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- PDB-5fcc: Structure of HutD from Pseudomonas fluorescens SBW25 (NaCl condition) -

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Basic information

Entry
Database: PDB / ID: 5fcc
TitleStructure of HutD from Pseudomonas fluorescens SBW25 (NaCl condition)
ComponentsHutD
KeywordsUNKNOWN FUNCTION / bicupin / histidine degradation
Function / homologyUncharacterised protein family HutD/Ves / HutD / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Protein Ves
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsJohnston, J.M. / Gerth, M.L. / Baker, E.N. / Lott, J.S. / Rainey, P.B.
CitationJournal: To Be Published
Title: Structure of HutD from Pseudomonas fluorescens
Authors: Gerth, M.L. / Liu, Y.H. / Zhang, X.-X. / Baker, E.N. / Lott, J.S. / Rainey, P.B. / Johnston, J.M.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Refinement description
Category: diffrn_source / pdbx_audit_support / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification
Revision 1.2Sep 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HutD
B: HutD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,84910
Polymers42,4982
Non-polymers3518
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-58 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.998, 81.998, 169.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HutD


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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Imidazole pH 6.5, 3 M NaCl, 150mM FG

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953692 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953692 Å / Relative weight: 1
ReflectionResolution: 1.94→81.998 Å / Num. obs: 43842 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 34.23 Å2 / Rsym value: 0.172 / Net I/σ(I): 21.3
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs
1.94-2.0422.22.871.313878262650.6112.871.3
2.04-2.1726.41.9270.415752559670.3791.9272.4
2.17-2.3226.71.1550.614933155990.2271.1554.2
2.32-2.527.70.757114466552280.1450.7576.2
2.5-2.7428.10.461.613666148640.0880.4610.4
2.74-3.0728.70.2323.212613543960.0440.23219.5
3.07-3.5428.50.0977.611136839090.0180.09741.9
3.54-4.3427.80.05712.39381033690.0110.05764.2
4.34-6.1327.60.0415.87320726510.0080.0480.2
6.13-81.998250.03614.53978015940.0070.03680.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PDB_EXTRACT3.15data extraction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ESG

3esg
PDB Unreleased entry


Resolution: 1.94→54.87 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 2236 5.11 %
Rwork0.2 --
obs0.202 43718 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.53 Å2
Refinement stepCycle: LAST / Resolution: 1.94→54.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 17 241 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012949
X-RAY DIFFRACTIONf_angle_d1.1163993
X-RAY DIFFRACTIONf_dihedral_angle_d14.4881721
X-RAY DIFFRACTIONf_chiral_restr0.061437
X-RAY DIFFRACTIONf_plane_restr0.006526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.98220.38751360.33782543X-RAY DIFFRACTION100
1.9822-2.02830.33041370.32292534X-RAY DIFFRACTION100
2.0283-2.0790.38691560.35312520X-RAY DIFFRACTION99
2.079-2.13530.29871350.27682543X-RAY DIFFRACTION100
2.1353-2.19810.29081210.25452579X-RAY DIFFRACTION100
2.1981-2.2690.28351360.2792549X-RAY DIFFRACTION100
2.269-2.35010.26811580.23432549X-RAY DIFFRACTION100
2.3501-2.44420.2851240.2422575X-RAY DIFFRACTION100
2.4442-2.55550.31051550.23142554X-RAY DIFFRACTION100
2.5555-2.69020.23551240.22892600X-RAY DIFFRACTION100
2.6902-2.85870.27651430.21392573X-RAY DIFFRACTION100
2.8587-3.07950.25711440.2162600X-RAY DIFFRACTION100
3.0795-3.38930.19741470.18562607X-RAY DIFFRACTION100
3.3893-3.87960.21091380.15972647X-RAY DIFFRACTION100
3.8796-4.88750.19991210.14392687X-RAY DIFFRACTION100
4.8875-54.89590.17711610.1742822X-RAY DIFFRACTION100

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