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- PDB-4tq5: Structure of a UbiA homolog from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 4tq5
TitleStructure of a UbiA homolog from Archaeoglobus fulgidus
Componentsprenyltransferase
KeywordsTRANSFERASE / prenyltransferase / membrane protein / Structural Genomics / New York Consortium on Membrane Protein Structure / NYCOMPS / PSI-Biology
Function / homologyUbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family / transferase activity, transferring alkyl or aryl (other than methyl) groups / plasma membrane / Bacteriochlorophyll synthase, 33 kDa subunit
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2023 Å
AuthorsHuang, H. / Levin, E.J. / Bai, Y. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK088057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098878 United States
American Heart Association12EIA8850017 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R12MZ United States
CitationJournal: Plos Biol. / Year: 2014
Title: Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1.
Authors: Huang, H. / Levin, E.J. / Liu, S. / Bai, Y. / Lockless, S.W. / Zhou, M.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9672
Polymers33,6751
Non-polymers2921
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.922, 61.922, 248.752
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein prenyltransferase /


Mass: 33674.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1648 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28625
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 4.12 Å3/Da / Density % sol: 70.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 12.5% PEG 20000, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionRedundancy: 21 % / Number: 197115 / Rmerge(I) obs: 0.128 / Χ2: 0.87 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 9401 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
8.675010.031.10219.6
6.898.6710.0511.10220.4
6.026.8910.0940.99821
5.476.0210.1320.98621.5
5.085.4710.1351.00321.6
4.785.0810.1251.02221.6
4.544.7810.1280.92822.1
4.344.5410.130.89321.8
4.184.3410.1360.82222
4.034.1810.1730.8422.2
3.914.0310.2370.81622.4
3.793.9110.2950.80321.8
3.693.7910.4070.78722.1
3.63.6910.4340.80122.2
3.523.610.5850.74822.3
3.453.5210.5780.76521.6
3.383.4510.8350.74220.5
3.313.3810.9620.74718.9
3.263.3110.9530.75617.8
3.23.2610.73715.9
ReflectionResolution: 3.2→50 Å / Num. obs: 9401 / % possible obs: 99.9 % / Redundancy: 21 % / Biso Wilson estimate: 88.16 Å2 / Rmerge(I) obs: 0.128 / Χ2: 0.874 / Net I/av σ(I): 27.727 / Net I/σ(I): 4.9 / Num. measured all: 197115
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.2-3.2615.94670.73798.7
3.26-3.3117.84390.7561000.953
3.31-3.3818.94640.7471000.962
3.38-3.4520.54820.7421000.835
3.45-3.5221.64370.7651000.578
3.52-3.622.34810.7481000.585
3.6-3.6922.24580.8011000.434
3.69-3.7922.14530.7871000.407
3.79-3.9121.84820.8031000.295
3.91-4.0322.44460.8161000.237
4.03-4.1822.24670.841000.173
4.18-4.34224680.8221000.136
4.34-4.5421.84670.8931000.13
4.54-4.7822.14770.9281000.128
4.78-5.0821.64721.0221000.125
5.08-5.4721.64631.0031000.135
5.47-6.0221.54760.9861000.132
6.02-6.89214930.9981000.094
6.89-8.6720.44821.1021000.051
8.67-5019.65271.1021000.03

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: SAD / Resolution: 3.2023→49.244 Å / FOM work R set: 0.6879 / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 36.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 1715 9.81 %Random
Rwork0.2512 15766 --
obs0.2548 17481 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.77 Å2 / Biso mean: 95.78 Å2 / Biso min: 61.17 Å2
Refinement stepCycle: final / Resolution: 3.2023→49.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 20 0 2169
Biso mean--108.62 --
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062234
X-RAY DIFFRACTIONf_angle_d0.9523051
X-RAY DIFFRACTIONf_chiral_restr0.033357
X-RAY DIFFRACTIONf_plane_restr0.004368
X-RAY DIFFRACTIONf_dihedral_angle_d13.776770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2023-3.29650.46621410.39381281142298
3.2965-3.40280.4241420.32121333147599
3.4028-3.52440.33471400.29321283142399
3.5244-3.66550.33311540.2961338149299
3.6655-3.83230.30871400.237813171457100
3.8323-4.03420.33251420.232612941436100
4.0342-4.28680.32421480.24391326147499
4.2868-4.61760.27331460.225512821428100
4.6176-5.08190.26291380.207213651503100
5.0819-5.81620.25721410.2512951436100
5.8162-7.3240.2581380.25313321470100
7.324-49.24960.24471450.24731320146599

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