PDB-8paj: Crystal Structure of a Squalene-Hopene cyclase from Archangium gephyra

ID or keywords:

Entry

Database: PDB / ID: 8paj

Title

Crystal Structure of a Squalene-Hopene cyclase from Archangium gephyra

Components

Squalene-hopene/tetraprenyl-beta-curcumene cyclase

Keywords

UNKNOWN FUNCTION / Squalene / Hopene / Cyclase

Function / homology

IMIDAZOLE / :

Function and homology information

Biological species

Archangium gephyra (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.46 Å

Authors

Worthy, H.L. / Isupov, M.N. / Littlechild, J.A. / Mitchell, D.E.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Structure of a mesophilic Squalene-Hopene Cyclases from Cystobacter fuscus and Archangium gephyra
Authors: Worthy, H.L. / Mitchell, D.E. / Isupov, M.N. / Littlechild, J.A.

History

Deposition	Jun 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 26, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8paj.cif.gz	736.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8paj.ent.gz	469.3 KB	Display	PDB format
PDBx/mmJSON format	8paj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8paj_validation.pdf.gz	475.4 KB	Display	wwPDB validaton report
Full document	8paj_full_validation.pdf.gz	487 KB	Display
Data in XML	8paj_validation.xml.gz	35.5 KB	Display
Data in CIF	8paj_validation.cif.gz	55 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pa/8paj ftp://data.pdbj.org/pub/pdb/validation_reports/pa/8paj	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Squalene-hopene/tetraprenyl-beta-curcumene cyclase

B: Squalene-hopene/tetraprenyl-beta-curcumene cyclase

hetero molecules

80.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Squalene-hopene/tetraprenyl-beta-curcumene cyclase

hetero molecules

defined by author
Evidence: gel filtration
40.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Squalene-hopene/tetraprenyl-beta-curcumene cyclase

hetero molecules

defined by author
40.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.958, 84.165, 87.968
Angle α, β, γ (deg.)	90.000, 94.204, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-809- HOH
2	1	B-766- HOH
3	1	B-826- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 30 - 374 / Label seq-ID: 11 - 355

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AB

#1: Protein	Squalene-hopene/tetraprenyl-beta-curcumene cyclase Mass: 39825.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archangium gephyra (bacteria) / Gene: ATI61_11568 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0G2ZXK3

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Non-polymers , 5 types, 787 molecules

#2: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₅N₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.11 %
Crystal grow	Temperature: 292 K / Method: microbatch Details: 0.1 M HEPES/MOPS [pH 7.5], 90 mM NaNO3, 90 mM Na2PO4, 90 mM (NH4)2SO4, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD PH range: 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 23, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976284 Å / Relative weight: 1
Reflection	Resolution: 1.46→43.87 Å / Num. obs: 117598 / % possible obs: 100 % / Redundancy: 6.2 % / CC_1/2: 0.997 / R_rim(I) all: 0.103 / Net I/σ(I): 9.2
Reflection shell	Resolution: 1.46→1.48 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5755 / CC_1/2: 0.694 / R_rim(I) all: 1.327 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.46→43.866 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.967 / SU B: 4.222 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1988	5924	5.063 %
R_work	0.1591	111090	-
all	0.161	-	-
obs	-	117014	99.985 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.52 Å²	-0 Å²	-0.29 Å²
2-	-	0.321 Å²	0 Å²
3-	-	-	0.239 Å²

Refinement step

Cycle: LAST / Resolution: 1.46→43.866 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5298	0	76	772	6146

