PDB Short entry for 1S6L HEADER LYASE 25-JAN-04 1S6L TITLE SOLUTION STRUCTURE OF MERB, THE ORGANOMERCURIAL LYASE INVOLVED IN THE TITLE 2 BACTERIAL MERCURY RESISTANCE SYSTEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKYLMERCURY LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORGANOMERCURIAL LYASE; COMPND 5 EC: 4.99.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MERB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PET21B KEYWDS LYASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.DI LELLO,G.C.BENISON,H.VALAFAR,K.E.PITTS,A.O.SUMMERS,P.LEGAULT, AUTHOR 2 J.G.OMICHINSKI REVDAT 3 06-JUL-11 1S6L 1 REMARK REVDAT 2 24-FEB-09 1S6L 1 VERSN REVDAT 1 19-APR-05 1S6L 0 JRNL AUTH P.DI LELLO,G.C.BENISON,H.VALAFAR,K.E.PITTS,A.O.SUMMERS, JRNL AUTH 2 P.LEGAULT,J.G.OMICHINSKI JRNL TITL NMR STRUCTURAL STUDIES REVEAL A NOVEL PROTEIN FOLD FOR MERB, JRNL TITL 2 THE ORGANOMERCURIAL LYASE INVOLVED IN THE BACTERIAL MERCURY JRNL TITL 3 RESISTANCE SYSTEM. JRNL REF BIOCHEMISTRY V. 43 8322 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15222745 JRNL DOI 10.1021/BI049669Z REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.DI LELLO,G.C.BENISON,J.G.OMICHINSKI,P.LEGAULT REMARK 1 TITL 1H, 15N, AND 13C RESONANCE ASSIGNMENT OF THE 23 KDA REMARK 1 TITL 2 ORGANOMERCURIAL LYASE MERB IN ITS FREE AND MERCURY-BOUND REMARK 1 TITL 3 FORMS REMARK 1 REF J.BIOMOL.NMR V. 29 457 2004 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 15213467 REMARK 1 DOI 10.1023/B:JNMR.0000032559.32474.A1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER, A.T., ADAMS, P.D., CLORE, G.M., GROS, P., REMARK 3 GROSSE-KUNSTLEVE, R.W., JIANG, J.S., KUSZEWSKI, J., REMARK 3 NILGES, M., PANNU, N.S., READ, R.J., RICE, L.M., REMARK 3 SIMONSON, T. AND WARREN, G.L. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE THREE-DIMENSIONAL STRUCTURES OF REMARK 3 MERB WERE DETERMINED USING A SET OF 1493 NOE-DERIVED DISTANCE REMARK 3 RESTRAINTS, 203 BACKBONE DIHEDRAL ANGLE (PHI AND PSI) RESTRAINTS, REMARK 3 5 CHI ANGLE RESTRAINTS, 36 HYDROGEN-BOND RESTRAINTS AND 298 ONE- REMARK 3 BOND RESIDUAL DIPOLAR COUPLING RESTRAINTS. REMARK 4 REMARK 4 1S6L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-04. REMARK 100 THE RCSB ID CODE IS RCSB021431. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE BUFFER REMARK 210 AND 10MM SODIUM CHLORIDE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0-1.5MM MERB [U-15N], 10MM REMARK 210 SODIUM PHOSPHATE BUFFER, 10MM REMARK 210 SODIUM CHLORIDE, 7.5MM DTT, 1MM REMARK 210 EDTA, 90%H2O, 10%D2O; 1.0-1.5MM REMARK 210 MERB [U-13C AND U-15N], 10MM REMARK 210 SODIUM PHOSPHATE BUFFER, 10MM REMARK 210 SODIUM CHLORIDE, 7.5MM DTT, 1MM REMARK 210 EDTA, 99.9% D2O; 1.3MM MERB [U- REMARK 210 13C AND U-15N], 10MM SODIUM REMARK 210 PHOSPHATE BUFFER, 10MM SODIUM REMARK 210 CHLORIDE, 7.5MM DTT, 1MM EDTA, 11 REMARK 210 MG/ML PF1 PHAGES, 90%H2O, 10%D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N-EDITED NOESY-HSQC; HNHA; REMARK 210 3D 13C-EDITED HMQC-NOESY; 4D 13C/ REMARK 210 13C-EDITED HMQC-NOESY-HMQC; 2D REMARK 210 IPAP-[1H-15N] HSQC; 3D TROSY- REMARK 210 BASED HNCO FOR MEASURAMENTS OF REMARK 210 ONE-BOND DIPOLAR COUPLINGS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, NMRPIPE, PIPP, NMRVIEW REMARK 210 5.0.4, CNS 1.