HEADER LIPOPROTEIN 03-MAR-08 2K1G TITLE SOLUTION NMR STRUCTURE OF LIPOPROTEIN SPR FROM ESCHERICHIA COLI K12. TITLE 2 NORTHEAST STRUCTURAL GENOMICS TARGET ER541-37-162 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOPROTEIN SPR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 63-188; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: SPR, YEIV, B2175, JW2163; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: ER541-37-162-21.1; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS SOLUTION NMR STRUCTURE, BACTERIAL LIPOPROTEIN, CYSTEINE PEPTIDASE, KEYWDS 2 NPLC/P60 FAMILY, CONSTRUCT OPTIMIZED, MEMBRANE, PALMITATE, KEYWDS 3 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 4 STRUCTURAL GENOMICS CONSORTIUM, NESG, LIPOPROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,P.ROSSI,L.ZHAO,M.JIANG,M.MAGLAQUI,R.XIAO,J.LIU,M.C.BARAN, AUTHOR 2 G.V.T.SWAPNA,Y.J.HUANG,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 7 01-MAY-24 2K1G 1 REMARK SEQADV REVDAT 6 13-JUL-11 2K1G 1 VERSN REVDAT 5 09-JUN-09 2K1G 1 REVDAT REVDAT 4 24-FEB-09 2K1G 1 VERSN REVDAT 3 13-JAN-09 2K1G 1 JRNL REVDAT 2 25-MAR-08 2K1G 1 SPRSDE REVDAT 1 18-MAR-08 2K1G 0 SPRSDE 25-MAR-08 2K1G 2JYX JRNL AUTH J.M.ARAMINI,P.ROSSI,Y.J.HUANG,L.ZHAO,M.JIANG,M.MAGLAQUI, JRNL AUTH 2 R.XIAO,J.LOCKE,R.NAIR,B.ROST,T.B.ACTON,M.INOUYE, JRNL AUTH 3 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE NLPC/P60 DOMAIN OF LIPOPROTEIN JRNL TITL 2 SPR FROM ESCHERICHIA COLI: STRUCTURAL EVIDENCE FOR A NOVEL JRNL TITL 3 CYSTEINE PEPTIDASE CATALYTIC TRIAD. JRNL REF BIOCHEMISTRY V. 47 9715 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18715016 JRNL DOI 10.1021/BI8010779 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, CNS 1.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 2525 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 138 DIHEDRAL ANGLE CONSTRAINTS, AND 48 HYDROGEN REMARK 3 BOND CONSTRAINTS (21.0 CONSTRAINTS PER RESIDUE, 7.1 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 37 TO 162 BY PSVS REMARK 3 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET REMARK 3 FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ REMARK 3 ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19, AND REMARK 3 USING NEUTRAL HISTIDINES AT POSITIONS 119 AND 131. REMARK 4 REMARK 4 2K1G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000100555. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.07 MM [U-100% 13C; U-100% 15N] REMARK 210 ER541-37-162, 20 MM MES, 100 MM REMARK 210 SODIUM CHLORIDE, 10 MM DTT, 5 MM REMARK 210 CALCIUM CHLORIDE, 0.02 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 1.07 MM REMARK 210 [U-100% 13C; U-100% 15N] ER541- REMARK 210 37-162, 20 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 10 MM DTT, 5 MM REMARK 210 CALCIUM CHLORIDE, 0.02 % SODIUM REMARK 210 AZIDE, 100% D2O; 1.03 MM [U-5% REMARK 210 13C; U-100% 15N] ER541-37-162, REMARK 210 20 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 10 MM DTT, 5 MM REMARK 210 CALCIUM CHLORIDE, 0.02 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D HN(COCA) REMARK 210 CB; 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-COSY; 3D SIMULTANEOUS CN REMARK 210 NOESY; 3D CCH-TOCSY AROMATIC; 3D REMARK 210 1H-13C NOESY AROMATIC; 3D CCCONH REMARK 210 TOCSY; 3D HCCH-TOCSY; 3D CCH- REMARK 210 TOCSY ALIPHATIC; 3D HNHA; 2D 1H- REMARK 210 13C HIGH RES. (L/V STEREO REMARK 210 ASSIGNMENT); 2D 1H-15N HETNOE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, AUTOASSIGN 2.4.0, REMARK 210 NMRPIPE 2.3, SPARKY 3.110, CYANA REMARK 210 2.1, CNS 1.2, AUTOSTRUCTURE REMARK 210 2.2.1, PSVS 1.3, PDBSTAT 5.