HEADER CHAPERONE/OXIDOREDUCTASE 01-MAY-07 2PQ4 TITLE NMR SOLUTION STRUCTURE OF NAPD IN COMPLEX WITH NAPA1-35 SIGNAL PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NAPD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PERIPLASMIC NITRATE REDUCTASE PRECURSOR; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: SIGNAL PEPTIDE: RESIDUES 1-35; COMPND 9 EC: 1.7.99.4; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 STRAIN: K12; SOURCE 4 GENE: NAPD, B2207, JW2195; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 11 STRAIN: K12; SOURCE 12 GENE: NAPA, B2206, JW2194; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS NAPD/NAPA1-35, MIXED BETA-ALPHA SANDWICH STRUCTURE, PROTEIN-PEPTIDE KEYWDS 2 COMPLEX, ALPHA-HELIX, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS KEYWDS 4 INITIATIVE, BSGI, CHAPERONE-OXIDOREDUCTASE COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.M.MINAILIUC,I.EKIEL,M.MILAD,MONTREAL-KINGSTON BACTERIAL STRUCTURAL AUTHOR 2 GENOMICS INITIATIVE (BSGI) REVDAT 3 16-MAR-22 2PQ4 1 REMARK SEQADV REVDAT 2 24-FEB-09 2PQ4 1 VERSN REVDAT 1 20-MAY-08 2PQ4 0 JRNL AUTH O.M.MINAILIUC,I.EKIEL,J.CHENG,M.MILAD,S.GANDHI,R.LAROCQUE, JRNL AUTH 2 M.CYGLER,A.MATTE JRNL TITL SOLUTION STRUCTURE OF NAPD, A PRIVATE CHAPERONE OF JRNL TITL 2 PERIPLASMIC NITRATE REDUCTASE NAPA/B, IN COMPLEX WITH JRNL TITL 3 NAPA1-35 SIGNAL PEPTIDE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, X-PLOR-NIH NMR 2.11.2 REMARK 3 AUTHORS : GUNTERT, P. (CYANA), SCHWIETERS, C.D., KUSZEWSKI, REMARK 3 J.J., TJANDRA, N., CLORE, G.M. (X-PLOR-NIH NMR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XPLOR-NIH NMR 2112 REFINE ALGORITHM FOR REMARK 3 STRUCTURE REFINEMENT REMARK 4 REMARK 4 2PQ4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042661. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 312.4 REMARK 210 PH : 5.9 REMARK 210 IONIC STRENGTH : 50MM NAHPO4, 0.150M NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.3 MM NAPD U-15N AND/OR U-13C, REMARK 210 1.6 MM NAPA1-35; 1.0-1.2 MM REMARK 210 NAPA1-35 U-15N AND/OR U-13C, 1.6- REMARK 210 2.0 MM NAPD REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N/13C- REMARK 210 FILTERED/EDITED NOESY; 2D_15N/ REMARK 210 13C-DOUBLE FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA/NEASY 1.5.5, XWINNMR 3.5, REMARK 210 NMRPIPE 2.2 REMARK 210 METHOD USED : CYANA2.1 TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 SER A 2 -166.99 52.58 REMARK 500 1 MET A 4 80.75 -175.71 REMARK 500 1 TRP A 8 -70.93 -104.04 REMARK 500 1 ALA A 42 54.38 -111.71 REMARK 500 1 SER A 44 14.50 -149.43 REMARK 500 1 TYR A 79 114.43 -179.26 REMARK 500 1 GLU A 84 -46.08 178.72 REMARK 500 1 GLU A 87 30.30 -177.61 REMARK 500 1 ARG B 5 -32.05 -177.73 REMARK 500 1 LEU B 23 -162.98 -66.17 REMARK 500 1 ALA B 29 -66.58 -129.65 REMARK 500 1 ARG B 30 94.62 -44.08 REMARK 500 2 MET A 4 84.59 -175.00 REMARK 500 2 THR A 6 118.44 -163.51 REMARK 500 2 TRP A 8 -69.73 -102.83 REMARK 500 2 ALA A 42 54.30 -111.99 REMARK 500 2 SER A 44 13.90 -148.28 REMARK 500 2 TYR A 79 109.82 -179.86 REMARK 500 2 GLU A 84 -38.76 -172.63 REMARK 500 2 GLN A 85 95.10 57.95 REMARK 500 2 SER B 4 -72.08 -152.26 REMARK 500 2 ARG B 5 -31.30 179.89 REMARK 500 2 LEU B 23 -162.75 -67.62 REMARK 500 2 PRO B 26 -89.81 -72.51 REMARK 500 2 VAL B 32 -32.33 179.50 REMARK 500 2 VAL B 33 106.79 -43.17 REMARK 500 3 SER A 2 -43.93 -157.48 REMARK 500 3 HIS A 3 -164.35 -175.98 REMARK 500 3 MET A 4 98.87 -177.93 REMARK 500 3 THR A 6 119.14 -166.77 REMARK 500 3 ALA A 42 54.25 -111.82 REMARK 500 3 SER A 44 14.91 -149.46 REMARK 500 3 TYR A 79 117.83 -179.31 REMARK 500 3 GLU A 84 -75.35 -175.18 REMARK 500 3 GLN A 85 84.25 -177.93 REMARK 500 3 GLU A 87 -39.24 -148.32 REMARK 500 3 LEU B 3 58.23 -69.65 REMARK 500 3 ARG B 5 -39.88 -158.79 REMARK 500 3 LEU B 23 -162.72 -67.08 REMARK 500 3 PRO B 26 -89.95 -72.05 REMARK 500 3 VAL B 28 -75.85 -77.14 REMARK 500 3 ALA B 29 28.77 -176.87 REMARK 500 3 ALA B 31 18.91 53.56 REMARK 500 4 HIS A 3 147.16 59.61 REMARK 500 4 MET A 4 92.67 -178.40 REMARK 500 4 THR A 6 116.30 -166.74 REMARK 500 4 TRP A 8 -71.86 -111.81 REMARK 500 4 ALA A 42 54.37 -111.86 REMARK 500 4 SER A 44 15.35 -150.62 REMARK 500 4 TYR A 79 107.89 -178.20 REMARK 500 REMARK 500 THIS ENTRY HAS 301 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 1 ARG A 21 0.18 SIDE CHAIN REMARK 500 1 ARG A 67 0.18 SIDE CHAIN REMARK 500 1 ARG B 5 0.32 SIDE CHAIN REMARK 500 1 ARG B 6 0.12 SIDE CHAIN REMARK 500 1 ARG B 30 0.22 SIDE CHAIN REMARK 500 2 ARG A 21 0.18 SIDE CHAIN REMARK 500 2 ARG A 67 0.31 SIDE CHAIN REMARK 500 2 ARG B 5 0.32 SIDE CHAIN REMARK 500 2 ARG B 6 0.31 SIDE CHAIN REMARK 500 2 ARG B 30 0.23 SIDE CHAIN REMARK 500 3 ARG A 21 0.18 SIDE CHAIN REMARK 500 3 ARG A 67 0.22 SIDE CHAIN REMARK 500 3 ARG B 5 0.16 SIDE CHAIN REMARK 500 3 ARG B 6 0.21 SIDE CHAIN REMARK 500 3 ARG B 30 0.31 SIDE CHAIN REMARK 500 4 ARG A 21 0.18 SIDE CHAIN REMARK 500 4 ARG A 67 0.18 SIDE CHAIN REMARK 500 4 ARG B 5 0.31 SIDE CHAIN REMARK 500 4 ARG B 6 0.20 SIDE CHAIN REMARK 500 4 ARG B 30 0.25 SIDE CHAIN REMARK 500 5 ARG A 21 0.20 SIDE CHAIN REMARK 500 5 ARG A 67 0.14 SIDE CHAIN REMARK 500 5 ARG B 5 0.23 SIDE CHAIN REMARK 500 5 ARG B 6 0.27 SIDE CHAIN REMARK 500 5 ARG B 30 0.32 SIDE CHAIN REMARK 500 6 ARG A 21 0.18 SIDE CHAIN REMARK 500 6 ARG A 67 0.27 SIDE CHAIN REMARK 500 6 ARG B 5 0.32 SIDE CHAIN REMARK 500 6 ARG B 6 0.09 SIDE CHAIN REMARK 500 6 ARG B 30 0.22 SIDE CHAIN REMARK 500 7 ARG A 21 0.14 SIDE CHAIN REMARK 500 7 ARG A 67 0.27 SIDE CHAIN REMARK 500 7 ARG B 5 0.15 SIDE CHAIN REMARK 500 7 ARG B 6 0.12 SIDE CHAIN REMARK 500 7 ARG B 30 0.21 SIDE CHAIN REMARK 500 8 ARG A 21 0.18 SIDE CHAIN REMARK 500 8 ARG A 67 0.27 SIDE CHAIN REMARK 500 8 ARG B 5 0.32 SIDE CHAIN REMARK 500 8 ARG B 6 0.12 SIDE CHAIN REMARK 500 8 ARG B 30 0.24 SIDE CHAIN REMARK 500 9 ARG A 21 0.28 SIDE CHAIN REMARK 500 9 ARG A 67 0.23 SIDE CHAIN REMARK 500 9 ARG B 5 0.10 SIDE CHAIN REMARK 500 9 ARG B 6 0.32 SIDE CHAIN REMARK 500 9 ARG B 30 0.31 SIDE CHAIN REMARK 500 10 ARG A 21 0.18 SIDE CHAIN REMARK 500 10 ARG A 67 0.32 SIDE CHAIN REMARK 500 10 ARG B 5 0.10 SIDE CHAIN REMARK 500 10 ARG B 6 0.10 SIDE CHAIN REMARK 500 10 ARG B 30 0.23 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 99 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NAPD_ECOLI RELATED DB: TARGETDB REMARK 900 RELATED ID: 2F79 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF NAPD DBREF 2PQ4 A 4 90 UNP P0A9I5 NAPD_ECOLI 1 87 DBREF 2PQ4 B 1 35 UNP P33937 NAPA_ECOLI 1 35 SEQADV 2PQ4 GLY A 1 UNP P0A9I5 EXPRESSION TAG SEQADV 2PQ4 SER A 2 UNP P0A9I5 EXPRESSION TAG SEQADV 2PQ4 HIS A 3 UNP P0A9I5 EXPRESSION TAG SEQRES 1 A 90 GLY SER HIS MET HIS THR ASN TRP GLN VAL CYS SER LEU SEQRES 2 A 90 VAL VAL GLN ALA LYS SER GLU ARG ILE SER ASP ILE SER SEQRES 3 A 90 THR GLN LEU ASN ALA PHE PRO GLY CYS GLU VAL ALA VAL SEQRES 4 A 90 SER ASP ALA PRO SER GLY GLN LEU ILE VAL VAL VAL GLU SEQRES 5 A 90 ALA GLU ASP SER GLU THR LEU ILE GLN THR ILE GLU SER SEQRES 6 A 90 VAL ARG ASN VAL GLU GLY VAL LEU ALA VAL SER LEU VAL SEQRES 7 A 90 TYR HIS GLN GLN GLU GLU GLN GLY GLU GLU THR PRO SEQRES 1 B 35 MET LYS LEU SER ARG ARG SER PHE MET LYS ALA ASN ALA SEQRES 2 B 35 VAL ALA ALA ALA ALA ALA ALA ALA GLY LEU SER VAL PRO SEQRES 3 B 35 GLY VAL ALA ARG ALA VAL VAL GLY GLN HELIX 1 1 LYS A 18 PHE A 32 1 15 HELIX 2 2 ASP A 55 VAL A 69 1 15 HELIX 3 3 ARG B 5 GLY B 22 1 18 SHEET 1 A 4 GLU A 36 VAL A 39 0 SHEET 2 A 4 GLN A 46 GLU A 52 -1 O VAL A 50 N GLU A 36 SHEET 3 A 4 VAL A 10 ALA A 17 -1 N LEU A 13 O VAL A 49 SHEET 4 A 4 VAL A 72 SER A 76 -1 O SER A 76 N VAL A 14 SHEET 1 B 4 GLU A 36 VAL A 39 0 SHEET 2 B 4 GLN A 46 GLU A 52 -1 O VAL A 50 N GLU A 36 SHEET 3 B 4 VAL A 10 ALA A 17 -1 N LEU A 13 O VAL A 49 SHEET 4 B 4 HIS A 80 GLN A 81 -1 O GLN A 81 N VAL A 10 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