3DCP | pdb_00003dcp

Crystal structure of the putative histidinol phosphatase hisK from Listeria monocytogenes. Northeast Structural Genomics Consortium target LmR141.

PDB DOI: https://doi.org/10.2210/pdb3DCP/pdb

Classification: HYDROLASE
Organism(s): Listeria monocytogenes serotype 4b str. H7858
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-04 Released: 2008-07-29
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Zhao, L., Mao, L., Foote, E.L., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.212 (Depositor), 0.226 (DCC)
R-Value Work:
0.193 (Depositor), 0.208 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6NLR

Literature

Crystal structure of the putative histidinol phosphatase hisK from Listeria monocytogenes.

Vorobiev, S.M., Su, M., Seetharaman, J., Zhao, L., Mao, L., Foote, E.L., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 99.07 kDa
Atom Count: 7,277
Modeled Residue Count: 821
Deposited Residue Count: 849
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidinol-phosphatase	A, B, C	283	Listeria monocytogenes serotype 4b str. H7858	Mutation(s): 0 Gene Names: hisK, LMOh7858_0629 EC: 3.1.3.15

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	D [auth A], G [auth B], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.212 (Depositor), 0.226 (DCC)
R-Value Work: 0.193 (Depositor), 0.208 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.278	α = 90
b = 191.278	β = 90
c = 48.051	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary