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

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Basic information

Entry
Database: PDB / ID: 8paj
TitleCrystal Structure of a Squalene-Hopene cyclase from Archangium gephyra
ComponentsSqualene-hopene/tetraprenyl-beta-curcumene cyclase
KeywordsUNKNOWN FUNCTION / Squalene / Hopene / Cyclase
Function / homologyIMIDAZOLE / :
Function and homology information
Biological speciesArchangium gephyra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsWorthy, H.L. / Isupov, M.N. / Littlechild, J.A. / Mitchell, D.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)104457 United Kingdom
CitationJournal: 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
DepositionJun 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Squalene-hopene/tetraprenyl-beta-curcumene cyclase
B: Squalene-hopene/tetraprenyl-beta-curcumene cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,85117
Polymers79,6512
Non-polymers1,20015
Water13,908772
1
A: Squalene-hopene/tetraprenyl-beta-curcumene cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4579
Polymers39,8261
Non-polymers6318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Squalene-hopene/tetraprenyl-beta-curcumene cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3958
Polymers39,8261
Non-polymers5697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-809-

HOH

21B-766-

HOH

31B-826-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

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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Components

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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 interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976284 Å / Relative weight: 1
ReflectionResolution: 1.46→43.87 Å / Num. obs: 117598 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rrim(I) all: 0.103 / Net I/σ(I): 9.2
Reflection shellResolution: 1.46→1.48 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5755 / CC1/2: 0.694 / Rrim(I) all: 1.327 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→43.866 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflection
Rfree0.1988 5924 5.063 %
Rwork0.1591 111090 -
all0.161 --
obs-117014 99.985 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0.29 Å2
2--0.321 Å20 Å2
3---0.239 Å2
Refinement stepCycle: LAST / Resolution: 1.46→43.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 76 772 6146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125992
X-RAY DIFFRACTIONr_bond_other_d0.0060.0165543
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6558241
X-RAY DIFFRACTIONr_angle_other_deg0.8351.57312721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.48586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98310879
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.06310292
X-RAY DIFFRACTIONr_chiral_restr0.0920.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027504
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021636
X-RAY DIFFRACTIONr_nbd_refined0.2070.21246
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1440.24925
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22812
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0640.22995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2553
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.246
X-RAY DIFFRACTIONr_nbd_other0.1250.2159
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.264
X-RAY DIFFRACTIONr_mcbond_it1.1381.3942878
X-RAY DIFFRACTIONr_mcbond_other1.1381.3942878
X-RAY DIFFRACTIONr_mcangle_it1.622.5123628
X-RAY DIFFRACTIONr_mcangle_other1.622.5133629
X-RAY DIFFRACTIONr_scbond_it1.191.6323114
X-RAY DIFFRACTIONr_scbond_other1.191.6333115
X-RAY DIFFRACTIONr_scangle_it1.6262.8884557
X-RAY DIFFRACTIONr_scangle_other1.6262.8894558
X-RAY DIFFRACTIONr_lrange_it2.8951007.30427497
X-RAY DIFFRACTIONr_lrange_other2.3661042.48426525
X-RAY DIFFRACTIONr_rigid_bond_restr3.629311535
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.0512162
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.080490.05009
12AX-RAY DIFFRACTIONLocal ncs0.080490.05009
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.46-1.4980.3454350.34181760.34286110.920.9181000.353
1.498-1.5390.3174700.31679480.31684180.9310.9291000.327
1.539-1.5830.3114390.29277040.29381430.9350.9421000.303
1.583-1.6320.2834000.27175180.27279190.9470.9599.98740.278
1.632-1.6860.2693960.22773300.22977260.9530.9671000.229
1.686-1.7450.2493650.20670760.20874440.9590.97399.95970.205
1.745-1.810.2263590.17668050.17871640.970.9811000.168
1.81-1.8840.1923170.15265820.15468990.9760.9861000.14
1.884-1.9680.1923440.15563160.15866600.9770.9851000.139
1.968-2.0640.1993260.14460470.14763730.9750.9881000.126
2.064-2.1750.1843040.13357080.13660170.980.9999.91690.114
2.175-2.3070.1952720.12954400.13257130.9770.9999.98250.11
2.307-2.4650.1752730.12751120.1353850.9820.991000.108
2.465-2.6620.1872490.12447570.12750060.9790.9911000.106
2.662-2.9150.1712590.12443620.12746220.9830.99199.97840.108
2.915-3.2570.1942000.13839980.14141980.9760.9881000.126
3.257-3.7580.1681800.1435020.14236820.9820.9891000.135
3.758-4.5940.1591760.12329740.12531510.9870.99199.96830.127
4.594-6.4620.172900.14923580.1524480.9840.9881000.154
6.462-43.8660.18670.1813410.1814090.9820.9899.9290.2
Refinement TLS params.

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

IDL11 (°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)
10.4654-0.147-0.16231.57360.04951.2246-0.0099-0.0234-0.03570.03030.0286-0.01720.02720.0632-0.01870.0153-0.00250.00930.0085-0.00040.021515.0457-21.119339.8917
20.5575-0.07830.03461.6451-0.07851.15150.00480.0195-0.0026-0.0320.003-0.01730.0063-0.0247-0.00780.0231-0.00170.01770.0014-0.00080.021421.9346-11.442183.506
Refinement TLS groupSelection: ALL

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