HEADER DNA BINDING PROTEIN 04-OCT-97 2EZK TITLE SOLUTION NMR STRUCTURE OF THE IBETA SUBDOMAIN OF THE MU END DNA TITLE 2 BINDING DOMAIN OF PHAGE MU TRANSPOSASE, REGULARIZED MEAN STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSPOSASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IBETA SUBDOMAIN, RESIDUES 77 - 174 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE MU; SOURCE 3 ORGANISM_TAXID: 10677 KEYWDS DNA-BINDING PROTEIN, TRANSPOSITION, TRANSPOSABLE ELEMENT, DNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,R.T.CLUBB,S.SCHUMAKER,A.M.GRONENBORN REVDAT 3 09-MAR-22 2EZK 1 KEYWDS REMARK REVDAT 2 24-FEB-09 2EZK 1 VERSN REVDAT 1 14-JAN-98 2EZK 0 JRNL AUTH S.SCHUMACHER,R.T.CLUBB,M.CAI,K.MIZUUCHI,G.M.CLORE, JRNL AUTH 2 A.M.GRONENBORN JRNL TITL SOLUTION STRUCTURE OF THE MU END DNA-BINDING IBETA SUBDOMAIN JRNL TITL 2 OF PHAGE MU TRANSPOSASE: MODULAR DNA RECOGNITION BY TWO JRNL TITL 3 TETHERED DOMAINS. JRNL REF EMBO J. V. 16 7532 1997 JRNL REFN ISSN 0261-4189 JRNL PMID 9405381 JRNL DOI 10.1093/EMBOJ/16.24.7532 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 IBETA SUBDOMAIN OF MU A TRANSPOSASE REMARK 3 WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND REMARK 3 IS BASED ON 1446 EXPERIMENTAL NMR RESTRAINTS: REMARK 3 255 SEQUENTIAL (|I- J|=1), 220 MEDIUM RANGE (1 < |I-J| <=5) REMARK 3 AND 252 LONG RANGE (|I-J| >5) INTERRESIDUES AND 234 REMARK 3 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; REMARK 3 52 DISTANCE RESTRAINTS FOR 26 BACKBONE H-BONDS;. REMARK 3 153 TORSION ANGLE RESTRAINTS REMARK 3 (94 PHI, 8 PSI, 36 CHI1 AND 15 CHI2); REMARK 3 58 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 180 REMARK 3 (92 CALPHA AND 88 CBETA) 13C 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 2EZK AND 29 STRUCTURES ARE PRESENTED IN ENTRY 2EZL, REMARK 3 AND THE EXPERIMENTAL RESTRAINTS IN R2EZKMR. IN THE REMARK 3 RESTRAINED REGULARIZED MEAN COORDINATES (2EZK) 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 THE STRUCTURES (2EZI) HAS NO MEANING. BEST FITTING TO REMARK 3 GENERATE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 89 - REMARK 3 166. RESIDUES 76 - 88 AND 167 - 174 AT THE N- AND REMARK 3 C-TERMINI ARE POORLY DEFINED BY THE EXPERIMENTAL DATA. REMARK 3 NOTE THE OCCUPANCY FIELD HAS NO MEANING. REMARK 3 REMARK 3 RMSD IN BONDS,ANGLES,IMPROPERS,CDIH,NOE,COUP: REMARK 3 2808E-03,0.871524,1.02906,0.295155,2.337017E-02,0.902726 REMARK 3 REMARK 3 SHIFTS RMS A, B: 1.04343, 1.11143 REMARK 4 REMARK 4 2EZK 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_1000178061. 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 : TRIPLE RESONANCE FOR ASSIGNMENT REMARK 210 OF PROTEIN: CBCA(CO)NH; CBCANH; REMARK 210 HBHA(CO)NH; C(CO)NH; H(CCO)NH; REMARK 210 HCCH-COSY; HCCH-TOCSY; HNHA; 15N- REMARK 210 SEPARATED HOHAHA; QUANTITATIVE J REMARK 210 CORRELATION FOR COUPLING REMARK 210 CONSTANTS; 3D 15N-SEPARATED NOE; REMARK 210 3D 13C-SEPARATED NOE AND ROE; 4D REMARK 210 15N/13C-SEPARATED NOE; 4D 13C/ REMARK 210 13C-SEPARATED NOE EXPERIMENTS 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 : 29 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : REGULARIZED MEAN STRUCTURE 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 GLY A 169 REMARK 465 ALA A 170 REMARK 465 SER A 171 REMARK 465 ARG A 172 REMARK 465 ARG A 173 REMARK 465 ASN A 174 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 O ARG A 89 H TRP A 93 1.53 REMARK 500 O GLU A 90 H SER A 94 1.58 REMARK 500 O TYR A 87 HH21 ARG A 89 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 ALA A 78 -116.53 -51.29 REMARK 500 PRO A 80 -167.04 -105.06 REMARK 500 HIS A 85 128.62 -176.59 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 146 0.09 SIDE CHAIN REMARK 500 ARG A 168 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EZL RELATED DB: PDB DBREF 2EZK A 77 174 UNP P07636 TRA_BPMU 77 174 SEQRES 1 A 99 MET ILE ALA ARG PRO THR LEU GLU ALA HIS ASP TYR ASP SEQRES 2 A 99 ARG GLU ALA LEU TRP SER LYS TRP ASP ASN ALA SER ASP SEQRES 3 A 99 SER GLN ARG ARG LEU ALA GLU LYS TRP LEU PRO ALA VAL SEQRES 4 A 99 GLN ALA ALA ASP GLU MET LEU ASN GLN GLY ILE SER THR SEQRES 5 A 99 LYS THR ALA PHE ALA THR VAL ALA GLY HIS TYR GLN VAL SEQRES 6 A 99 SER ALA SER THR LEU ARG ASP LYS TYR TYR GLN VAL GLN SEQRES 7 A 99 LYS PHE ALA LYS PRO ASP TRP ALA ALA ALA LEU VAL ASP SEQRES 8 A 99 GLY ARG GLY ALA SER ARG ARG ASN HELIX 1 1 GLU A 90 ASN A 98 1 9 HELIX 2 2 ASP A 101 ASN A 122 1 22 HELIX 3 3 THR A 127 HIS A 137 1 11 HELIX 4 4 ALA A 142 LYS A 154 1 13 HELIX 5 5 LYS A 157 VAL A 165 1 9 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