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- PDB-4low: Structure and identification of a pterin dehydratase-like protein... -

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Basic information

Entry
Database: PDB / ID: 4low
TitleStructure and identification of a pterin dehydratase-like protein as a RuBisCO assembly factor in the alpha-carboxysome
ComponentsacRAF
KeywordsUNKNOWN FUNCTION / PCD / pterin-4a-carbinolamine dehydratase-like
Function / homology
Function and homology information


4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / tetrahydrobiopterin biosynthetic process
Similarity search - Function
Transcriptional coactivator/pterin dehydratase / Pterin 4 alpha carbinolamine dehydratase / Pterin 4 alpha carbinolamine dehydratase superfamily / Pterin 4 alpha carbinolamine dehydratase / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / NICKEL (II) ION / 4a-hydroxytetrahydrobiopterin dehydratase
Similarity search - Component
Biological speciesThiomonas intermedia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsWheatley, N.M. / Gidaniyan, S.D. / Cascio, D. / Yeates, T.O.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and Identification of a Pterin Dehydratase-like Protein as a Ribulose-bisphosphate Carboxylase/Oxygenase (RuBisCO) Assembly Factor in the alpha-Carboxysome.
Authors: Wheatley, N.M. / Sundberg, C.D. / Gidaniyan, S.D. / Cascio, D. / Yeates, T.O.
History
DepositionJul 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Structure summary
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acRAF
B: acRAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,83510
Polymers19,4412
Non-polymers3948
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-14 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.110, 51.110, 60.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein acRAF


Mass: 9720.723 Da / Num. of mol.: 2 / Fragment: UNP residues 7-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiomonas intermedia (bacteria) / Strain: K12 / Gene: Tint_0125 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5X340
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.05 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 17.5% PEG3350, 800 mM ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.3→51.11 Å / Num. obs: 36178 / % possible obs: 96.9 %

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXEmodel building
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.3→51.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.9578 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.054 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 1809 5 %RANDOM
Rwork0.2025 ---
obs0.2025 36178 93.92 %-
Displacement parametersBiso max: 174 Å2 / Biso mean: 32.3605 Å2 / Biso min: 13.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.942 Å20 Å20 Å2
2---0.942 Å20 Å2
3---1.884 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.3→51.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 20 117 1405
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d451SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes217HARMONIC5
X-RAY DIFFRACTIONt_it1365HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion170SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1676SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1365HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1842HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion4.19
X-RAY DIFFRACTIONt_other_torsion17.07
LS refinement shellResolution: 1.3→1.34 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2412 125 4.98 %
Rwork0.2115 2383 -
all0.2129 2508 -
obs--93.92 %
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)
11.3304-0.2072-0.2360.7694-0.46941.4455-0.0748-0.0277-0.04430.01490.01710.08150.0532-0.16940.0577-0.0537-0.01870.0093-0.0364-0.01050.020910.376618.380569.9063
21.00750.06550.39231.2857-1.45743.88370.02890.1193-0.1298-0.26490.0770.04490.6907-0.2704-0.1059-0.0141-0.0339-0.0259-0.0648-0.021-0.038628.3979.29462.305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 89
2X-RAY DIFFRACTION2{ B|* }B4 - 87

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