PDB Short entry for 2EZH HEADER DNA BINDING PROTEIN 25-JUL-97 2EZH TITLE SOLUTION NMR STRUCTURE OF THE IGAMMA SUBDOMAIN OF THE MU END DNA TITLE 2 BINDING DOMAIN OF MU PHAGE TRANSPOSASE, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSPOSASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IGAMMA SUBDOMAIN, RESIDUES 174 - 247; COMPND 5 OTHER_DETAILS: MUA OF PHAGE MU TRANSPOSASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE MU; SOURCE 3 ORGANISM_TAXID: 10677 KEYWDS DNA-BINDING PROTEIN, TRANSPOSITION, DNA BINDING PROTEIN EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,R.T.CLUBB,S.SCHUMAKER,A.M.GRONENBORN REVDAT 3 09-MAR-22 2EZH 1 KEYWDS REMARK REVDAT 2 24-FEB-09 2EZH 1 VERSN REVDAT 1 03-DEC-97 2EZH 0 JRNL AUTH R.T.CLUBB,S.SCHUMACHER,K.MIZUUCHI,A.M.GRONENBORN,G.M.CLORE JRNL TITL SOLUTION STRUCTURE OF THE I GAMMA SUBDOMAIN OF THE MU END JRNL TITL 2 DNA-BINDING DOMAIN OF PHAGE MU TRANSPOSASE. JRNL REF J.MOL.BIOL. V. 273 19 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9367742 JRNL DOI 10.1006/JMBI.1997.1312 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR (SEE ABOVE)), BRUNGER (X-PLOR (SEE REMARK 3 ABOVE)) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE 3D STRUCTURE OF THE IGAMMA SUBDOMAIN OF MU A REMARK 3 TRANSPOSASE WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR REMARK 3 NMR AND IS BASED ON 1293 EXPERIMENTAL NMR RESTRAINTS: REMARK 3 264 SEQUENTIAL (|I- J|=1), 282 MEDIUM RANGE (1 < |I-J| <=5) REMARK 3 AND 178 LONG RANGE (|I-J| >5) INTERRESIDUES AND 245 REMARK 3 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; REMARK 3 40 DISTANCE RESTRAINTS FOR 20 BACKBONE H-BONDS; REMARK 3 108 TORSION ANGLE RESTRAINTS; 47 THREE-BOND HN-HA COUPLING REMARK 3 CONSTANT RESTRAINTS; AND 129 (66 CALPHA AND 63 CBETA) 13C REMARK 3 SHIFT RESTRAINTS. REMARK 3 REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED REMARK 3 ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, REMARK 3 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO REMARK 3 INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. REMARK 3 MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL REMARK 3 SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B REMARK 3 106, 92-96) RESTRAINTS, AND A CONFORMATIONAL DATABASE REMARK 3 POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI. 5, REMARK 3 1067-1080; KUSZEWSKI ET AL. (1997) J. MAGN. RESON 125, REMARK 3 171-177). REMARK 3 REMARK 3 THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN REMARK 3 ENTRY 2EZH AND 30 STRUCTURES ARE PRESENTED IN ENTRY 2EZI, REMARK 3 AND THE EXPERIMENTAL RESTRAINTS IN 2EZHMR. IN THE REMARK 3 RESTRAINED REGULARIZED MEAN COORDINATES (2EZH) THE LAST REMARK 3 COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE REMARK 3 INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN REMARK 3 COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA REMARK 3 STRUCTURES (2EZI) HAS NO MEANING. BEST FITTING TO GENERATE REMARK 3 THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 180 - REMARK 3 240. NOTE THAT THE OCCUPANCY FIELD HAS NO MEANING. REMARK 4 REMARK 4 2EZH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178059. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SEE BELOW REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX500; AMX600 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 : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 RES C SSSEQI REMARK 465 MET A 173 REMARK 465 ASN A 174 REMARK 465 VAL A 175 REMARK 465 HIS A 176 REMARK 465 LYS A 177 REMARK 465 GLU A 243 REMARK 465 HIS A 244 REMARK 465 ALA A 245 REMARK 465 LEU A 246 REMARK 465 MET A 247 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 OD2 ASP A 181 H SER A 217 1.59 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 ASP A 181 108.55 -46.42 REMARK 500 LEU A 231 -84.06 -61.99 REMARK 500 ASP A 232 158.77 179.84 REMARK 500 GLU A 241 87.85 -48.41 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 ARG A 212 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EZI RELATED DB: PDB DBREF 2EZH A 174 247 UNP P07636 TRA_BPMU 174 247 SEQRES 1 A 75 MET ASN VAL HIS LYS SER GLU PHE ASP GLU ASP ALA TRP SEQRES 2 A 75 GLN PHE LEU ILE ALA ASP TYR LEU ARG PRO GLU LYS PRO SEQRES 3 A 75 ALA PHE ARG LYS CYS TYR GLU ARG LEU GLU LEU ALA ALA SEQRES 4 A 75 ARG GLU HIS GLY TRP SER ILE PRO SER ARG ALA THR ALA SEQRES 5 A 75 PHE ARG ARG ILE GLN GLN LEU ASP GLU ALA MET VAL VAL SEQRES 6 A 75 ALA CYS ARG GLU GLY GLU HIS ALA LEU MET HELIX 1 1 GLU A 182 TYR A 192 1 11 HELIX 2 2 PHE A 200 HIS A 214 1 15 HELIX 3 3 ARG A 221 LEU A 231 1 11 HELIX 4 4 GLU A 233 ARG A 240 1 8 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