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- PDB-4hd1: Crystal structure of squalene synthase HpnC from Alicyclobacillus... -

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Basic information

Entry
Database: PDB / ID: 4hd1
TitleCrystal structure of squalene synthase HpnC from Alicyclobacillus acidocaldarius
ComponentsSqualene synthase HpnC
KeywordsTRANSFERASE / MCSG / STRUCTURAL GENOMICS / PSI-BIOLOGY / Midwest Center for Structural Genomics
Function / homology
Function and homology information


15-cis-phytoene synthase / geranylgeranyl-diphosphate geranylgeranyltransferase activity / farnesyl-diphosphate farnesyltransferase activity / squalene synthase activity / biosynthetic process
Similarity search - Function
Hydroxysqualene synthase HpnC / Squalene/phytoene synthase / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Squalene synthase HpnC
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsChang, C. / Bearden, J. / Li, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of squalene synthase HpnC from Alicyclobacillus acidocaldarius
Authors: Chang, C. / Bearden, J. / Li, H. / Joachimiak, A.
History
DepositionOct 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Squalene synthase HpnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3182
Polymers33,2221
Non-polymers961
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.803, 124.803, 95.042
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Squalene synthase HpnC


Mass: 33222.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: ATCC 27009 / DSM 446 / 104-1A / Gene: Aaci_2442 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C8WSG3, 15-cis-phytoene synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium Fluoride, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 17606 / Num. obs: 17122 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 49.5
Reflection shellResolution: 2.4→2.42 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 2.7 / Num. unique all: 427 / % possible all: 14.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
CNSphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→33.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.503 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.223
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 866 5.1 %RANDOM
Rwork0.198 ---
all0.2004 17091 --
obs0.2004 17091 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 280.39 Å2 / Biso mean: 79.1422 Å2 / Biso min: 41.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0.49 Å20 Å2
2---0.99 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 5 43 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192173
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9652938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1355264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.33321.405121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45815359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5941537
X-RAY DIFFRACTIONr_chiral_restr0.0710.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211719
X-RAY DIFFRACTIONr_rigid_bond_restr2.51932172
X-RAY DIFFRACTIONr_sphericity_free21.93525
X-RAY DIFFRACTIONr_sphericity_bonded12.56952150
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 54 -
Rwork0.272 1055 -
all-1109 -
obs-1109 98.23 %
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)
11.6710.76231.37814.68710.04691.2313-0.1139-0.3056-0.0662-0.18390.2278-0.2155-0.0259-0.345-0.1140.4623-0.0285-0.19730.4540.1220.53984.18243.167
215.6579-0.68559.77350.1849-1.137110.09180.11911.94940.6329-0.1948-0.21720.04321.14922.17010.09811.2778-0.1315-0.51550.67390.17510.527738.34374.16254.335
33.0131-2.17431.13492.22750.91795.02770.1756-0.2891-0.0936-0.19660.1418-0.0097-0.0702-0.2493-0.31750.4494-0.0352-0.12570.43370.04620.487345.69282.7751.402
40.36970.85531.49116.76814.79886.9930.1479-0.0354-0.02240.4102-0.29360.41680.2787-0.56610.14570.538-0.0314-0.24930.40970.0010.57640.57568.36540.291
548.93364.438841.002584.209220.916538.4431.09151.80390.6139-5.8893-2.85138.99810.36420.89541.75981.8807-0.275-1.36220.6131-0.10561.511439.08160.42831.053
60.7706-3.44221.56320.3966-2.17837.7790.23060.0991-0.007-1.2331-0.51070.35460.25010.20410.28020.6593-0.0044-0.27940.4461-0.13150.32945.71368.41729.574
70.11540.0359-0.0432.6812-1.54320.90130.07740.13060.1833-0.33070.02110.05960.17210.0107-0.09850.59390.0246-0.12310.49760.06960.515948.99980.53733.874
80.78541.1604-0.44343.5991-0.04120.5198-0.00160.2236-0.1245-0.09790.0158-0.23220.0902-0.1175-0.01430.62220.0489-0.23840.3602-0.12410.440452.18659.19141.804
90.76640.5852-0.12061.18070.78711.13550.0120.0720.0260.11560.0063-0.03380.2398-0.0118-0.01830.5939-0.0123-0.22240.3545-0.05580.450350.91863.08750.63
1017.4041-25.495616.113137.539-23.643814.99230.717-0.0954-0.5051-1.3423-0.03270.79160.8815-0.065-0.68431.152-0.0515-0.41990.2652-0.06410.577653.32241.88955.711
1119.875312.6988-1.75018.1222-1.11330.1622-0.28120.3012-1.2705-0.11560.1755-0.83840.0477-0.04550.10581.5683-0.5099-0.20150.3953-0.21050.44141.71440.56553.449
120.44110.8323-0.28372.01980.23491.73680.06070.01190.03360.23150.0088-0.0860.2871-0.1013-0.06960.5726-0.0355-0.25650.3835-0.02190.480352.92463.53361.097
133.92512.0425-3.48169.6212-0.27313.5237-0.2479-0.1635-0.12070.5683-0.11750.49540.4652-0.10280.36540.8122-0.3526-0.19690.4573-0.140.398943.22853.43864.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 23
2X-RAY DIFFRACTION2A24 - 28
3X-RAY DIFFRACTION3A29 - 43
4X-RAY DIFFRACTION4A44 - 57
5X-RAY DIFFRACTION5A58 - 63
6X-RAY DIFFRACTION6A64 - 72
7X-RAY DIFFRACTION7A73 - 97
8X-RAY DIFFRACTION8A98 - 130
9X-RAY DIFFRACTION9A131 - 184
10X-RAY DIFFRACTION10A185 - 190
11X-RAY DIFFRACTION11A191 - 201
12X-RAY DIFFRACTION12A202 - 247
13X-RAY DIFFRACTION13A248 - 261

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