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	5992
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.016	5543
X-RAY DIFFRACTION	r_angle_refined_deg	1.539	1.655	8241
X-RAY DIFFRACTION	r_angle_other_deg	0.835	1.573	12721
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.819	5	798
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.48	5	86
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.983	10	879
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.063	10	292
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	853
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	7504
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1636
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	1246
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.144	0.2	4925
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	2812
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.064	0.2	2995
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	553
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.138	0.2	46
X-RAY DIFFRACTION	r_nbd_other	0.125	0.2	159
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.108	0.2	64
X-RAY DIFFRACTION	r_mcbond_it	1.138	1.394	2878
X-RAY DIFFRACTION	r_mcbond_other	1.138	1.394	2878
X-RAY DIFFRACTION	r_mcangle_it	1.62	2.512	3628
X-RAY DIFFRACTION	r_mcangle_other	1.62	2.513	3629
X-RAY DIFFRACTION	r_scbond_it	1.19	1.632	3114
X-RAY DIFFRACTION	r_scbond_other	1.19	1.633	3115
X-RAY DIFFRACTION	r_scangle_it	1.626	2.888	4557
X-RAY DIFFRACTION	r_scangle_other	1.626	2.889	4558
X-RAY DIFFRACTION	r_lrange_it	2.895	1007.304	27497
X-RAY DIFFRACTION	r_lrange_other	2.366	1042.484	26525
X-RAY DIFFRACTION	r_rigid_bond_restr	3.629	3	11535
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.08	0.05	12162

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08049	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08049	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.46-1.498	0.345	435	0.341	8176	0.342	8611	0.92	0.918	100	0.353
1.498-1.539	0.317	470	0.316	7948	0.316	8418	0.931	0.929	100	0.327
1.539-1.583	0.311	439	0.292	7704	0.293	8143	0.935	0.942	100	0.303
1.583-1.632	0.283	400	0.271	7518	0.272	7919	0.947	0.95	99.9874	0.278
1.632-1.686	0.269	396	0.227	7330	0.229	7726	0.953	0.967	100	0.229
1.686-1.745	0.249	365	0.206	7076	0.208	7444	0.959	0.973	99.9597	0.205
1.745-1.81	0.226	359	0.176	6805	0.178	7164	0.97	0.981	100	0.168
1.81-1.884	0.192	317	0.152	6582	0.154	6899	0.976	0.986	100	0.14
1.884-1.968	0.192	344	0.155	6316	0.158	6660	0.977	0.985	100	0.139
1.968-2.064	0.199	326	0.144	6047	0.147	6373	0.975	0.988	100	0.126
2.064-2.175	0.184	304	0.133	5708	0.136	6017	0.98	0.99	99.9169	0.114
2.175-2.307	0.195	272	0.129	5440	0.132	5713	0.977	0.99	99.9825	0.11
2.307-2.465	0.175	273	0.127	5112	0.13	5385	0.982	0.99	100	0.108
2.465-2.662	0.187	249	0.124	4757	0.127	5006	0.979	0.991	100	0.106
2.662-2.915	0.171	259	0.124	4362	0.127	4622	0.983	0.991	99.9784	0.108
2.915-3.257	0.194	200	0.138	3998	0.141	4198	0.976	0.988	100	0.126
3.257-3.758	0.168	180	0.14	3502	0.142	3682	0.982	0.989	100	0.135
3.758-4.594	0.159	176	0.123	2974	0.125	3151	0.987	0.991	99.9683	0.127
4.594-6.462	0.172	90	0.149	2358	0.15	2448	0.984	0.988	100	0.154
6.462-43.866	0.18	67	0.18	1341	0.18	1409	0.982	0.98	99.929	0.2

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4654	-0.147	-0.1623	1.5736	0.0495	1.2246	-0.0099	-0.0234	-0.0357	0.0303	0.0286	-0.0172	0.0272	0.0632	-0.0187	0.0153	-0.0025	0.0093	0.0085	-0.0004	0.0215	15.0457	-21.1193	39.8917
2	0.5575	-0.0783	0.0346	1.6451	-0.0785	1.1515	0.0048	0.0195	-0.0026	-0.032	0.003	-0.0173	0.0063	-0.0247	-0.0078	0.0231	-0.0017	0.0177	0.0014	-0.0008	0.0214	21.9346	-11.4421	83.506

Refinement TLS group

Selection: ALL

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