10 20 30 40 50 60 70 80 2JN0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER MEMBRANE PROTEIN 15-DEC-06 2JN0
TITLE SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA TITLE 2 COLI. NORTHEAST STRUCTURAL GENOMICS TARGET ER382A.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL LIPOPROTEIN YGDR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HYPOTHETICAL LIPOPROTEIN YGDR, RESIDUES 2-53; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YGDR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: ER382A-21.2
KEYWDS SOLUTION NMR STRUCTURE, HYPOTHETICAL LIPOPROTEIN, PSI-2 KEYWDS 2 TARGET, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, MEMBRANE KEYWDS 4 PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR P.ROSSI,C.X.CHEN,M.JIANG,K.CUNNINGHAM,L.MA,R.XIAO,J.C.LIU, AUTHOR 2 M.BARAN,G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)
REVDAT 2 24-FEB-09 2JN0 1 VERSN REVDAT 1 01-MAY-07 2JN0 0
JRNL AUTH P.ROSSI,C.X.CHEN,M.JIANG,K.CUNNINGHAM,L.MA,R.XIAO, JRNL AUTH 2 J.LIU,M.C.BARAN,G.V.T.SWAPNA,T.B.ACTON,B.ROST, JRNL AUTH 3 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM JRNL TITL 2 ESCHERICHIA COLI. NORTHEAST STRUCTURAL GENOMICS JRNL TITL 3 TARGET ER382A. JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNSSOLVE 1.1, X-PLOR 2.11.2, PROCHECK NMR 3.51, REMARK 3 MOLPROBITY 3.01, QUEEN 1.1, PSVS 1.3 REMARK 3 AUTHORS : BRUNGER, ET. AL. (CNSSOLVE), CLORE ET. AL. (X- REMARK 3 PLOR), LASKOWSKI, MACARTHUR (PROCHECK NMR), REMARK 3 LOVELL, RICHARDSON ET. AL. (MOLPROBITY), REMARK 3 NABUURS, VUISTER (QUEEN), BHATTACHARYA, REMARK 3 MONTELIONE (PSVS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NOESY ASSIGNMENT MADE WITH ITERATIVE REMARK 3 METHOD USING CNS, HYPER (DIHEDRAL) AND DYANA FOLLOWED BY NIH- REMARK 3 XPLOR FOR SIMMULATED ANNEALING MD. CONVERGED STRUCTURES WERE REMARK 3 FURTHER MINIMIZED USING CNS IN EXPLICIT H2O SHELL (NILGES REMARK 3 PROTOCOL). FULL LENGTH SEQUENCE WAS CARRIED THROUGH THE REMARK 3 REFINEMENT PROTOCOL. COORDINATES FROM DISORDERED REGIONS, REMARK 3 INCLUDING HEXHIS TAG, WERE NOT REPORTED. STRUCTURE IS BASED ON REMARK 3 439 CONSTRAINTS (216 LONG RANGE), 43 DIHEDRAL AND 20 H-BOND.
REMARK 4 REMARK 4 2JN0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-06. REMARK 100 THE RCSB ID CODE IS RCSB100036.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.17 MM [U-100% 13C, U-100% REMARK 210 15N] ER382A, 10 MM DTT, 5 MM REMARK 210 CACL2, 0.1 M NACL, 20 MM MES, REMARK 210 0.02 % SODIUM AZIDE, 95% H2O, REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-13C REMARK 210 HSQC, 3D HNCO, 3D HNCACB, 3D REMARK 210 HBHA(CO)NH, 3D 1H-15N NOESY, REMARK 210 3D 1H-13C NOESY, 3D HCCH- REMARK 210 TOCSY, 3D HN(CO)CACB, 3D HCCH- REMARK 210 COSY, 3D CCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOSTRUCTURE 2.1.1, NMRPIPE, REMARK 210 