10 20 30 40 50 60 70 80 2KMN - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/ANTIBIOTIC 01-AUG-09 2KMN
TITLE SOLUTION STRUCTURE OF PEPTIDE DEFORMYLASE COMPLEXED WITH TITLE 2 ACTINONIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDF, POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: DEF, FMS, B3287, JW3248; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22
KEYWDS PEPTIDE DEFORMYLASE, NMR, ACTINONIN, HYDROLASE, IRON, METAL- KEYWDS 2 BINDING, PROTEIN BIOSYNTHESIS, HYDROLASE/ANTIBIOTIC COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR C.A.MCELROY,C.D.AMERO,D.W.BYERLY,M.P.FOSTER
REVDAT 1 25-AUG-09 2KMN 0
JRNL AUTH C.A.MCELROY,C.D.AMERO,D.W.BYERLY,M.P.FOSTER JRNL TITL SOLUTION STRUCTURE OF PEPTIDE DEFORMYLASE COMPLEXED JRNL TITL 2 WITH ACTINONIN JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.D.AMERO,D.W.BYERLY,C.A.MCELROY,A.SIMMONS, REMARK 1 AUTH 2 M.P.FOSTER REMARK 1 TITL LIGAND-INDUCED CHANGES IN THE STRUCTURE AND REMARK 1 TITL 2 DYNAMICS OF ESCHERICHIA COLI PEPTIDE DEFORMYLASE. REMARK 1 REF BIOCHEMISTRY V. 48 7595 2009 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 19627112 REMARK 1 DOI 10.1021/BI900600B
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KMN COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-09. REMARK 100 THE RCSB ID CODE IS RCSB101309.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6-1.0 MM [U-100% 13C; U- REMARK 210 100% 15N] PROTEIN-1, 1.2 MM REMARK 210 ACTINONIN-2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 1H-15N TOCSY; 3D 1H-15N NOESY; REMARK 210 3D HNHA; 3D HNHB; 3D C(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, CNS 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: 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 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 3 -147.47 -80.46 REMARK 500 1 ALA A 48 -57.24 -26.82 REMARK 500 1 ASP A 52 25.51 80.13 REMARK 500 1 ARG A 56 75.63 -64.67 REMARK 500 1 ASP A 61 31.86 -145.12 REMARK 500 1 SER A 63 65.75 -55.80 REMARK 500 1 ASN A 65 -139.47 -163.28 REMARK 500 1 ARG A 69 63.77 -179.94 REMARK 500 1 PRO A 94 49.25 -72.40 REMARK 500 2 LEU A 3 -143.43 -79.10 REMARK 500 2 PRO A 9 52.48 -92.68 REMARK 500 2 ARG A 56 69.03 -63.01 REMARK 500 2 SER A 63 81.19 -37.56 REMARK 500 2 ASN A 65 -141.87 -165.99 REMARK 500 2 ARG A 66 38.48 -83.57 REMARK 500 2 GLU A 68 61.78 -111.27 REMARK 500 3 LEU A 3 -148.76 -83.10 REMARK 500 3 PRO A 9 52.13 -93.17 REMARK 500 3 ARG A 56 68.65 -63.13 REMARK 500 3 ASN A 65 -66.16 -161.99 REMARK 500 3 ARG A 66 -36.75 -130.99 REMARK 500 3 ARG A 69 69.20 173.65 REMARK 500 3 PRO A 94 -148.42 -63.05 REMARK 500 4 ASP