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- PDB-6jc4: Crystal structure of the urease accessory protein UreF from Klebs... -

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Basic information

Entry
Database: PDB / ID: 6jc4
TitleCrystal structure of the urease accessory protein UreF from Klebsiella pneumoniae
ComponentsUrease accessory protein UreF
KeywordsMETAL BINDING PROTEIN / Nickel-binding / urease accessory protein
Function / homologyUrease accessory protein UreF / UreF domain superfamily / UreF / nickel cation binding / cytoplasm / Urease accessory protein UreF / Urease accessory protein UreF
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWu, W. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570128 China
Ministry of Science and Technology (China)2014CB560709 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Structural characterization of the urease accessory protein UreF from Klebsiella pneumoniae.
Authors: Liu, S. / Wu, W. / Zhao, Q. / Liang, H. / Che, S. / Zhang, H. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: Urease accessory protein UreF
B: Urease accessory protein UreF
C: Urease accessory protein UreF
D: Urease accessory protein UreF


Theoretical massNumber of molelcules
Total (without water)114,8484
Polymers114,8484
Non-polymers00
Water6,323351
1
A: Urease accessory protein UreF
D: Urease accessory protein UreF


Theoretical massNumber of molelcules
Total (without water)57,4242
Polymers57,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-16 kcal/mol
Surface area16940 Å2
MethodPISA
2
B: Urease accessory protein UreF
C: Urease accessory protein UreF


Theoretical massNumber of molelcules
Total (without water)57,4242
Polymers57,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-16 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.886, 121.886, 63.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 200 / Label seq-ID: 34 - 233

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Urease accessory protein UreF


Mass: 28712.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: ureF, ureF_1, ureF_2, NCTC204_02890, NCTC5052_03968, NCTC8849_05426, NCTC9637_01222, NCTC9661_01459, SAMEA104305404_01442, SAMEA24002668_02244
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X3G2L5, UniProt: A6TE44*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% (w/v) PEG-8000, 0.1M CHES, pH 9.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 41752 / % possible obs: 100 % / Redundancy: 13.5 % / Rpim(I) all: 0.034 / Net I/σ(I): 27.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 9.9 / Num. unique obs: 2055 / Rpim(I) all: 0.142 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.03 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.196 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.232 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24172 1984 4.8 %RANDOM
Rwork0.19971 ---
obs0.20166 39735 99.88 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.3→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 0 351 6715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175976
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.6358880
X-RAY DIFFRACTIONr_angle_other_deg1.3561.56613744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36420.101396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.912151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2791576
X-RAY DIFFRACTIONr_chiral_restr0.0830.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3721.8623196
X-RAY DIFFRACTIONr_mcbond_other2.3711.8623195
X-RAY DIFFRACTIONr_mcangle_it3.4162.7833988
X-RAY DIFFRACTIONr_mcangle_other3.4152.7833989
X-RAY DIFFRACTIONr_scbond_it3.7852.4333336
X-RAY DIFFRACTIONr_scbond_other3.7842.4333337
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.733.4544893
X-RAY DIFFRACTIONr_long_range_B_refined7.7123.7657953
X-RAY DIFFRACTIONr_long_range_B_other7.68723.4647871
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A65230.08
12B65230.08
21A64430.09
22C64430.09
31A64050.1
32D64050.1
41B64920.08
42C64920.08
51B64570.09
52D64570.09
61C64600.08
62D64600.08
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 147 -
Rwork0.197 2930 -
obs--99.84 %
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)
11.4627-0.43560.53160.8726-0.13331.3361-0.04070.2732-0.1197-0.07650.027-0.0724-0.06930.08980.01370.05320.00590.02270.1037-0.01850.041254.335-27.6-7.223
21.5246-0.8619-0.48311.73940.40182.0836-0.1142-0.1610.04040.40340.0756-0.19130.0252-0.04020.03860.1308-0.0071-0.03440.05-0.00760.037489.349-9.97310.199
30.78290.76090.39712.54940.47731.6537-0.01290.09330.0389-0.4646-0.0596-0.19110.0463-0.09080.07250.14480.01910.04550.07510.00280.058388.084-4.415-16.908
41.22460.55050.28991.66210.90832.85120.0967-0.2945-0.2160.2094-0.0563-0.0794-0.04690.0255-0.04030.09290.0054-0.00760.08890.05250.043948.917-29.24619.853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 200
2X-RAY DIFFRACTION2B1 - 200
3X-RAY DIFFRACTION3C1 - 200
4X-RAY DIFFRACTION4D1 - 200

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