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- PDB-4z42: Crystal structure of urease from Yersinia enterocolitica -

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Basic information

Entry
Database: PDB / ID: 4z42
TitleCrystal structure of urease from Yersinia enterocolitica
Components
  • Urease subunit alpha
  • Urease subunit beta
  • Urease subunit gamma
KeywordsHYDROLASE / urease / urea degradation / nitrogen metabolism
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit ...Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Ribbon / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesYersinia enterocolitica W22703 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsStuder, G. / Jakob, R.P. / Mahi, M.A. / Wiesand, U. / Schwede, T. / Maier, T.
CitationJournal: To Be Published
Title: Crystal structure of urease from Yersinia enterocolitica
Authors: Studer, G. / Jakob, R.P. / Mahi, M.A. / Wiesand, U. / Schwede, T. / Maier, T.
History
DepositionApr 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
D: Urease subunit gamma
E: Urease subunit beta
F: Urease subunit alpha
G: Urease subunit gamma
H: Urease subunit beta
I: Urease subunit alpha
J: Urease subunit gamma
K: Urease subunit beta
L: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,00520
Polymers360,53512
Non-polymers4708
Water1,964109
1
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
D: Urease subunit gamma
E: Urease subunit beta
F: Urease subunit alpha
G: Urease subunit gamma
H: Urease subunit beta
I: Urease subunit alpha
J: Urease subunit gamma
K: Urease subunit beta
L: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
D: Urease subunit gamma
E: Urease subunit beta
F: Urease subunit alpha
G: Urease subunit gamma
H: Urease subunit beta
I: Urease subunit alpha
J: Urease subunit gamma
K: Urease subunit beta
L: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
D: Urease subunit gamma
E: Urease subunit beta
F: Urease subunit alpha
G: Urease subunit gamma
H: Urease subunit beta
I: Urease subunit alpha
J: Urease subunit gamma
K: Urease subunit beta
L: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,083,01560
Polymers1,081,60636
Non-polymers1,40924
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Unit cell
Length a, b, c (Å)157.200, 157.200, 774.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-714-

HOH

21L-715-

HOH

31L-722-

HOH

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Components

#1: Protein
Urease subunit gamma / / Urea amidohydrolase subunit gamma


Mass: 11063.837 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Yersinia enterocolitica W22703 (bacteria) / References: UniProt: F4MWM9, urease
#2: Protein
Urease subunit beta / / Urea amidohydrolase subunit beta


Mass: 17926.947 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Yersinia enterocolitica W22703 (bacteria) / References: UniProt: F4MWM8, urease
#3: Protein
Urease subunit alpha / / Urea amidohydrolase subunit alpha


Mass: 61143.055 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Yersinia enterocolitica W22703 (bacteria) / References: UniProt: F4MWM7, urease
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 % / Description: bipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2, 0.1M Sodium HEPES pH 7.5, 30%(v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.01→43.3 Å / Num. all: 85049 / Num. obs: 84998 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 64.43 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.5
Reflection shellResolution: 3.01→3.19 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.8 / % possible all: 96.4

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FWB

1fwb


Resolution: 3.01→29.71 Å / Cor.coef. Fo:Fc: 0.7679 / Cor.coef. Fo:Fc free: 0.7262 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.496
RfactorNum. reflection% reflectionSelection details
Rfree0.2976 3666 5 %RANDOM
Rwork0.2769 ---
obs0.278 73319 99.48 %-
Displacement parametersBiso mean: 100.84 Å2
Baniso -1Baniso -2Baniso -3
1-7.4973 Å20 Å20 Å2
2--7.4973 Å20 Å2
3----14.9946 Å2
Refine analyzeLuzzati coordinate error obs: 1.013 Å
Refinement stepCycle: LAST / Resolution: 3.01→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47265 0 8 109 47382
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00847713HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9486391HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d13174SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes627HARMONIC2
X-RAY DIFFRACTIONt_gen_planes7156HARMONIC5
X-RAY DIFFRACTIONt_it47713HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion2.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3218SEMIHARMONIC5
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_contact52349SEMIHARMONIC4
LS refinement shellResolution: 3.01→3.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2954 256 4.99 %
Rwork0.2798 4876 -
all0.2806 5132 -
obs--99.48 %
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)
1-0.23221.38860.326110.97440.34510.36230.0268-0.11980.23320.03870.03610.0588-0.11720.198-0.0629-0.0138-0.2252-0.0675-0.4466-0.37660.392722.2521-27.884383.656
25.09780.4584-1.7123-1.16992.0914.6457-0.18710.03930.13090.14120.231-0.30860.0380.2588-0.0439-0.1032-0.5769-0.0999-0.1031-0.10380.486654.7328-54.523467.8742
30.19260.09171.38441.15281.69112.0052-0.062-0.28690.5870.70050.0023-0.3975-0.25480.09750.05970.1981-0.3202-0.1113-0.113-0.4152-0.13620.0389-60.117998.4944
41.0062-0.2474-3.151910.49584.23950-0.01110.07380.3311-0.0507-0.1276-0.0883-0.2023-0.17230.13870.32740.1356-0.0228-0.5064-0.29830.3662-3.1686-22.660477.2413
57.9546-2.2421.98538.1689-2.04890.02690.06720.14960.2445-0.26950.07250.3859-0.509-0.4058-0.13960.08080.4308-0.0379-0.19620.28210.1701-28.9613-36.120843.0254
62.36492.0752-0.33953.29780.02550.47570.0240.20621.0771-0.10860.1518-0.3207-0.72660.1905-0.17580.1403-0.06930.1412-0.48160.0990.605915.1274-44.340155.9913
7-1.28240.89950.70035.2956.5082.4770.0151-0.1820.0010.12240.0013-0.0728-0.138-0.0579-0.01640.1171-0.0501-0.0438-0.4161-0.3757-0.17512.8955-31.9507101.538
83.5689-2.0605-1.4892-3.5689-0.34285.954-0.0054-0.0850.04510.1102-0.03990.06230.04640.01330.04540.2149-0.01550.04840.1887-0.169-0.4122-12.4205-66.8793125.015
91.0623-0.9082-1.04471.7641.20570.1222-0.0444-0.20410.79790.48540.13470.4796-0.1829-0.0081-0.09030.10360.22060.1937-0.2927-0.23910.3797-21.4376-49.583382.5852
10-3.25631.8801-2.49463.25630.20218.3185-0.13470.27290.1504-0.11890.1086-0.02840.01280.16840.02610.2945-0.15850.18980.11290.2115-0.554412.0743-81.3185-2.6
118.97482.9308-2.86470.999-3.81734.46660.05710.0609-0.0561-0.2731-0.1468-0.2632-0.2380.16630.0896-0.1772-0.42340.27020.06990.140.032239.2275-57.331524.1001
120.1047-0.34371.19822.8298-1.70641.3357-0.05880.3440.6809-1.19440.08920.1344-0.19340.0328-0.03040.47260.0647-0.01820.0310.3405-0.5665-6.7677-65.356122.8557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }

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