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- PDB-5uft: Crystal Structure of a Nitrogen-fixing NifU-like protein (N-termi... -

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Basic information

Entry
Database: PDB / ID: 5uft
TitleCrystal Structure of a Nitrogen-fixing NifU-like protein (N-terminal) from Brucella abortus
ComponentsNitrogen-fixing NifU-like, N-terminal
KeywordsMETAL BINDING PROTEIN / SSGCID / Brucella abortus / iron ion binding / iron-sulfur cluster binding/assembly / NifU / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyNIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / iron-sulfur cluster assembly / iron-sulfur cluster binding / iron ion binding / Nitrogen-fixing NifU-like, N-terminal
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Nitrogen-fixing NifU-like protein (N-terminal) from Brucella abortus
Authors: Dranow, D.M. / Mayclin, S.J. / Buchko, G.W. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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: Nitrogen-fixing NifU-like, N-terminal


Theoretical massNumber of molelcules
Total (without water)16,4111
Polymers16,4111
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.960, 42.960, 149.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nitrogen-fixing NifU-like, N-terminal


Mass: 16410.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: BAB1_1096 / Plasmid: BrabA.17776.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YQ04
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: BrabA.17776.a.A1.PB00075 at 15 mg/ml mixed 1:1 with an equal volume CSHT (b10): 30% (w/v) PEG-4000, 0.1 M Tris-HCl, pH=8.5, 0.2 M sodium acetate hydrate, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.35→29.799 Å / Num. obs: 7179 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.88 % / Biso Wilson estimate: 52.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 23.28
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.35-2.417.2180.5583.610.91100
2.41-2.487.1720.4624.160.9241100
2.48-2.557.1810.375.380.9751100
2.55-2.637.1410.2348.070.9831100
2.63-2.717.0880.2397.910.9791100
2.71-2.817.1630.17610.340.992199.8
2.81-2.927.0230.13513.570.991100
2.92-3.037.1740.09718.050.996199.8
3.03-3.176.960.07322.530.997199.8
3.17-3.327.0770.05927.640.9981100
3.32-3.56.7860.04932.740.9981100
3.5-3.726.7290.04138.540.9981100
3.72-3.976.7160.03442.280.9991100
3.97-4.296.5640.03345.420.9991100
4.29-4.76.4280.03147.840.9991100
4.7-5.266.6210.02749.560.9991100
5.26-6.076.4180.02646.7411100
6.07-7.436.0890.02448.180.9991100
7.43-10.515.8070.0250.711100
10.51-29.7994.7310.02343.260.999189.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qq4

2qq4


Resolution: 2.35→29.799 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.95
RfactorNum. reflection% reflection
Rfree0.2594 696 10.02 %
Rwork0.2246 --
obs0.228 6948 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.43 Å2 / Biso mean: 65.3505 Å2 / Biso min: 46.96 Å2
Refinement stepCycle: final / Resolution: 2.35→29.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 0 15 1089
Biso mean---57.59 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021095
X-RAY DIFFRACTIONf_angle_d0.4221483
X-RAY DIFFRACTIONf_chiral_restr0.039170
X-RAY DIFFRACTIONf_plane_restr0.003197
X-RAY DIFFRACTIONf_dihedral_angle_d13.573672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3501-2.53150.32591290.31331156128591
2.5315-2.78610.31631290.29981178130795
2.7861-3.18880.38551380.29041246138498
3.1888-4.0160.28661420.234512941436100
4.016-29.80130.19621580.17861378153699
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)
11.15371.12551.05253.8364-0.16972.9274-0.19030.8666-0.21380.20710.54940.1418-0.0814-0.4915-0.20160.32170.06940.0460.92540.15760.53937.608121.958657.1997
24.66271.69380.71915.9794.99355.05510.6995-1.06080.34220.3405-0.36030.12540.0871-0.9512-0.07380.46470.0050.02931.31780.2930.525-9.21313.620754.0201
33.0084-0.40210.94820.2866-0.43551.31220.02570.30470.8243-0.1776-0.2288-0.1266-0.0069-0.3826-0.73830.4370.17230.08321.51950.23510.6733-6.769720.052763.076
43.70290.69881.0072.88570.57163.442-0.42670.37051.06580.00880.07250.211-0.8116-0.65870.31090.5760.2032-0.01410.99370.22410.73235.685534.196560.5016
52.25591.75860.68273.59740.98432.3849-0.17080.55260.14330.01720.2866-0.1917-0.1485-0.2739-0.02850.3310.0925-0.01530.88290.17760.50758.790224.012661.5904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 104 through 143 )A104 - 143
2X-RAY DIFFRACTION2chain 'A' and (resid 0 through 7 )A0 - 7
3X-RAY DIFFRACTION3chain 'A' and (resid 8 through 15 )A8 - 15
4X-RAY DIFFRACTION4chain 'A' and (resid 16 through 38 )A16 - 38
5X-RAY DIFFRACTION5chain 'A' and (resid 39 through 103 )A39 - 103

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