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, WITH A REMARK 210 COMBINATION OF TORSION ANGLE REMARK 210 DYNAMICS AND CARTESIAN DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 55 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED MODELS ARE THE 20 REMARK 210 STRUCTURES WITH NO UPPER BOUND REMARK 210 VIOLATION GREATER THAT 0.3 REMARK 210 ARMSTRONGS AND NO DIHEDRAL ANGLE REMARK 210 RESTRAINT VIOLATION GREATER THAN REMARK 210 2 DEGREES AND WITH THE LOWEST REMARK 210 ENERGIES. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 PRO A 5 REMARK 465 TYR A 6 REMARK 465 ILE A 7 REMARK 465 LEU A 8 REMARK 465 GLU A 9 REMARK 465 LEU A 10 REMARK 465 LEU A 11 REMARK 465 THR A 12 REMARK 465 SER A 13 REMARK 465 VAL A 14 REMARK 465 ASN A 15 REMARK 465 ARG A 16 REMARK 465 THR A 17 REMARK 465 ASN A 18 REMARK 465 GLY A 19 REMARK 465 THR A 20 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 ALA A 142 H PHE A 165 1.49 REMARK 500 H SER A 115 O VAL A 124 1.52 REMARK 500 H VAL A 143 O VAL A 187 1.55 REMARK 500 H ALA A 142 O PHE A 165 1.57 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 LEU A 24 35.69 -98.43 REMARK 500 1 PRO A 36 109.08 -56.01 REMARK 500 1 LYS A 67 -104.06 66.06 REMARK 500 1 LEU A 76 -85.32 65.16 REMARK 500 1 ARG A 79 85.71 44.47 REMARK 500 1 GLU A 80 23.62 -168.07 REMARK 500 1 ASP A 88 -70.37 60.16 REMARK 500 1 ASP A 89 34.39 -166.94 REMARK 500 1 ILE A 102 -46.41 -151.31 REMARK 500 1 PHE A 103 79.02 -156.92 REMARK 500 1 GLU A 132 -163.29 179.60 REMARK 500 1 GLN A 134 20.75 -148.21 REMARK 500 1 ALA A 135 86.69 -171.94 REMARK 500 1 ALA A 139 79.15 -68.42 REMARK 500 1 ALA A 151 39.12 -150.31 REMARK 500 1 ASP A 153 -176.07 -59.37 REMARK 500 1 ARG A 155 -50.73 177.29 REMARK 500 1 GLN A 156 -46.86 -163.40 REMARK 500 1 PHE A 158 66.59 61.42 REMARK 500 1 CYS A 160 -75.32 -143.50 REMARK 500 1 LEU A 181 -176.18 -63.76 REMARK 500 1 LEU A 184 122.05 62.65 REMARK 500 1 SER A 208 165.23 60.57 REMARK 500 1 SER A 209 87.24 -150.79 REMARK 500 1 THR A 211 -62.91 -176.47 REMARK 500 2 ASP A 22 149.89 -174.74 REMARK 500 2 LEU A 24 -166.82 62.19 REMARK 500 2 ALA A 60 32.07 -99.75 REMARK 500 2 LYS A 67 -104.01 66.41 REMARK 500 2 TYR A 74 90.83 -162.22 REMARK 500 2 ASP A 88 -72.54 61.89 REMARK 500 2 ASP A 89 37.70 -158.05 REMARK 500 2 ILE A 102 -40.80 -174.67 REMARK 500 2 PHE A 103 65.48 -172.02 REMARK 500 2 ALA A 119 -51.07 -123.27 REMARK 500 2 GLU A 132 -162.02 178.56 REMARK 500 2 GLN A 134 18.59 -142.72 REMARK 500 2 ALA A 135 86.45 -171.57 REMARK 500 2 PRO A 148 -168.23 -75.75 REMARK 500 2 GLN A 149 115.70 -174.27 REMARK 500 2 GLU A 150 30.87 -149.19 REMARK 500 2 ALA A 151 36.41 -174.91 REMARK 500 2 ASP A 153 31.70 -156.74 REMARK 500 2 ARG A 155 -74.42 -160.32 REMARK 500 2 GLN A 156 39.40 -140.81 REMARK 500 2 PHE A 158 -68.38 -90.08 REMARK 500 2 CYS A 160 -50.79 80.03 REMARK 500 2 HIS A 161 48.05 -109.06 REMARK 500 2 HIS A 178 29.89 -145.79 REMARK 500 2 LEU A 181 -176.87 -57.07 REMARK 500 REMARK 500 THIS ENTRY HAS 503 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6047 RELATED DB: BMRB REMARK 900 1H, 15N, AND 13C RESONANCE ASSIGNMENT OF MERB IN THE FREE REMARK 900 FORM DBREF 1S6L A 1 212 UNP P77072 MERB_ECOLI 1 212 SEQRES 1 A 212 MET LYS LEU ALA PRO TYR ILE LEU GLU LEU LEU THR SER SEQRES 2 A 212 VAL ASN ARG THR ASN GLY THR ALA ASP LEU LEU VAL PRO SEQRES 3 A 212 LEU LEU ARG GLU LEU ALA LYS GLY ARG PRO VAL SER ARG SEQRES 4 A 212 THR THR LEU ALA GLY ILE LEU ASP TRP PRO ALA GLU ARG SEQRES 5 A 212 VAL ALA ALA VAL LEU GLU GLN ALA THR SER THR GLU TYR SEQRES 6 A 212 ASP LYS ASP GLY ASN ILE ILE GLY TYR GLY LEU THR LEU SEQRES 7 A 212 ARG GLU THR SER TYR VAL PHE GLU ILE ASP ASP ARG ARG SEQRES 8 A 212 LEU TYR ALA TRP CYS ALA LEU ASP THR LEU ILE PHE PRO SEQRES 9 A 212 ALA LEU ILE GLY ARG THR ALA ARG VAL SER SER HIS CYS SEQRES 10 A 212 ALA ALA THR GLY ALA PRO VAL SER LEU THR VAL SER PRO SEQRES 11 A 212 SER GLU ILE GLN ALA VAL GLU PRO ALA GLY MET ALA VAL SEQRES 12 A 212 SER LEU VAL LEU PRO GLN GLU ALA ALA ASP VAL ARG GLN SEQRES 13 A 212 SER PHE CYS CYS HIS VAL HIS PHE PHE ALA SER VAL PRO SEQRES 14 A 212 THR ALA GLU ASP TRP ALA SER LYS HIS GLN GLY LEU GLU SEQRES 15 A 212 GLY LEU ALA ILE VAL SER VAL HIS GLU ALA PHE GLY LEU SEQRES 16 A 212 GLY GLN GLU PHE ASN ARG HIS LEU LEU GLN THR MET SER SEQRES 17 A 212 SER ARG THR PRO HELIX 1 1 VAL A 25 LYS A 33 1 9 HELIX 2 2 SER A 38 ASP A 47 1 10 HELIX 3 3 PRO A 49 GLU A 58 1 10 HELIX 4 4 PHE A 103 GLY A 108 1 6 HELIX 5 5 SER A 167 LYS A 177 1 11 HELIX 6 6 VAL A 189 GLN A 205 1 17 SHEET 1 A 2 TYR A 65 ASP A 66 0 SHEET 2 A 2 ASN A 70 ILE A 71 -1 O ASN A 70 N ASP A 66 SHEET 1 B 5 ARG A 90 ALA A 94 0 SHEET 2 B 5 TYR A 83 ILE A 87 -1 N PHE A 85 O LEU A 92 SHEET 3 B 5 ALA A 111 HIS A 116 -1 O ARG A 112 N GLU A 86 SHEET 4 B 5 PRO A 123 VAL A 128 -1 O VAL A 124 N SER A 115 SHEET 5 B 5 ILE A 133 GLU A 137 -1 O GLU A 137 N SER A 125 SHEET 1 C 3 HIS A 163 PHE A 165 0 SHEET 2 C 3 ALA A 142 LEU A 145 -1 N ALA A 142 O PHE A 165 SHEET 3 C 3 ALA A 185 SER A 188 -1 O VAL A 187 N VAL A 143 CISPEP 1 GLU A 137 PRO A 138 1 0.06 CISPEP 2 GLU A 137 PRO A 138 2 -0.12 CISPEP 3 GLU A 137 PRO A 138 3 0.14 CISPEP 4 GLU A 137 PRO A 138 4 -0.02 CISPEP 5 GLU A 137 PRO A 138 5 -0.29 CISPEP 6 GLU A 137 PRO A 138 6 0.10 CISPEP 7 GLU A 137 PRO A 138 7 0.10 CISPEP 8 GLU A 137 PRO A 138 8 0.02 CISPEP 9 GLU A 137 PRO A 138 9 -0.44 CISPEP 10 GLU A 137 PRO A 138 10 -0.05 CISPEP 11 GLU A 137 PRO A 138 11 -0.21 CISPEP 12 GLU A 137 PRO A 138 12 -0.06 CISPEP 13 GLU A 137 PRO A 138 13 0.01 CISPEP 14 GLU A 137 PRO A 138 14 0.03 CISPEP 15 GLU A 137 PRO A 138 15 -0.20 CISPEP 16 GLU A 137 PRO A 138 16 0.00 CISPEP 17 GLU A 137 PRO A 138 17 0.17 CISPEP 18 GLU A 137 PRO A 138 18 0.12 CISPEP 19 GLU A 137 PRO A 138 19 -0.15 CISPEP 20 GLU A 137 PRO A 138 20 0.12 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