4Z5Q

Crystal structure of the LnmZ cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140 at 1.8 A resolution

PDB DOI: https://doi.org/10.2210/pdb4Z5Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces atroolivaceus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-04-02 Released: 2015-08-12
Deposition Author(s): Ma, M., Lohman, J., Rudolf, J., Miller, M.D., Cao, H., Osipiuk, J., Joachimiak, A., Phillips Jr., G.N., Shen, B., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.159 (Depositor), 0.170 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the LnmZ cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140

Ma, M., Lohman, J., Rudolf, J., Miller, M.D., Cao, H., Osipiuk, J., Joachimiak, A., Phillips Jr., G.N., Shen, B.

To be published.

Macromolecule Content

Total Structure Weight: 48.51 kDa
Atom Count: 3,226
Modelled Residue Count: 364
Deposited Residue Count: 423
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 hydroxylase	A	423	Streptomyces atroolivaceus	Mutation(s): 0 Gene Names: LnmZ
UniProt
Find proteins for Q8GGM6 (Streptomyces atroolivaceus) Explore Q8GGM6 Go to UniProtKB: Q8GGM6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GGM6
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.159 (Depositor), 0.170 (DCC)
R-Value Observed: 0.161 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34z5q

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.307	α = 90
b = 83.434	β = 97.67
c = 48.192	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA106150

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Refinement description
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary