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- PDB-5v00: Structure of HutD from Pseudomonas fluorescens SBW25 (Formate con... -

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Basic information

Entry
Database: PDB / ID: 5v00
TitleStructure of HutD from Pseudomonas fluorescens SBW25 (Formate condition)
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / bicupin / histidine degradation
Function / homology
Function and homology information


Uncharacterised protein family HutD/Ves / HutD / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Protein Ves
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, Y. / Johnston, J.M. / Gerth, M.L. / Baker, E.N. / Lott, J.S. / Rainey, P.B.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Foundation for Research Science and Technology New Zealand
Health Research Council (HRC) New Zealand
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas.
Authors: Gerth, M.L. / Liu, Y. / Jiao, W. / Zhang, X.X. / Baker, E.N. / Lott, J.S. / Rainey, P.B. / Johnston, J.M.
History
DepositionFeb 27, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMar 15, 2017ID: 3ESG
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,14214
Polymers42,4982
Non-polymers64412
Water7,242402
1
A: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,14214
Polymers42,4982
Non-polymers64412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y+1/2,-z+1/41
Buried area3910 Å2
ΔGint-11 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.863, 82.863, 174.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsDimer by size exclusion

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Components

#1: Protein Uncharacterized protein


Mass: 21248.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain SBW25) (bacteria)
Strain: SBW25 / Gene: PFLU_0360 / Production host: Escherichia coli (E. coli) / References: UniProt: C3K802
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 3.52 Å3/Da / Density % sol: 65.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Ammonium formate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→74.85 Å / Num. obs: 57596 / % possible obs: 98.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.037 / Χ2: 1.241 / Net I/σ(I): 35.11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.79-1.856.90.290.975188.7
1.85-1.937.60.2051.0561100
1.93-2.027.60.1481.1661100
2.02-2.127.60.1131.2861100
2.12-2.267.70.0841.3941100
2.26-2.437.70.0691.4711100
2.43-2.677.70.0531.2411100
2.67-3.068.60.0431.3531100
3.06-3.8615.60.0331.3651100
3.86-50150.0291.077199.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLL

1yll


Resolution: 1.8→74.85 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.705 / SU ML: 0.054 / SU R Cruickshank DPI: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 2911 5.1 %RANDOM
Rwork0.167 ---
obs0.1684 54479 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.3 Å2 / Biso mean: 27.762 Å2 / Biso min: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→74.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 42 402 3279
Biso mean--39.57 38.56 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192990
X-RAY DIFFRACTIONr_bond_other_d0.0020.022751
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.954040
X-RAY DIFFRACTIONr_angle_other_deg1.08636337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97622.867143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52515483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8961531
X-RAY DIFFRACTIONr_chiral_restr0.1330.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
LS refinement shellResolution: 1.795→1.842 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 217 -
Rwork0.236 3817 -
all-4034 -
obs--96.25 %

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