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY REMARK 210 AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING REMARK 210 TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE REMARK 210 ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS REMARK 210 WERE DETERMINED USING CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 210 OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED REMARK 210 USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE REMARK 210 FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. REMARK 210 COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): REMARK 210 BACKBONE, 97.9%, SIDE CHAIN, 94.2%, AROMATICS, 91.8%, REMARK 210 STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 83.3% REMARK 210 . FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 37 TO 162, PSVS REMARK 210 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: REMARK 210 38-58,61-93,96-113,118-124,128-159: (A) RMSD (ORDERED RESIDUES): REMARK 210 BB, 0.5, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR REMARK 210 ORDERED RESIDUES: MOST FAVORED, 88.4%, ADDITIONALLY ALLOWED, REMARK 210 11.5%, GENEROUSLY ALLOWED, 0.1%, DISALLOWED, 0.0%. (C) PROCHECK REMARK 210 SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.46/-1.49, ALL, REMARK 210 -0.27/-1.60. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 18.98/-1.73. REMARK 210 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 37- REMARK 210 162): RECALL, 0.985, PRECISION, 0.925, F-MEASURE, 0.954, DP- REMARK 210 SCORE, 0.816. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 8. THE REMARK 210 C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT REMARK 210 INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED REMARK 210 FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE REMARK 210 NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 37,59-60,94-95,114- REMARK 210 117,125-127,160-162. 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 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 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 VAL A 38 82.61 -68.29 REMARK 500 1 PRO A 85 -161.54 -74.25 REMARK 500 1 ASN A 126 -82.04 65.00 REMARK 500 1 ASN A 127 -3.01 -141.34 REMARK 500 1 SER A 135 -71.25 -90.29 REMARK 500 1 TYR A 152 104.45 -55.98 REMARK 500 2 PRO A 85 -173.17 -67.56 REMARK 500 2 ARG A 104 -160.91 -112.17 REMARK 500 2 ASN A 126 -80.08 60.45 REMARK 500 2 GLU A 154 -166.56 177.30 REMARK 500 2 ARG A 161 94.31 -60.99 REMARK 500 3 LYS A 52 -1.45 -57.82 REMARK 500 3 PRO A 85 -179.02 -66.01 REMARK 500 3 ARG A 104 -122.13 -137.49 REMARK 500 3 THR A 116 45.44 -145.47 REMARK 500 3 SER A 136 -51.78 -138.42 REMARK 500 3 VAL A 138 96.34 -64.23 REMARK 500 3 ASN A 