SPARKY, MOLMOL, CNS, PROCHECK, REMARK 210 XPLOR-NIH, DIANA, QUEEN 1.1 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 : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY. MONOMER IN SOLUTION BY NMR TC = 8.2 +/- 1.0 NS REMARK 210 (1D T1/T1RHO +/- FIT STD). POSSIBLE CIS PEPTIDE RES. 20K-21P. REMARK 210 COULD NOT BE ANAMBIGUOSLY ESTABLISHED DUE TO SPECTRAL OVERLAP. REMARK 210 COORDINATES REPORTED FROM RESIDUE 4 TO 53 SECTION BASED ON REMARK 210 ORDER PARAMETER. MANUAL RESONANCE ASSIGNMENT. 13C AND 15N REMARK 210 EDITED NOESY WERE WERE ASSIGNED USING AUTOSTRUCTURE. DIHEDRAL REMARK 210 ANGLE RESTRAINTS DETERMINED BY HYPER AND TALOS. ASSIGNMENT REMARK 210 STATS (EXCLUDING C-TERM TAG): BACKBONE 80.4%, SIDECHAIN 77.7%, REMARK 210 AROMATIC (SC) 100%, VL METHYL STEREOSP. 80%. STRUCTURE QUALITY REMARK 210 FACTOR PSVS 1.3: ORDERED RESIDUES RANGES B-STRAND (14-16, 6-9, REMARK 210 47-49, 22-24, 29-33, 39-43, 65, 50-51, 56-57) [S(PHI)+S(PSI)]> REMARK 210 1.8. RMSD 0.6 BB, 1.1 ALL HEAVY ATOMS. RAMA: 84.1% MOST FAV, REMARK 210 13.6% ADDTL.ALL.,2.2% GEN. ALL.,0.1% DISALL. PROCHECK (PSI- REMARK 210 PHI): 0.75/-2.64 (RAW/Z), PROCHECK (ALL): -0.6/-3.55 (RAW/Z), REMARK 210 MOLPROBITY CLASH: 23.61/- 2.53 (RAW/Z). RPF SCORES ALL REMARK 210 ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): REMARK 210 RECALL: 0.925, PRECISION: 0.916, F-MEASURE: 0.921, DP-SCORE: REMARK 210 0.731. MONOMER BY LIGHT SCATTERING
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 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 SER A 2 REMARK 465 SER A 3 REMARK 465 LEU A 54 REMARK 465 GLU A 55 REMARK 465 HIS A 56 REMARK 465 HIS A 57 REMARK 465 HIS A 58 REMARK 465 HIS A 59 REMARK 465 HIS A 60 REMARK 465 HIS A 61
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 THR A 27 -35.52 -137.74 REMARK 500 1 SER A 48 -72.40 -105.94 REMARK 500 2 VAL A 6 139.32 -172.74 REMARK 500 2 LYS A 20 52.29 170.31 REMARK 500 2 SER A 48 -64.70 -92.58 REMARK 500 2 ILE A 51 117.55 71.19 REMARK 500 3 TYR A 5 -158.12 -142.16 REMARK 500 3 VAL A 6 177.92 62.35 REMARK 500 3 LYS A 20 78.44 71.63 REMARK 500 3 ILE A 50 -32.64 -173.15 REMARK 500 3 ILE A 51 99.76 65.23 REMARK 500 4 LYS A 20 132.76 77.13 REMARK 500 4 ILE A 51 14.74 -144.72 REMARK 500 5 LYS A 20 78.45 72.63 REMARK 500 5 SER A 48 -63.66 -93.08 REMARK 500 5 ILE A 50 -74.28 -130.69 REMARK 500 6 LYS A 20 79.70 72.95 REMARK 500 6 SER A 48 -64.29 -99.63 REMARK 500 6 ILE A 50 -77.23 -112.64 REMARK 500 7 VAL A 6 132.67 -175.95 REMARK 500 7 LYS A 20 76.69 92.83 REMARK 500 7 SER A 48 -62.41 -152.56 REMARK 500 7 GLU A 52 -74.33 -52.83 REMARK 500 8 LYS A 20 78.46 72.71 REMARK 500 8 SER A 48 -73.46 -128.71 REMARK 500 8 GLU A 52 -93.02 61.61 REMARK 500 9 VAL A 6 83.71 39.35 REMARK 500 9 LYS A 20 85.98 162.52 REMARK 500 9 SER A 48 -61.53 -126.92 REMARK 500 9 ILE A 50 -57.11 -134.94 REMARK 500 9 GLU A 52 -70.69 -57.01 REMARK 500 10 TYR A 5 -8.12 -168.76 REMARK 500 10 LYS A 20 95.42 79.49 REMARK 500 10 SER A 48 -66.83 -137.21 REMARK 500 11 LYS A 20 76.98 91.61 REMARK 500 11 SER A 48 -78.11 -109.01 REMARK 500 12 VAL A 6 159.07 70.46 REMARK 500 12 ASP A 11 29.55 -76.76 REMARK 500 12 LYS A 20 65.62 157.86 REMARK 500 13 VAL A 6 120.17 73.14 REMARK 500 13 LYS A 10 -59.81 -28.12 REMARK 500 13 LYS A 20 75.10 67.78 REMARK 500 13 SER A 48 -68.88 -91.11 REMARK 500 13 GLN A 49 147.85 -179.49 REMARK 500 13 GLU A 52 49.62 -87.00 REMARK 500 14 TYR A 5 112.22 -160.50 REMARK 500 14 VAL A 6 154.82 65.43 REMARK 500 14 LYS A 20 73.49 69.46 REMARK 500 14 SER A 48 -65.49 -130.80 REMARK 500 15 LYS A 20 71.52 71.94 REMARK 500 15 GLN A 36 7.39 -150.15 REMARK 500 15 SER A 48 -78.94 -151.45 REMARK 500 15 ILE A 50 17.20 -141.01 REMARK 500 15 ILE A 51 -66.98 -125.25 REMARK 500 16 LYS A 10 -55.02 -29.14 REMARK 500 16 LYS A 20 90.39 73.76 REMARK 500 16 ASP A 34 175.49 -54.85 REMARK 500 17 LYS A 20 72.30 71.15 REMARK 500 17 SER A 48 -76.73 -117.57 REMARK 500 17 ILE A 51 162.31 61.63 REMARK 500 18 LYS A 20 70.30 82.61 REMARK 500 18 SER A 48 -75.15 -146.44 REMARK 500 18 GLU A 52 -165.22 66.92 REMARK 500 19 VAL A 6 115.17 71.25 REMARK 500 19 LYS A 20 73.20 73.19 REMARK 500 19 SER A 48 -70.13 -125.01 REMARK 500 19 ILE A 50 -69.31 -98.76 REMARK 500 19 GLU A 52 96.90 -68.44 REMARK 500 20 TYR A 5 105.99 -160.58 REMARK 500 20 SER A 48 -69.83 -157.55 REMARK 500 20 ILE A 50 -45.39 -144.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 19 LYS A 20 4 140.99 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15079 RELATED DB: BMRB REMARK 900 RELATED ID: ER382A RELATED DB: TARGETDB
DBREF 2JN0 A 2 53 UNP P65294 YGDR_ECOLI 21 72
SEQADV 2JN0 MET A 1 UNP P65294 CLONING ARTIFACT SEQADV 2JN0 LEU A 54 UNP P65294 CLONING ARTIFACT SEQADV 2JN0 GLU A 55 UNP P65294 CLONING ARTIFACT SEQADV 2JN0 HIS A 56 UNP P65294 EXPRESSION TAG SEQADV 2JN0 HIS A 57 UNP P65294 EXPRESSION TAG SEQADV 2JN0 HIS A 58 UNP P65294 EXPRESSION TAG SEQADV 2JN0 HIS A 59 UNP P65294 EXPRESSION TAG SEQADV 2JN0 HIS A 60 UNP P65294 EXPRESSION TAG SEQADV 2JN0 HIS A 61 UNP P65294 EXPRESSION TAG
SEQRES 1 A 61 MET SER SER ASP TYR VAL MET ALA THR LYS ASP GLY ARG SEQRES 2 A 61 MET ILE LEU THR ASP GLY LYS PRO GLU ILE ASP ASP ASP SEQRES 3 A 61 THR GLY LEU VAL SER TYR HIS ASP GLN GLN GLY ASN ALA SEQRES 4 A 61 MET GLN ILE ASN ARG ASP ASP VAL SER GLN ILE ILE GLU SEQRES 5 A 61 ARG LEU GLU HIS HIS HIS HIS HIS HIS
SHEET 1 A 3 MET A 14 LEU A 16 0 SHEET 2 A 3 VAL A 6 THR A 9 -1 N MET A 7 O ILE A 15 SHEET 3 A 3 VAL A 47 GLN A 49 -1 O GLN A 49 N ALA A 8 SHEET 1 B 3 GLU A 22 ILE A 23 0 SHEET 2 B 3 LEU A 29 HIS A 33 -1 O SER A 31 N GLU A 22 SHEET 3 B 3 ALA A 39 ASN A 43 -1 O MET A 40 N TYR A 32
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