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- PDB-3tj8: Crystal structure of Helicobacter pylori UreE bound to Ni2+ -

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Basic information

Entry
Database: PDB / ID: 3tj8
TitleCrystal structure of Helicobacter pylori UreE bound to Ni2+
ComponentsUrease accessory protein ureE
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


urea metabolic process / nickel cation binding / unfolded protein binding / protein folding / protein-containing complex assembly / cytoplasm
Similarity search - Function
UreE urease accessory, N-terminal / Urease accessory protein UreE, C-terminal domain / Urease accessory protein UreE / UreE urease accessory, N-terminal domain superfamily / UreE urease accessory protein, N-terminal domain / UreE urease accessory protein, C-terminal domain / UreE urease accessory protein, N-terminal domain / UreE, C-terminal domain / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain ...UreE urease accessory, N-terminal / Urease accessory protein UreE, C-terminal domain / Urease accessory protein UreE / UreE urease accessory, N-terminal domain superfamily / UreE urease accessory protein, N-terminal domain / UreE urease accessory protein, C-terminal domain / UreE urease accessory protein, N-terminal domain / UreE, C-terminal domain / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / Alpha-Beta Plaits / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / NICKEL (II) ION / Urease accessory protein UreE
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsBanaszak, K. / Bellucci, M. / Zambelli, B. / Rypniewski, W.R. / Ciurli, S.
CitationJournal: Biochem.J. / Year: 2012
Title: Crystallographic and X-ray absorption spectroscopic characterization of Helicobacter pylori UreE bound to Ni2+ and Zn2+ reveals a role for the disordered C-terminal arm in metal trafficking.
Authors: Banaszak, K. / Martin-Diaconescu, V. / Bellucci, M. / Zambelli, B. / Rypniewski, W. / Maroney, M.J. / Ciurli, S.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urease accessory protein ureE
B: Urease accessory protein ureE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,39413
Polymers38,8752
Non-polymers51911
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-20 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.552, 117.145, 98.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-189-

HOH

21B-253-

HOH

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Components

#1: Protein Urease accessory protein ureE


Mass: 19437.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureE, HP_0070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09064
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO GB ABM16833.1

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 4.0M sodium formate, 0.1M sodium acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91885 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 15, 2010
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91885 Å / Relative weight: 1
ReflectionResolution: 1.59→58.57 Å / Num. all: 51702 / Num. obs: 51702 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rsym value: 0.049 / Net I/σ(I): 24.9
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.448 / % possible all: 87.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TJ8

3tj8


Resolution: 1.591→58.57 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.887 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21115 2629 5.1 %RANDOM
Rwork0.18498 ---
obs0.18629 48955 97.69 %-
all-48955 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.591→58.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 31 154 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222474
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5761.9793353
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03224.074108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19115440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3081517
X-RAY DIFFRACTIONr_chiral_restr0.1870.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211831
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.6411.51557
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52322483
X-RAY DIFFRACTIONr_scbond_it4.0273917
X-RAY DIFFRACTIONr_scangle_it6.2354.5857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 168 -
Rwork0.315 3242 -
obs--89.03 %
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)
15.1589-0.744-0.38462.61760.21942.7124-0.00250.0344-0.28780.2288-0.0130.39330.0559-0.48920.01550.13330.00230.01220.13760.01070.1635-15.882615.8713-14.9695
23.3712-2.2936-0.8883.09271.52393.5991-0.01210.02060.34680.1535-0.0170.1257-0.3517-0.21940.02910.18240.03640.01760.13140.00520.2201-15.347724.9558-14.752
35.687-1.1358-0.70751.4552-0.02212.1585-0.06510.092-0.18740.13850.00840.2899-0.0075-0.3020.05670.0807-0.0014-0.00040.068-0.00220.1004-11.41915.0714-15.6013
41.9767-0.70410.27292.3165-0.64171.7004-0.03970.05470.0519-0.0332-0.1533-0.1831-0.1390.18520.1930.0821-0.0181-0.03720.07150.04710.060511.795112.4225-5.4848
52.59871.7445-1.29055.2005-2.77754.129-0.02120.1079-0.0512-0.0092-0.0661-0.1539-0.16050.38540.08730.0719-0.0179-0.03950.12560.01270.046411.05213.1252-12.8565
65.3462-0.59590.19021.4723-0.47673.2325-0.0977-0.0839-0.12870.0491-0.0209-0.0183-0.00070.14040.11860.0957-0.007-0.020.05620.03340.08594.674212.0697-12.1328
77.07321.5771-4.211826.9697-1.746422.93630.15980.0128-0.2791-0.27020.1779-1.06610.71190.0277-0.33770.19570.03520.05830.13190.04190.213842.549324.36286.3324
86.3349-0.3753-0.15952.6556-0.00023.7702-0.21720.2004-0.1154-0.13750.195-0.17670.68210.10420.02220.3086-0.0429-0.09440.09540.04010.188236.106515.821814.687
91.97340.7592-2.27473.3021-0.68934.68460.00960.1140.0731-0.21730.0918-0.4190.2477-0.0467-0.10140.1934-0.0061-0.06680.10820.02810.181537.476121.291412.7247
101.39620.18110.64041.73371.26851.8392-0.0206-0.25380.16520.1735-0.24320.0947-0.10590.02350.26380.1251-0.0936-0.05450.1850.0140.06719.459613.75517.2156
112.78382.34720.03614.76630.06842.8664-0.0176-0.22880.28910.3073-0.16470.5351-0.1272-0.03030.18230.1512-0.0432-0.05410.17780.03740.158210.684613.512310.524
124.5855-0.40840.96621.99330.89860.71330.03030.15710.2245-0.0341-0.1231-0.0631-0.04250.01160.09290.2295-0.0692-0.0810.2460.08970.243320.017416.11217.8959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2A31 - 53
3X-RAY DIFFRACTION3A54 - 82
4X-RAY DIFFRACTION4A83 - 107
5X-RAY DIFFRACTION5A108 - 128
6X-RAY DIFFRACTION6A129 - 149
7X-RAY DIFFRACTION7B1 - 6
8X-RAY DIFFRACTION8B7 - 32
9X-RAY DIFFRACTION9B33 - 77
10X-RAY DIFFRACTION10B78 - 103
11X-RAY DIFFRACTION11B104 - 133
12X-RAY DIFFRACTION12B134 - 152

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