A 52 30.04 75.36 REMARK 500 4 ARG A 56 70.74 -64.26 REMARK 500 4 SER A 63 80.50 -38.05 REMARK 500 4 ASN A 65 -132.99 -164.64 REMARK 500 4 ARG A 69 76.08 170.67 REMARK 500 4 PRO A 94 49.75 -76.46 REMARK 500 5 PRO A 9 50.20 -91.86 REMARK 500 5 ASP A 52 31.52 79.35 REMARK 500 5 ARG A 56 69.06 -62.74 REMARK 500 5 ASN A 65 -131.80 -165.88 REMARK 500 5 ARG A 69 65.73 -176.62 REMARK 500 5 PRO A 94 48.43 -75.20 REMARK 500 5 GLU A 95 9.27 82.88 REMARK 500 6 LEU A 3 -159.30 -79.01 REMARK 500 6 ALA A 48 -54.59 -29.85 REMARK 500 6 ARG A 56 68.62 -64.11 REMARK 500 6 ASP A 61 28.56 -142.58 REMARK 500 6 SER A 63 84.59 -37.05 REMARK 500 6 ASN A 65 -85.76 -164.10 REMARK 500 6 ARG A 69 70.53 171.22 REMARK 500 6 PRO A 94 -144.43 -61.75 REMARK 500 7 LEU A 3 -158.69 -79.68 REMARK 500 7 ALA A 48 -56.16 -29.31 REMARK 500 7 ASP A 52 35.27 77.13 REMARK 500 7 ARG A 56 74.55 -62.81 REMARK 500 7 SER A 63 76.38 -39.95 REMARK 500 7 ASN A 65 -136.14 -164.41 REMARK 500 7 ARG A 69 76.28 172.48 REMARK 500 7 PRO A 94 47.67 -78.24 REMARK 500 7 GLU A 95 4.66 80.22 REMARK 500 8 PRO A 9 51.19 -92.35 REMARK 500 8 ALA A 48 -57.99 -28.51 REMARK 500 8 ARG A 56 72.52 -61.79 REMARK 500 8 SER A 63 81.51 -42.42 REMARK 500 8 ARG A 66 -91.13 -161.34 REMARK 500 8 GLU A 68 101.38 71.78 REMARK 500 8 ARG A 69 64.11 175.20 REMARK 500 8 PRO A 94 47.08 -75.68 REMARK 500 9 ALA A 48 -56.82 -27.21 REMARK 500 9 ASP A 52 33.06 77.51 REMARK 500 9 ARG A 56 72.46 -64.37 REMARK 500 9 SER A 63 89.77 -34.10 REMARK 500 9 ASN A 65 -85.19 -168.16 REMARK 500 9 ARG A 69 71.79 175.39 REMARK 500 9 PRO A 94 48.93 -73.32 REMARK 500 10 LEU A 3 -141.25 -79.09 REMARK 500 10 PRO A 9 51.68 -92.14 REMARK 500 10 ARG A 56 68.10 -61.78 REMARK 500 10 ASP A 61 37.78 -141.82 REMARK 500 10 SER A 63 86.87 -34.08 REMARK 500 10 ASN A 65 -74.58 -164.75 REMARK 500 10 ARG A 69 66.76 173.89 REMARK 500 10 PRO A 94 -146.54 -62.63 REMARK 500 11 ALA A 48 -55.74 -27.06 REMARK 500 11 ASP A 52 34.05 77.43 REMARK 500 11 ARG A 56 72.38 -65.13 REMARK 500 11 SER A 63 85.58 -34.42 REMARK 500 11 ASN A 65 -79.04 -165.17 REMARK 500 11 ARG A 69 68.61 175.02 REMARK 500 11 PRO A 94 48.48 -73.10 REMARK 500 12 ASN A 24 -168.66 -105.76 REMARK 500 12 ASP A 52 32.37 78.96 REMARK 500 12 ARG A 56 70.82 -63.34 REMARK 500 12 SER A 63 83.28 -38.02 REMARK 500 12 ASN A 65 -127.97 -163.87 REMARK 500 13 PRO A 9 55.48 -98.18 REMARK 500 13 ASP A 52 32.40 77.75 REMARK 500 13 ARG A 56 70.69 -62.84 REMARK 500 13 SER A 63 89.32 -35.29 REMARK 500 13 ASN A 65 -76.51 -165.60 REMARK 500 13 ARG A 69 68.83 178.23 REMARK 500 13 PRO A 94 47.73 -75.36 REMARK 500 14 ALA A 48 -56.15 -29.70 REMARK 500 14 ASP A 52 32.89 76.53 REMARK 500 14 ARG A 56 72.40 -65.37 REMARK 500 14 ASP A 61 34.12 -146.11 REMARK 500 14 SER A 63 77.71 -38.26 REMARK 500 14 ASN A 65 -84.99 -165.51 REMARK 500 14 ARG A 69 62.10 -174.92 REMARK 500 14 PRO A 94 47.70 -75.51 REMARK 500 15 ALA A 48 -56.76 -28.73 REMARK 500 15 HIS A 54 49.18 -75.84 REMARK 500 15 ARG A 56 75.14 -62.46 REMARK 500 15 ASP A 61 27.60 -140.16 REMARK 500 15 SER A 63 85.40 -35.95 REMARK 500 15 ASN A 65 -67.10 -133.84 REMARK 500 15 ARG A 66 -42.86 -133.27 REMARK 500 15 ARG A 69 66.76 177.17 REMARK 500 15 PRO A 94 44.84 -71.96 REMARK 500 16 PRO A 9 54.12 -93.49 REMARK 500 16 ASP A 52 31.45 79.11 REMARK 500 16 ARG A 56 69.04 -64.66 REMARK 500 16 SER A 63 78.84 -36.33 REMARK 500 16 ASN A 65 -126.30 -167.25 REMARK 500 16 ARG A 69 71.84 177.12 REMARK 500 16 PRO A 94 48.09 -74.87 REMARK 500 17 LEU A 3 -169.51 -79.87 REMARK 500 17 PRO A 9 52.38 -93.22 REMARK 500 17 ARG A 56 70.99 -65.02 REMARK 500 17 ASP A 61 39.84 -145.29 REMARK 500 17 SER A 63 74.70 -55.35 REMARK 500 17 ASN A 65 -72.86 -122.01 REMARK 500 17 ASP A 67 116.62 -161.25 REMARK 500 17 LEU A 91 -17.31 -48.62 REMARK 500 17 PRO A 94 -145.98 -62.11 REMARK 500 18 LEU A 3 -161.81 -79.53 REMARK 500 18 ARG A 56 66.72 -64.50 REMARK 500 18 SER A 63 78.25 -38.88 REMARK 500 18 ASN A 65 -138.23 -163.30 REMARK 500 18 PRO A 94 49.16 -70.98 REMARK 500 19 PRO A 9 51.84 -93.49 REMARK 500 19 ALA A 48 -56.50 -26.90 REMARK 500 19 ARG A 56 68.34 -59.83 REMARK 500 19 VAL A 62 -161.33 -79.46 REMARK 500 19 ASN A 65 -119.22 -165.84 REMARK 500 20 LEU A 3 -165.97 -79.74 REMARK 500 20 ALA A 48 -54.43 -28.61 REMARK 500 20 ASP A 52 30.07 77.46 REMARK 500 20 ARG A 56 69.30 -64.00 REMARK 500 20 SER A 63 81.59 -38.35 REMARK 500 20 ASN A 65 -139.98 -165.12 REMARK 500 20 ARG A 69 72.03 173.29 REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 148 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 HIS A 132 NE2 93.9 REMARK 620 3 HIS A 136 NE2 86.8 123.9 REMARK 620 4 BB2 A 149 O4 95.6 116.0 119.8 REMARK 620 5 BB2 A 149 N1 139.4 75.8 131.8 57.3 REMARK 620 6 BB2 A 149 O2 164.1 96.5 97.2 69.0 34.6 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 148 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 A 149
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5404 RELATED DB: BMRB REMARK 900 BACKBONE AND SIDE CHAIN ASSIGNMENTS OF PEPTIDE DEFORMYLASE REMARK 900 COMPLEXED WITH ACTINONIN
DBREF 2KMN A 1 147 UNP P0A6K3 DEF_ECOLI 2 148
