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
(ATOM LINES ARE NOT SHOWN.)
END
