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- PDB-4tq4: Structure of a UbiA homolog from Archaeoglobus fulgidus bound to ... -

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Basic information

Entry
Database: PDB / ID: 4tq4
TitleStructure of a UbiA homolog from Archaeoglobus fulgidus bound to DMAPP and Mg2+
Componentsprenyltransferase
KeywordsTRANSFERASE / prenyltransferase / membrane protein / Structural Genomics / New York Consortium on Membrane Protein Structure / NYCOMPS / PSI-Biology
Function / homology: / UbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family / transferase activity, transferring alkyl or aryl (other than methyl) groups / metal ion binding / plasma membrane / DIMETHYLALLYL DIPHOSPHATE / Bacteriochlorophyll synthase, 33 kDa subunit
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5025 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 / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._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 / _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prenyltransferase
B: prenyltransferase
C: prenyltransferase
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,75216
Polymers133,5734
Non-polymers1,17912
Water48627
1
A: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6884
Polymers33,3931
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13230 Å2
MethodPISA
2
B: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6884
Polymers33,3931
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13500 Å2
MethodPISA
3
C: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6884
Polymers33,3931
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13310 Å2
MethodPISA
4
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6884
Polymers33,3931
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.605, 218.922, 65.292
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
prenyltransferase


Mass: 33393.184 Da / Num. of mol.: 4
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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 34% PEG 400, 100 mM Tris-HCL, 100 mM NaCl, 100 mM MgCl2, 1-oleoyl-rac-glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2014
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 51825 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 44.31 Å2 / Rmerge(I) obs: 0.116 / Χ2: 0.9 / Net I/av σ(I): 9.063 / Net I/σ(I): 6.6 / Num. measured all: 173584
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.542.90.67225210.81798.6
2.54-2.593.10.64526320.82799.4
2.59-2.643.10.58725550.91699.2
2.64-2.693.30.5426050.92699
2.69-2.753.30.45325670.99699.3
2.75-2.823.10.39325931.02898.4
2.82-2.893.40.36625661.00699.7
2.89-2.963.50.31725951.01399.7
2.96-3.053.50.27826080.99199.5
3.05-3.153.50.24425960.96599.5
3.15-3.263.50.226170.93599.5
3.26-3.393.30.1725920.95199.1
3.39-3.553.20.14425440.92998.8
3.55-3.733.60.12425990.86899.8
3.73-3.973.50.1126080.8399.7
3.97-4.273.50.08725960.82199.2
4.27-4.73.20.07326010.79898.5
4.7-5.383.50.06725970.83499.7
5.38-6.783.40.05925970.84399.2
6.78-503.50.06926360.71198.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQ3

4tq3


Resolution: 2.5025→39.083 Å / FOM work R set: 0.7897 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 2550 4.93 %Random
Rwork0.2152 49203 --
obs0.2173 51753 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.48 Å2 / Biso mean: 51.3 Å2 / Biso min: 25.93 Å2
Refinement stepCycle: final / Resolution: 2.5025→39.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9041 0 64 27 9132
Biso mean--58.21 48.35 -
Num. residues----1155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089364
X-RAY DIFFRACTIONf_angle_d1.16712799
X-RAY DIFFRACTIONf_chiral_restr0.0451473
X-RAY DIFFRACTIONf_plane_restr0.0061563
X-RAY DIFFRACTIONf_dihedral_angle_d15.2313226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5025-2.55060.29731040.23962338244285
2.5506-2.60260.27881280.24272812294099
2.6026-2.65920.32171510.23592710286199
2.6592-2.72110.26991270.21732807293499
2.7211-2.78910.26551530.212647280099
2.7891-2.86450.26251360.21222787292399
2.8645-2.94870.26291340.203927812915100
2.9487-3.04390.26531510.21592773292499
3.0439-3.15260.26321390.21122740287999
3.1526-3.27880.22271250.224327802905100
3.2788-3.42790.25191380.22962783292199
3.4279-3.60850.27271510.22382709286099
3.6085-3.83450.25781510.222227682919100
3.8345-4.13020.32521290.23952758288799
4.1302-4.54530.25451650.22332741290698
4.5453-5.20170.23781430.214227322875100
5.2017-6.54860.28131670.22172796296399
6.5486-39.08730.19311580.16712741289999

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