4GYF | pdb_00004gyf

Crystal structure of histidinol phosphate phosphatase (HISK) from Lactococcus lactis subsp. lactis Il1403 complexed with ZN, L-histidinol and phosphate

PDB DOI: https://doi.org/10.2210/pdb4GYF/pdb
Entry: 4GYF supersedes: 3UMU

Classification: HYDROLASE
Organism(s): Lactococcus lactis subsp. lactis Il1403
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-09-05 Released: 2013-02-06
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Ghodge, S., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.186 (Depositor), 0.185 (DCC)
R-Value Work:
0.160 (Depositor), 0.162 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of histidinol phosphate phosphatase (HISK) from Lactococcus lactis subsp. lactis Il1403 complexed with ZN, L-histidinol and phosphate

Fedorov, A.A., Fedorov, E.V., Ghodge, S., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 34.43 kDa
Atom Count: 2,471
Modeled Residue Count: 263
Deposited Residue Count: 284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidinol-phosphatase	A	284	Lactococcus lactis subsp. lactis Il1403	Mutation(s): 3 Gene Names: hisK, LL1216, L37351 EC: 3.1.3.15
UniProt
Find proteins for Q02150 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q02150 Go to UniProtKB: Q02150
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02150
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HSO Query on HSO Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	L-histidinol C₆ H₁₂ N₃ O ZQISRDCJNBUVMM-YFKPBYRVSA-O		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	P [auth A], Q [auth A], R [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL 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 J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.186 (Depositor), 0.185 (DCC)
R-Value Work: 0.160 (Depositor), 0.162 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.661	α = 90
b = 86.679	β = 90
c = 45.08	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

This entry supersedes: 3UMU

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2015-06-24
Changes: Non-polymer description
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection