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- PDB-4tq6: Structure of a UbiA homolog from Archaeoglobus fulgidus bound to Cd2+ -

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Basic information

Entry
Database: PDB / ID: 4tq6
TitleStructure of a UbiA homolog from Archaeoglobus fulgidus bound to Cd2+
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 / : / Bacteriochlorophyll synthase, 33 kDa subunit
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.0678 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
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
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_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prenyltransferase
B: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,68610
Polymers66,7862
Non-polymers8998
Water00
1
A: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8435
Polymers33,3931
Non-polymers4504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-21 kcal/mol
Surface area12370 Å2
MethodPISA
2
B: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8435
Polymers33,3931
Non-polymers4504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-21 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.938, 89.871, 341.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 15 - 301 / Label seq-ID: 15 - 301

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein prenyltransferase


Mass: 33393.184 Da / Num. of mol.: 2
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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd

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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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 30% PEG 550 MME, 100 mM MES, 100 mM CdCl2, 5 mM MgCl2

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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: Jul 13, 2013
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: 3.067→42.336 Å / Num. all: 15560 / Num. obs: 15560 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 106.22 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.068 / Rsym value: 0.043 / Net I/av σ(I): 14.347 / Net I/σ(I): 15.8 / Num. measured all: 49271
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.067-3.233.30.6431.1728822240.4460.6432.499.3
3.23-3.433.30.3422.1701821350.250.342499.7
3.43-3.673.30.1823.8659220280.1350.1826.999.9
3.67-3.963.20.17611318970.0760.111.599.7
3.96-4.343.20.05213.5555417630.0440.05218.299.7
4.34-4.853.10.03818.4479115510.0340.03824.699.4
4.85-5.63.10.03817.5425713950.0350.03825.898.7
5.6-6.8630.03220.1354511950.030.03227.398.8
6.86-9.730.01831.127239140.0150.01839.697
9.7-42.33630.01350.913904580.0130.01347.885.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREPphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQ5

4tq5


Resolution: 3.0678→42.336 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.301 772 4.97 %Random
Rwork0.2651 14747 --
obs0.2669 15519 98.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.07 Å2 / Biso mean: 100.8228 Å2 / Biso min: 53.51 Å2
Refinement stepCycle: final / Resolution: 3.0678→42.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 8 0 4056
Biso mean--154.49 --
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094175
X-RAY DIFFRACTIONf_angle_d1.4745735
X-RAY DIFFRACTIONf_chiral_restr0.06681
X-RAY DIFFRACTIONf_plane_restr0.01698
X-RAY DIFFRACTIONf_dihedral_angle_d13.011356
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2280X-RAY DIFFRACTION3.744TORSIONAL
12B2280X-RAY DIFFRACTION3.744TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0678-3.25990.46491320.43852435256799
3.2599-3.51150.36941240.353124482572100
3.5115-3.86470.33361420.288224142556100
3.8647-4.42340.33721360.250224972633100
4.4234-5.5710.24961180.24812479259799
5.571-42.33970.26571200.23422474259493

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