PDB Short entry for 2LYR HEADER DNA BINDING PROTEIN 19-SEP-12 2LYR TITLE NOE-BASED 3D STRUCTURE OF THE MONOMERIC PARTIALLY-FOLDED INTERMEDIATE TITLE 2 OF CYLR2 AT 259K (-14 CELSIUS DEGREES) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYLR2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE TRANSCRIPTION REGULATOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 GENE: CYLR2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS CYLR2, DNA BINDING PROTEIN, NOE-BASED STRUCTURE, PROTEIN FOLDING, KEYWDS 2 COLD DENATURATION, CYTOLYSIN REPRESSOR 2, HELIX-TURN-HELIX, KEYWDS 3 PARTIALLY FOLDED EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.JAREMKO,L.JAREMKO,H.KIM,M.CHO,C.D.SCHWIETERS,K.GILLER,S.BECKER, AUTHOR 2 M.ZWECKSTETTER REVDAT 4 14-JUN-23 2LYR 1 REMARK REVDAT 3 03-APR-13 2LYR 1 JRNL REVDAT 2 27-FEB-13 2LYR 1 JRNL REVDAT 1 20-FEB-13 2LYR 0 JRNL AUTH M.JAREMKO,L.JAREMKO,H.Y.KIM,M.K.CHO,C.D.SCHWIETERS,K.GILLER, JRNL AUTH 2 S.BECKER,M.ZWECKSTETTER JRNL TITL COLD DENATURATION OF A PROTEIN DIMER MONITORED AT ATOMIC JRNL TITL 2 RESOLUTION. JRNL REF NAT.CHEM.BIOL. V. 9 264 2013 JRNL REFN ISSN 1552-4450 JRNL PMID 23396077 JRNL DOI 10.1038/NCHEMBIO.1181 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0, X-PLOR NIH 2.26 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000102997. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 259 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.6 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.52 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 600 MM SODIUM CHLORIDE, REMARK 210 50 MM HEPES, 93 % H2O, 7 % D2O, REMARK 210 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D HCCH-TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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: 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 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 HZ3 LYS A 13 OG1 THR A 55 1.32 REMARK 500 O LEU A 57 H PHE A 61 1.42 REMARK 500 O ALA A 21 H GLU A 25 1.45 REMARK 500 OE1 GLU A 35 HG SER A 42 1.47 REMARK 500 O ASN A 32 HZ1 LYS A 36 1.47 REMARK 500 O SER A 27 HG1 THR A 30 1.49 REMARK 500 OE1 GLU A 19 HH TYR A 52 1.50 REMARK 500 O ILE A 9 H LYS A 13 1.52 REMARK 500 O ASN A 4 H LEU A 6 1.52 REMARK 500 O SER A 18 H ALA A 22 1.53 REMARK 500 O ASP A 59 HE21 GLN A 62 1.53 REMARK 500 HZ2 LYS A 13 O ASN A 54 1.53 REMARK 500 OD1 ASN A 32 HZ2 LYS A 36 1.54 REMARK 500 HH11 ARG A 28 OE2 GLU A 35 1.54 REMARK 500 O ILE A 49 H LEU A 53 1.55 REMARK 500 O LYS A 7 HH11 ARG A 10 1.55 REMARK 500 O GLN A 62 HE21 GLN A 64 1.57 REMARK 500 HG SER A 16 OE2 GLU A 19 1.57 REMARK 500 O ILE A 34 H LYS A 38 1.58 REMARK 500 O SER A 42 H ALA A 46 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 1 ILE A 3 -154.54 -93.94 REMARK 500 1 LYS A 14 42.42 36.45 REMARK 500 1 SER A 27 -14.77 -46.38 REMARK 500 1 GLN A 64 76.92 52.57 REMARK 500 2 SER A 27 -13.69 -45.87 REMARK 500 2 GLN A 62 48.76 -61.30 REMARK 500 2 GLN A 64 75.55 -109.74 REMARK 500 3 ILE A 3 46.96 -65.07 REMARK 500 3 ARG A 28 -30.56 -38.84 REMARK 500 3 LEU A 53 49.74 -71.10 REMARK 500 3 ASN