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- PDB-4tq3: Structure of a UbiA homolog from Archaeoglobus fulgidus bound to ... -

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Basic information

Entry
Database: PDB / ID: 4tq3
TitleStructure of a UbiA homolog from Archaeoglobus fulgidus bound to GPP 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 / GERANYL DIPHOSPHATE / Bacteriochlorophyll synthase, 33 kDa subunit
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4076 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)135,02416
Polymers133,5734
Non-polymers1,45112
Water45025
1
A: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7564
Polymers33,3931
Non-polymers3633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13290 Å2
MethodPISA
2
B: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7564
Polymers33,3931
Non-polymers3633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13450 Å2
MethodPISA
3
C: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7564
Polymers33,3931
Non-polymers3633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13420 Å2
MethodPISA
4
D: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7564
Polymers33,3931
Non-polymers3633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13310 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-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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, sitting 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-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2014
RadiationMonochromator: Single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 54488 / % possible obs: 92.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.33 Å2 / Rmerge(I) obs: 0.101 / Χ2: 0.937 / Net I/av σ(I): 8.725 / Net I/σ(I): 8.8 / Num. measured all: 182679
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.443.30.48826760.88491.7
2.44-2.493.40.45826370.89888.9
2.49-2.533.40.39626320.91691.1
2.53-2.593.40.34726770.97189.3
2.59-2.643.40.31326021.0590
2.64-2.73.40.26626281.08488.4
2.7-2.773.40.22925871.10389.9
2.77-2.853.40.21926321.13388.7
2.85-2.933.40.18226011.1288.3
2.93-3.023.40.17226461.08989.8
3.02-3.133.30.1526440.98790.8
3.13-3.263.30.12827140.99490.9
3.26-3.413.30.11327390.92193.5
3.41-3.593.30.127600.85294.6
3.59-3.813.20.09528500.79996.4
3.81-4.13.20.09328580.79697.6
4.1-4.523.20.08728470.895.9
4.52-5.173.10.07328390.86397.1
5.17-6.513.40.07529750.82299.4
6.51-1003.80.06229440.73298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4TQ5

4tq5


Resolution: 2.4076→30.338 Å / FOM work R set: 0.803 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 2745 5.04 %Random
Rwork0.2212 51691 --
obs0.223 54436 92.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.38 Å2 / Biso mean: 44.64 Å2 / Biso min: 24.8 Å2
Refinement stepCycle: final / Resolution: 2.4076→30.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8876 0 84 25 8985
Biso mean--45.57 38.66 -
Num. residues----1135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089212
X-RAY DIFFRACTIONf_angle_d1.1912589
X-RAY DIFFRACTIONf_chiral_restr0.0461450
X-RAY DIFFRACTIONf_plane_restr0.0061535
X-RAY DIFFRACTIONf_dihedral_angle_d15.8643157
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4076-2.44910.30881290.25492387251685
2.4491-2.49360.27351430.23442511265490
2.4936-2.54150.28611350.22512487262291
2.5415-2.59340.28911250.22132569269490
2.5934-2.64970.27571210.21752476259790
2.6497-2.71130.29681160.20462520263688
2.7113-2.77910.25641390.20462461260089
2.7791-2.85420.26361350.20762501263689
2.8542-2.93810.25821270.20182484261189
2.9381-3.03290.26021320.22042539267190
3.0329-3.14110.2781320.22172499263191
3.1411-3.26680.2691230.24372595271891
3.2668-3.41530.26291380.23312599273793
3.4153-3.5950.26071360.22762626276295
3.595-3.81990.29791480.23652685283396
3.8199-4.11420.29061290.24342755288498
4.1142-4.5270.2441600.22352707286796
4.527-5.17920.22021460.21652682282897
5.1792-6.51460.27581700.23512801297199
6.5146-30.33990.18851610.18142807296899

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