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(-) Description

Title :  STRUCTURE OF XOO1075, A PEPTIDE DEFORMYLASE FROM XANTHOMONAS ORYZAE PV ORYZAE, IN COMPLEX WITH FRAGMENT 134
 
Authors :  H. P. T. Ngo, L. W. Kang
Date :  28 Jul 15  (Deposition) - 03 Aug 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Peptide Deformylase, Xanthomonas, Fragment, Metallopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. T. Ngo, L. W. Kang
Structure Of Xoo1075, A Peptide Deformylase From Xanthomona Oryzae Pv Oryzae, In Complex With Fragment 134
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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
156K1Ligand/Ion3-(2-METHYL-1,3-THIAZOL-4-YL)ANILINE
2ACT1Ligand/IonACETATE ION
3CD3Ligand/IonCADMIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
156K2Ligand/Ion3-(2-METHYL-1,3-THIAZOL-4-YL)ANILINE
2ACT2Ligand/IonACETATE ION
3CD-1Ligand/IonCADMIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:99 , HIS A:141 , GLU A:142 , HIS A:145 , HOH A:348binding site for residue CD A 201
2AC2SOFTWAREHIS A:43 , GLU A:128 , GLU A:130binding site for residue CD A 202
3AC3SOFTWAREGLU A:37 , GLU A:132 , HOH A:369binding site for residue CD A 203
4AC4SOFTWARELEU A:14 , ARG A:149 , LEU A:150 , SER A:153 , ASP A:159 , HOH A:306 , HOH A:349binding site for residue ACT A 204
5AC5SOFTWARETRP A:96 , GLU A:97 , GLY A:98 , PHE A:134 , HIS A:141 , GLU A:142binding site for residue 56K A 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5CWX)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               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
                 5cwx A   1 MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSYD 170
                                    10        20        30        40        50        60  ||    79        89        99       109       119       129       139       149       159       169 
                                                                                         63|                                                                                                 
                                                                                          73
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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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 5cwy 5cx0 5cxj 5cy7 5cy8 5e5d

(-) Related Entries Specified in the PDB File

5cp0 5cpd 5cvk 5cvp 5cvq 5cwy 5cx0 5cxj 5cy7 5cy8