5HXT | pdb_00005hxt

Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with IPP and DMSPP

PDB DOI: https://doi.org/10.2210/pdb5HXT/pdb

Classification: TRANSFERASE
Organism(s): Solanum habrochaites
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-01-31 Released: 2017-04-05
Deposition Author(s): Lee, C.C., Chan, Y.T., Wang, A.H.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.249 (Depositor), 0.209 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure and Potential Head-to-Middle Condensation Function of a Z,Z-Farnesyl Diphosphate Synthase

Chan, Y.T., Ko, T.P., Yao, S.H., Chen, Y.W., Lee, C.C., Wang, A.H.J.

(2017) ACS Omega 2: 930-936

DOI: https://doi.org/10.1021/acsomega.6b00562

Macromolecule Content

Total Structure Weight: 54.9 kDa
Atom Count: 4,002
Modeled Residue Count: 447
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic	A, B	233	Solanum habrochaites	Mutation(s): 2 Gene Names: ZFPS EC: 2.5.1.92
UniProt
Find proteins for B8XA40 (Solanum habrochaites) Explore B8XA40 Go to UniProtKB: B8XA40
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8XA40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O4B Query on O4B Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DST Query on DST Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C₅ H₁₂ O₆ P₂ S ZWFWSISPSBLNGO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
IPR Query on IPR Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	ISOPENTYL PYROPHOSPHATE C₅ H₁₄ O₇ P₂ IPFXNYPSBSIFOB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.249 (Depositor), 0.209 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.981	α = 90
b = 66.321	β = 90
c = 128.939	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Lee, C.C.

Chan, Y.T.

Wang, A.H.J.

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 2.0: 2019-10-16
Changes: Data collection, Database references, Non-polymer description, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

5HXT | pdb_00005hxt

Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with IPP and DMSPP

Literature

Crystal Structure and Potential Head-to-Middle Condensation Function of a Z,Z-Farnesyl Diphosphate Synthase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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