SEQRES 1 A 147 SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG LEU SEQRES 2 A 147 ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA GLU SEQRES 3 A 147 ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET TYR SEQRES 4 A 147 ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL ASP SEQRES 5 A 147 ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU ASN SEQRES 6 A 147 ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU LEU SEQRES 7 A 147 GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS LEU SEQRES 8 A 147 SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA GLU SEQRES 9 A 147 LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS PRO SEQRES 10 A 147 PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS ILE SEQRES 11 A 147 GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE MET SEQRES 12 A 147 ASP TYR LEU SER
HET ZN A 148 1 HET BB2 A 149 62
HETNAM ZN ZINC ION HETNAM BB2 ACTINONIN
HETSYN BB2 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2- HETSYN 2 BB2 HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL- HETSYN 3 BB2 PROPYL]-AMIDE
FORMUL 2 ZN ZN 2+ FORMUL 3 BB2 C19 H35 N3 O5
HELIX 1 1 ASN A 24 GLU A 41 1 18 HELIX 2 2 THR A 49 ASP A 52 5 4 HELIX 3 3 GLY A 124 VAL A 138 1 15 HELIX 4 4 LEU A 141 LEU A 146 5 6
SHEET 1 A 5 GLY A 45 ALA A 47 0 SHEET 2 A 5 ILE A 57 ILE A 60 -1 O VAL A 59 N LEU A 46 SHEET 3 A 5 LEU A 70 GLU A 88 -1 O LEU A 70 N ILE A 60 SHEET 4 A 5 ALA A 98 LEU A 111 -1 O ARG A 102 N THR A 84 SHEET 5 A 5 PRO A 117 ASP A 123 -1 O ALA A 122 N VAL A 106
LINK SG CYS A 90 ZN ZN A 148 1555 1555 2.03 LINK NE2 HIS A 132 ZN ZN A 148 1555 1555 2.37 LINK NE2 HIS A 136 ZN ZN A 148 1555 1555 2.38 LINK ZN ZN A 148 O4 BB2 A 149 1555 1555 2.35 LINK ZN ZN A 148 N1 BB2 A 149 1555 1555 2.34 LINK ZN ZN A 148 O2 BB2 A 149 1555 1555 2.34
CISPEP 1 ILE A 8 PRO A 9 1 -0.31 CISPEP 2 ILE A 8 PRO A 9 2 0.14 CISPEP 3 ILE A 8 PRO A 9 3 0.44 CISPEP 4 ILE A 8 PRO A 9 4 -0.38 CISPEP 5 ILE A 8 PRO A 9 5 0.18 CISPEP 6 ILE A 8 PRO A 9 6 -0.15 CISPEP 7 ILE A 8 PRO A 9 7 -0.33 CISPEP 8 ILE A 8 PRO A 9 8 0.09 CISPEP 9 ILE A 8 PRO A 9 9 -0.57 CISPEP 10 ILE A 8 PRO A 9 10 0.17 CISPEP 11 ILE A 8 PRO A 9 11 -0.32 CISPEP 12 ILE A 8 PRO A 9 12 -0.51 CISPEP 13 ILE A 8 PRO A 9 13 0.29 CISPEP 14 ILE A 8 PRO A 9 14 -0.28 CISPEP 15 ILE A 8 PRO A 9 15 -0.42 CISPEP 16 ILE A 8 PRO A 9 16 0.32 CISPEP 17 ILE A 8 PRO A 9 17 0.20 CISPEP 18 ILE A 8 PRO A 9 18 -0.30 CISPEP 19 ILE A 8 PRO A 9 19 0.24 CISPEP 20 ILE A 8 PRO A 9 20 -0.49
SITE 1 AC1 5 GLN A 50 CYS A 90 HIS A 132 HIS A 136 SITE 2 AC1 5 BB2 A 149 SITE 1 AC2 17 GLY A 43 ILE A 44 GLY A 45 GLN A 50 SITE 2 AC2 17 VAL A 59 ILE A 60 GLU A 87 GLU A 88 SITE 3 AC2 17 GLY A 89 CYS A 90 LEU A 91 ARG A 97 SITE 4 AC2 17 CYS A 129 HIS A 132 GLU A 133 HIS A 136 SITE 5 AC2 17 ZN A 148
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