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- PDB-3tj9: Crystal structure of Helicobacter pylori UreE bound to Zn2+ -

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Basic information

Entry
Database: PDB / ID: 3tj9
TitleCrystal structure of Helicobacter pylori UreE bound to Zn2+
ComponentsUrease accessory protein ureE
KeywordsMETAL BINDING PROTEIN / urease accessory 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 / Urease accessory protein UreE
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.521 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 / 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_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Urease accessory protein ureE
D: Urease accessory protein ureE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9277
Polymers77,7504
Non-polymers1773
Water3,369187
1
A: Urease accessory protein ureE
B: Urease accessory protein ureE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9874
Polymers38,8752
Non-polymers1112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Urease accessory protein ureE
D: Urease accessory protein ureE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9413
Polymers38,8752
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.343, 109.343, 280.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Urease accessory protein ureE


Mass: 19437.547 Da / Num. of mol.: 4
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTYR 22 AGREES WITH THE SEQUENCE IN 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4.0M sodium formate, 0.1M sodium cacodylate pH 6.5, 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: 1.2818, 1.2832, 1.2765
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 15, 2010
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28181
21.28321
31.27651
ReflectionResolution: 2.52→50 Å / Num. obs: 34454 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rsym value: 0.092 / Net I/σ(I): 22.4
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1654 / Rsym value: 0.43 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
Auto-Rickshaw"three wavelength MAD"phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.521→19.83 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 16.226 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24484 1051 3.1 %RANDOM
Rwork0.20261 ---
obs0.20389 33219 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.521→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 5 187 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9756474
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1315612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39724.518197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94615818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3971525
X-RAY DIFFRACTIONr_chiral_restr0.1140.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213535
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_it0.9021.53071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75924900
X-RAY DIFFRACTIONr_scbond_it3.30131707
X-RAY DIFFRACTIONr_scangle_it5.8214.51574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.521→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 69 -
Rwork0.331 2366 -
obs--99.31 %
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)
12.9799-1.8419-0.23485.0484-2.55283.98310.1511-0.31240.34830.4254-0.1027-0.2908-0.80520.3916-0.04840.1841-0.12220.03610.1365-0.04490.107542.6895-26.3344-16.2474
22.77650.4838-0.92111.9986-0.26452.91810.05860.0507-0.13-0.1015-0.0451-0.09640.0194-0.0081-0.01360.0274-0.038-0.0180.10960.01350.082637.6877-49.9378-6.4869
32.76553.1171-0.43678.1392-0.81541.68130.2229-0.2849-0.68510.642-0.6495-0.85810.24310.49480.42660.5114-0.2384-0.12270.44680.20110.384535.6138-70.214325.8683
43.99660.30191.94842.3615-1.42345.67680.2738-0.35450.09750.3985-0.3329-0.145-0.0162-0.05410.05910.1284-0.1499-0.00340.19570.00350.113334.8231-47.995712.8239
50.55090.1827-1.429711.1434.41646.05390.42550.03010.0125-1.9559-0.33510.2851-2.4348-0.0485-0.09041.1429-0.02240.00140.3479-0.07040.207162.8915-14.33616.0752
61.3396-0.6447-0.35593.84341.20643.66420.0023-0.13320.0659-0.05040.11160.0121-0.41540.0366-0.11390.05140.00020.00240.1087-0.0350.084165.6952-34.22628.8328
78.14432.4254-1.07249.7274-0.765715.52860.0422-1.2769-1.74181.2382-0.23610.22442.9414-0.28120.19390.7916-0.07410.01530.37050.17730.732154.5292-71.77480.1608
83.72850.56790.68732.29531.27892.06260.0283-0.0498-0.3340.19010.02340.06610.3536-0.0389-0.05160.07870.0243-0.02390.126-0.0050.1261.6857-52.8566-5.1431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION2A77 - 149
3X-RAY DIFFRACTION3B1 - 76
4X-RAY DIFFRACTION4B77 - 153
5X-RAY DIFFRACTION5C1 - 53
6X-RAY DIFFRACTION6C54 - 154
7X-RAY DIFFRACTION7D1 - 55
8X-RAY DIFFRACTION8D56 - 154

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