3DWR | pdb_00003dwr

Leishmania major coproporphyrinogen III oxidase with bound ligand

PDB DOI: https://doi.org/10.2210/pdb3DWR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania major
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-22 Released: 2008-09-09
Deposition Author(s): Le Trong, I., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.186 (Depositor), 0.195 (DCC)
R-Value Work:
0.163 (Depositor), 0.176 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Leishmania major coproporphyrinogen III oxidase with bound ligand

Merritt, E.A., Le Trong, I., Larson, E.T., Shibata, S., Zhang, Z., Anderson, L., Ross, J., Verlinde, C.L.M.J., Buckner, F.S., Van Voorhis, W.C., Hol, G.J.W., Fan, E.

To be published.

Macromolecule Content

Total Structure Weight: 71.95 kDa
Atom Count: 5,051
Modeled Residue Count: 561
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproporphyrinogen III oxidase	A, B	309	Leishmania major	Mutation(s): 0 Gene Names: LMAJ006828, LmjF06.1270 EC: 1.3.3.3
UniProt
Find proteins for P84155 (Leishmania major) Explore P84155 Go to UniProtKB: P84155
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84155
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0PA Query on 0PA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B]	cyclopentylacetic acid C₇ H₁₂ O₂ YVHAIVPPUIZFBA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.186 (Depositor), 0.195 (DCC)
R-Value Work: 0.163 (Depositor), 0.176 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.487	α = 90
b = 48.06	β = 90.06
c = 84.442	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Le Trong, I.

Merritt, E.A.

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description