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(-) Description

Title :  STRUCTURE OF XOO1075, A PEPTIDE DEFORMYASE FROM XANTHOMONAS ORYZAE PV. ORYZE, IN COMPLEX WITH FRAGMENT 493
 
Authors :  H. P. T. Ngo, L. W. Kang
Date :  27 Jul 15  (Deposition) - 03 Aug 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Peptide Deformylase, Xanthomonas, Fragment, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. T. Ngo, L. W. Kang
Structure Of Xoo1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, In Complex With Fragment 493
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, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
156E1Ligand/IonETHYL N-[(5-METHYLTHIOPHEN-3-YL)CARBONYL]GLYCINATE
2ACT1Ligand/IonACETATE ION
3CD5Ligand/IonCADMIUM ION
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
156E2Ligand/IonETHYL N-[(5-METHYLTHIOPHEN-3-YL)CARBONYL]GLYCINATE
2ACT2Ligand/IonACETATE ION
3CD-1Ligand/IonCADMIUM ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:99 , HIS A:141 , HIS A:145 , CD A:204binding site for residue CD A 201
2AC2SOFTWAREGLU A:37 , GLU A:132 , HOH A:446binding site for residue CD A 202
3AC3SOFTWAREHIS A:43 , GLU A:128 , GLU A:130 , HOH A:369 , HOH A:429binding site for residue CD A 203
4AC4SOFTWAREGLN A:51 , HIS A:141 , GLU A:142 , HIS A:145 , CD A:201 , HOH A:427binding site for residue CD A 204
5AC5SOFTWAREALA A:42 , HIS A:43 , TYR A:69 , GLY A:98 , CYS A:99 , LEU A:100 , ARG A:137 , HIS A:141 , GLU A:142 , HOH A:302binding site for residue 56E A 205
6AC6SOFTWARELEU A:14 , GLY A:148 , ARG A:149 , LEU A:150 , SER A:153 , ASP A:159 , HOH A:307 , HOH A:392binding site for residue ACT A 206
7AC7SOFTWARELEU A:14 , HOH A:370 , HOH A:388 , HOH A:389 , HOH A:447 , HOH A:469binding site for residue NA A 207
8AC8SOFTWARELEU A:105 , ASP A:164 , HOH A:424 , HOH A:438binding site for residue CD A 208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CVK)

(-) 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
(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:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee.........eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cvk A   1 MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEARYPEAPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSYDL 171
                                    10        20        30        40        50        60    ||  72        82        92       102       112       122       132       142       152       162         
                                                                                           65|                                                                                                       
                                                                                            68
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5cvp 5cvq 5cwx 5cwy 5cx0 5cxj 5cy7 5cy8 5e5d

(-) Related Entries Specified in the PDB File

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