153 -69.10 -91.35 REMARK 500 3 LEU A 159 99.36 -67.36 REMARK 500 4 VAL A 38 97.15 -64.38 REMARK 500 4 ASP A 39 105.34 -58.04 REMARK 500 4 THR A 116 -59.12 -141.02 REMARK 500 4 ASN A 126 78.33 55.34 REMARK 500 4 ASN A 127 -41.04 70.20 REMARK 500 5 ASN A 37 89.08 -67.23 REMARK 500 5 LYS A 52 85.23 46.46 REMARK 500 5 GLN A 79 -69.34 -94.90 REMARK 500 5 ARG A 104 -159.01 -118.12 REMARK 500 5 SER A 115 -42.35 -165.23 REMARK 500 5 VAL A 138 95.77 -68.39 REMARK 500 5 ASN A 153 -60.80 -92.57 REMARK 500 6 ASP A 39 97.88 -56.93 REMARK 500 6 LYS A 52 109.08 -59.09 REMARK 500 6 GLN A 79 -68.22 -108.39 REMARK 500 6 PRO A 85 -175.62 -66.03 REMARK 500 6 THR A 105 96.46 -58.47 REMARK 500 6 GLU A 154 -173.02 -177.57 REMARK 500 7 LYS A 52 109.83 -59.81 REMARK 500 7 GLU A 78 -72.99 -73.24 REMARK 500 7 ARG A 86 48.80 -82.66 REMARK 500 7 ARG A 104 -162.33 -111.96 REMARK 500 7 SER A 115 -59.62 -151.81 REMARK 500 7 ASN A 153 -62.43 -98.07 REMARK 500 7 SER A 160 -61.58 -98.43 REMARK 500 8 LYS A 52 95.37 -64.85 REMARK 500 8 PRO A 85 -172.67 -67.45 REMARK 500 8 SER A 115 -38.42 -132.86 REMARK 500 8 ASN A 127 17.18 51.53 REMARK 500 8 HIS A 131 -166.37 -161.72 REMARK 500 8 ASN A 153 -69.59 -94.65 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ER541 RELATED DB: TARGETDB DBREF 2K1G A 37 162 UNP P0AFV4 SPR_ECOLI 63 188 SEQADV 2K1G MET A 36 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G LEU A 163 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G GLU A 164 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G HIS A 165 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G HIS A 166 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G HIS A 167 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G HIS A 168 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G HIS A 169 UNP P0AFV4 EXPRESSION TAG SEQADV 2K1G HIS A 170 UNP P0AFV4 EXPRESSION TAG SEQRES 1 A 135 MET ASN VAL ASP VAL LYS SER ARG ILE MET ASP GLN TYR SEQRES 2 A 135 ALA ASP TRP LYS GLY VAL ARG TYR ARG LEU GLY GLY SER SEQRES 3 A 135 THR LYS LYS GLY ILE ASP CYS SER GLY PHE VAL GLN ARG SEQRES 4 A 135 THR PHE ARG GLU GLN PHE GLY LEU GLU LEU PRO ARG SER SEQRES 5 A 135 THR TYR GLU GLN GLN GLU MET GLY LYS SER VAL SER ARG SEQRES 6 A 135 SER ASN LEU ARG THR GLY ASP LEU VAL LEU PHE ARG ALA SEQRES 7 A 135 GLY SER THR GLY ARG HIS VAL GLY ILE TYR ILE GLY ASN SEQRES 8 A 135 ASN GLN PHE VAL HIS ALA SER THR SER SER GLY VAL ILE SEQRES 9 A 135 ILE SER SER MET ASN GLU PRO TYR TRP LYS LYS ARG TYR SEQRES 10 A 135 ASN GLU ALA ARG ARG VAL LEU SER ARG SER LEU GLU HIS SEQRES 11 A 135 HIS HIS HIS HIS HIS HELIX 1 1 ASP A 39 LYS A 52 1 14 HELIX 2 2 ASP A 67 GLN A 79 1 13 HELIX 3 3 SER A 87 GLN A 92 1 6 HELIX 4 4 GLU A 93 GLY A 95 5 3 HELIX 5 5 SER A 99 LEU A 103 5 5 HELIX 6 6 GLU A 145 ARG A 151 1 7 SHEET 1 A 6 LYS A 96 VAL A 98 0 SHEET 2 A 6 TYR A 152 ARG A 157 -1 O ALA A 155 N VAL A 98 SHEET 3 A 6 ASP A 107 ALA A 113 -1 N LEU A 110 O GLU A 154 SHEET 4 A 6 GLY A 117 GLY A 125 -1 O TYR A 123 N ASP A 107 SHEET 5 A 6 GLN A 128 SER A 133 -1 O VAL A 130 N ILE A 122 SHEET 6 A 6 GLY A 137 SER A 142 -1 O ILE A 139 N HIS A 131 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 MODEL 1