HEADER MEMBRANE PROTEIN 15-DEC-06 2JN0 TITLE SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA COLI. TITLE 2 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 TARGET, KEYWDS 2 STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, NESG, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.ROSSI,C.X.CHEN,M.JIANG,K.CUNNINGHAM,L.MA,R.XIAO,J.C.LIU,M.BARAN, AUTHOR 2 G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 4 14-JUN-23 2JN0 1 REMARK REVDAT 3 05-FEB-20 2JN0 1 REMARK SEQADV 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,J.LIU, JRNL AUTH 2 M.C.BARAN,G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA JRNL TITL 2 COLI. NORTHEAST STRUCTURAL GENOMICS TARGET ER382A. JRNL REF TO BE PUBLISHED JRNL REFN 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), NABUURS, REMARK 3 VUISTER (QUEEN), BHATTACHARYA, 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 DEPOSITION ID IS D_1000100036. 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% 15N] REMARK 210 ER382A, 10 MM DTT, 5 MM CACL2, REMARK 210 0.1 M NACL, 20 MM MES, 0.02 % REMARK 210 SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCACB; 3D HBHA(CO) REMARK 210 NH; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HCCH-TOCSY; 3D HN(COCA) REMARK 210 CB; 3D HCCH-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 SPECTROSCOPY. REMARK 210 MONOMER IN SOLUTION BY NMR TC = 8.2 +/- 1.0 NS (1D T1/T1RHO +/- REMARK 210 FIT STD). POSSIBLE CIS PEPTIDE RES. 20K-21P. COULD NOT BE REMARK 210 ANAMBIGUOSLY ESTABLISHED DUE TO SPECTRAL OVERLAP. COORDINATES REMARK 210 REPORTED FROM RESIDUE 4 TO 53 SECTION BASED ON ORDER PARAMETER. REMARK 210 MANUAL RESONANCE ASSIGNMENT. 13C AND 15N EDITED NOESY WERE WERE REMARK 210 ASSIGNED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS REMARK 210 DETERMINED BY HYPER AND TALOS. ASSIGNMENT STATS (EXCLUDING C- REMARK 210 TERM TAG): BACKBONE 80.4%, SIDECHAIN 77.7%, AROMATIC (SC) 100%, REMARK 210 VL METHYL STEREOSP. 80%. STRUCTURE QUALITY FACTOR PSVS 1.3: REMARK 210 ORDERED RESIDUES RANGES B-STRAND (14-16, 6-9, 47-49, 22-24, 29- REMARK 210 33, 39-43, 65, 50-51, 56-57) [S(PHI)+S(PSI)]>1.8. RMSD 0.6 BB, REMARK 210 1.1 ALL HEAVY ATOMS. RAMA: 84.1% MOST FAV, 13.6% ADDTL.ALL.,2.2% REMARK 210 GEN. ALL.,0.1% DISALL. PROCHECK (PSI-PHI): 0.75/-2.64 (RAW/Z), REMARK 210 PROCHECK (ALL): -0.6/-3.55 (RAW/Z), MOLPROBITY CLASH: 23.61/- REMARK 210 2.53 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY REMARK 210 PEAKLISTS TO STRUCTURE): RECALL: 0.925, PRECISION: 0.916, F- REMARK 210 MEASURE: 0.921, DP-SCORE: 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 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 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: 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 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 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 REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS. 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 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20