A 54 72.37 -27.87 REMARK 500 3 THR A 55 117.06 -166.14 REMARK 500 3 PHE A 61 67.22 38.57 REMARK 500 3 TRP A 63 113.04 -36.99 REMARK 500 4 ILE A 3 -51.50 -160.03 REMARK 500 4 ASN A 54 28.76 44.69 REMARK 500 4 PRO A 56 46.47 -59.45 REMARK 500 4 TRP A 63 160.58 161.31 REMARK 500 5 ILE A 3 47.52 -84.27 REMARK 500 5 LYS A 14 22.96 47.85 REMARK 500 5 PHE A 61 11.24 -67.40 REMARK 500 5 TRP A 63 -175.85 83.32 REMARK 500 6 ASN A 5 102.70 -17.94 REMARK 500 6 ASN A 54 93.74 -54.22 REMARK 500 6 PHE A 61 75.00 -66.04 REMARK 500 7 ASN A 4 40.00 -69.38 REMARK 500 7 SER A 27 -13.56 -49.73 REMARK 500 7 ASN A 54 64.38 -65.57 REMARK 500 7 GLN A 62 160.46 -40.84 REMARK 500 7 GLN A 64 72.23 19.92 REMARK 500 7 PRO A 65 24.76 -70.58 REMARK 500 8 ILE A 3 -176.64 -68.22 REMARK 500 8 ASN A 4 98.30 46.83 REMARK 500 8 LYS A 13 24.09 -77.40 REMARK 500 8 GLU A 25 29.18 49.32 REMARK 500 8 SER A 27 -15.23 -44.71 REMARK 500 8 ASN A 54 63.16 -63.49 REMARK 500 8 PRO A 56 58.69 -66.40 REMARK 500 8 PHE A 61 178.35 45.06 REMARK 500 9 ASN A 54 81.58 -47.45 REMARK 500 9 PHE A 61 134.00 63.56 REMARK 500 10 SER A 27 -13.96 -40.53 REMARK 500 10 TYR A 52 -139.72 -101.21 REMARK 500 10 LEU A 53 -26.28 56.93 REMARK 500 10 PHE A 61 111.08 87.54 REMARK 500 11 ASN A 4 5.75 -171.11 REMARK 500 11 LYS A 14 46.59 38.07 REMARK 500 11 TYR A 51 15.81 42.00 REMARK 500 11 LEU A 53 53.64 -62.44 REMARK 500 11 THR A 55 113.24 -166.66 REMARK 500 REMARK 500 THIS ENTRY HAS 104 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 4 ARG A 10 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GZU RELATED DB: PDB REMARK 900 STRUCTURE OF THE SAME PROTEIN USING INTERMONOMER DISTANCES FROM REMARK 900 PARAMAGNETIC RELAXATION ENHANCEMENT AND NMR DIPOLAR COUPLINGS REMARK 900 RELATED ID: 1UTX RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE SAME PROTEIN AT 1.9 A RESOLUTION REMARK 900 RELATED ID: 2XI8 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE SAME PROTEIN AT 1.21 A RESOLUTION REMARK 900 RELATED ID: 2XIU RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MTSL-TAGGED CYLR2 REMARK 900 RELATED ID: 2XJ3 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF T55C MUTANT OF CYLR2 REMARK 900 RELATED ID: 2LYJ RELATED DB: PDB REMARK 900 RELATED ID: 2LYK RELATED DB: PDB REMARK 900 RELATED ID: 2LYL RELATED DB: PDB REMARK 900 RELATED ID: 2LYP RELATED DB: PDB REMARK 900 RELATED ID: 2LYQ RELATED DB: PDB REMARK 900 RELATED ID: 2LYS RELATED DB: PDB REMARK 900 RELATED ID: 17897 RELATED DB: BMRB DBREF 2LYR A 1 66 UNP Q8VL32 Q8VL32_ENTFL 1 66 SEQRES 1 A 66 MET ILE ILE ASN ASN LEU LYS LEU ILE ARG GLU LYS LYS SEQRES 2 A 66 LYS ILE SER GLN SER GLU LEU ALA ALA LEU LEU GLU VAL SEQRES 3 A 66 SER ARG GLN THR ILE ASN GLY ILE GLU LYS ASN LYS TYR SEQRES 4 A 66 ASN PRO SER LEU GLN LEU ALA LEU LYS ILE ALA TYR TYR SEQRES 5 A 66 LEU ASN THR PRO LEU GLU ASP ILE PHE GLN TRP GLN PRO SEQRES 6 A 66 GLU HELIX 1 1 ASN A 5 LYS A 13 1 9 HELIX 2 2 SER A 16 LEU A 23 1 8 HELIX 3 3 SER A 27 TYR A 39 1 13 HELIX 4 4 SER A 42 ASN A 54 1 13 HELIX 5 5 PRO A 56 PHE A 61 1 6 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