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- PDB-3qkc: CRYSTAL STRUCTURE OF geranyl diphosphate synthase small subunit f... -

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Basic information

Entry
Database: PDB / ID: 3qkc
TitleCRYSTAL STRUCTURE OF geranyl diphosphate synthase small subunit from Antirrhinum majus
ComponentsGeranyl diphosphate synthase small subunit
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homologydimethylallyltranstransferase / dimethylallyltranstransferase activity / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha / Geranyl diphosphate synthase small subunit
Function and homology information
Biological speciesAntirrhinum majus (snapdragon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 2.2 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of geranyl diphosphate synthase small subunit from Antirrhinum majus
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Geranyl diphosphate synthase small subunit
A: Geranyl diphosphate synthase small subunit


Theoretical massNumber of molelcules
Total (without water)60,0012
Polymers60,0012
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-38 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.199, 48.789, 61.593
Angle α, β, γ (deg.)66.690, 89.280, 89.980
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Geranyl diphosphate synthase small subunit


Mass: 30000.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Antirrhinum majus (snapdragon) / Gene: AAS82859 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q6QLV2, dimethylallyltranstransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 1.4 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 2.9 % / Av σ(I) over netI: 23.18 / Number: 80462 / Rmerge(I) obs: 0.073 / Χ2: 2.5 / D res high: 2.05 Å / D res low: 50 Å / Num. obs: 28005 / % possible obs: 97.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.565096.410.0611.1382.9
4.425.5698.810.0476.1582.8
3.864.4298.510.0423.6722.9
3.513.8698.810.0483.4492.9
3.253.5198.610.0552.4962.9
3.063.2598.410.0712.3832.9
2.913.0698.710.0821.9932.9
2.782.9198.210.1041.7972.9
2.682.7897.910.141.7632.9
2.582.6897.810.1621.5012.9
2.52.5898.110.1861.4762.9
2.432.597.610.2231.4692.9
2.372.4397.510.2611.3793
2.312.3797.110.3181.3822.9
2.262.3197.610.3921.3262.9
2.212.2696.810.4411.2512.9
2.162.2196.910.5131.2112.9
2.122.1697.110.6181.1862.8
2.092.1294.410.6431.1242.6
2.052.0987.710.6981.1372.4
ReflectionResolution: 2.05→50 Å / Num. obs: 28005 / % possible obs: 97.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.073 / Χ2: 2.503 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.092.40.69812131.13787.7
2.09-2.122.60.64313921.12494.4
2.12-2.162.80.61814231.18697.1
2.16-2.212.90.51313691.21196.9
2.21-2.262.90.44113851.25196.8
2.26-2.312.90.39214451.32697.6
2.31-2.372.90.31813831.38297.1
2.37-2.4330.26114131.37997.5
2.43-2.52.90.22313911.46997.6
2.5-2.582.90.18614161.47698.1
2.58-2.682.90.16214311.50197.8
2.68-2.782.90.1413701.76397.9
2.78-2.912.90.10414331.79798.2
2.91-3.062.90.08214531.99398.7
3.06-3.252.90.07114182.38398.4
3.25-3.512.90.05513832.49698.6
3.51-3.862.90.04814443.44998.8
3.86-4.422.90.04214433.67298.5
4.42-5.562.80.04714026.15898.8
5.56-502.90.06139811.13896.4

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRRfactor: 50.18 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.56 Å
Translation2.5 Å34.56 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 2.2→19.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.942 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.393 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 1160 5.1 %RANDOM
Rwork0.2093 ---
obs0.2132 22916 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 67.12 Å2 / Biso mean: 50.622 Å2 / Biso min: 17.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0.04 Å20.01 Å2
2--0.07 Å20.09 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 0 79 3997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223980
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9865364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1185510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69423.882170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83115722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4131530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212958
X-RAY DIFFRACTIONr_mcbond_it0.68310.52530
X-RAY DIFFRACTIONr_mcangle_it1.501504042
X-RAY DIFFRACTIONr_scbond_it2.174501450
X-RAY DIFFRACTIONr_scangle_it0.0764.51322
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 74 -
Rwork0.258 1576 -
all-1650 -
obs--97 %
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)
11.1945-0.1142-0.3691.77890.52733.52970.00390.1570.0861-0.18190.06590.01280.14060.1572-0.06980.0329-0.0025-0.01560.04450.0290.04574.759910.14752.7469
21.23840.2263-0.54681.8205-0.44493.4176-0.0052-0.19340.08550.17130.0398-0.00570.1524-0.1424-0.03460.03380.0019-0.01910.0544-0.0310.0501-1.652410.152431.3789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B-10 - 9999
2X-RAY DIFFRACTION2A-10 - 9999

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