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(-) Description

Title :  STRUCTURE OF XOO1075, A PEPTIDE DEFORMYLASE FROM XANTHOMONAS ORYZE PV ORYZE, IN COMPLEX WITH FRAGMENT 275
 
Authors :  H. P. T. Ngo, L. W. Kang
Date :  30 Jul 15  (Deposition) - 03 Aug 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  A Peptide Deformylase, Xanthomonas, Fragment, Metallopeptidase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. T. Ngo, L. W. Kang
Structure Of Xoo1075, A Peptide Deformylase From Xanthomona Oryze Pv Oryze, In Complex With Fragment 275
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 42-212
    Gene: DEF, XOO1075
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE KACC10331
    Organism Taxid: 291331
    Strain: KACC10331
    Synonym: PDF,POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
156U1Ligand/Ion2-(DIFLUOROMETHYL)-1H-BENZIMIDAZOLE
2ACT1Ligand/IonACETATE ION
3CD3Ligand/IonCADMIUM ION
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
156U2Ligand/Ion2-(DIFLUOROMETHYL)-1H-BENZIMIDAZOLE
2ACT2Ligand/IonACETATE ION
3CD-1Ligand/IonCADMIUM ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:99 , HIS A:141 , HIS A:145 , HOH A:304binding site for residue CD A 201
2AC2SOFTWARELEU A:14 , GLY A:148 , ARG A:149 , LEU A:150 , SER A:153 , ASP A:159 , HOH A:303binding site for residue ACT A 202
3AC3SOFTWAREHIS A:43 , GLU A:128 , GLU A:130 , HOH A:323 , HOH A:394binding site for residue CD A 203
4AC4SOFTWAREGLU A:37 , GLU A:132 , HOH A:325binding site for residue CD A 204
5AC5SOFTWAREVAL A:45 , ARG A:68 , TYR A:69 , GLY A:98 , CYS A:99 , HIS A:141 , GLU A:142 , HOH A:302binding site for residue 56U A 205
6AC6SOFTWARELEU A:14 , HOH A:349 , HOH A:353 , HOH A:385 , HOH A:395 , HOH A:407binding site for residue NA A 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CY7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CY7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CY7)

(-) Exons   (0, 0)

(no "Exon" information available for 5CY7)

(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee...........eeeeeeeeeeeee....eeeeee.......eeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cy7 A   1 MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEASERYPEAPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSYDL 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5CY7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CY7)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5H3Z2_XANOR | Q5H3Z2: 4nt8 5cp0 5cpd 5cvk 5cvp 5cvq 5cwx 5cwy 5cx0 5cxj 5cy8 5e5d

(-) Related Entries Specified in the PDB File

5cp0 5cpd 5cvk 5cvp 5cvq 5cwx 5cwy 5cx0 5cxj 5cy8