEQRES 2 A 55 HIS THR GLY GLU VAL ILE GLU THR LYS GLY GLY ASN HIS SEQRES 3 A 55 LYS THR LEU LYS GLU TRP LYS ALA LYS TRP GLY PRO GLU SEQRES 4 A 55 ALA VAL GLU SER TRP ALA THR LEU LEU GLY HIS HIS HIS SEQRES 5 A 55 HIS HIS HIS SEQRES 1 B 12 DC DG DC DA DT DA DT DA DT DG DC DG SEQRES 1 C 12 DC DG DC DA DT DA DT DA DT DG DC DG HELIX 1 1 HIS A 101 TRP A 111 1 11 HELIX 2 2 GLY A 112 TRP A 119 1 8 SHEET 1 A 3 VAL A 93 THR A 96 0 SHEET 2 A 3 VAL A 82 LYS A 86 -1 N LYS A 83 O THR A 96 SHEET 3 A 3 ALA A 120 LEU A 123 -1 O LEU A 123 N VAL A 82 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 267 0 0 2 3 0 0 6 0 0 0 7 END