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- PDB-3ny0: Crystal Structure of UreE from Helicobacter pylori (Ni2+ bound form) -

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Basic information

Entry
Database: PDB / ID: 3ny0
TitleCrystal Structure of UreE from Helicobacter pylori (Ni2+ bound form)
ComponentsUrease accessory protein ureE
KeywordsMETAL BINDING PROTEIN / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / urease maturation 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
NICKEL (II) ION / Urease accessory protein UreE
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsShi, R. / Munger, C. / Assinas, A. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Biochemistry / Year: 2010
Title: Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites
Authors: Shi, R. / Munger, C. / Asinas, A. / Benoit, S.L. / Miller, E. / Matte, A. / Maier, R.J. / Cygler, M.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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)77,7095
Polymers77,6504
Non-polymers591
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-42 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.057, 91.057, 202.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Urease accessory protein ureE


Mass: 19412.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 43504 / Gene: HP_0070, ureE / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09064
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 13% PEG 20000, 0.1M MES pH 5.5, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.4849 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4849 Å / Relative weight: 1
ReflectionResolution: 3.1→46.63 Å / Num. obs: 14069 / % possible obs: 85.7 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.096 / Χ2: 1.226 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.215.70.2936171.22138.9
3.21-3.346.60.2978361.25352.4
3.34-3.497.20.25511391.30970.8
3.49-3.6880.22615001.23493.3
3.68-3.9110.30.20215971.25799.1
3.91-4.2111.80.15416251.29499.7
4.21-4.6311.90.11216321.35299.7
4.63-5.311.90.09416371.18799.7
5.3-6.6711.70.08416821.18199.8
6.67-5010.80.04918041.04799.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LA0

3la0


Resolution: 3.09→46.63 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 51.461 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.591 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.299 695 4.9 %RANDOM
Rwork0.2453 ---
obs0.2477 14043 85.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 121.52 Å2 / Biso mean: 93.598 Å2 / Biso min: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å20 Å2
2--3.57 Å20 Å2
3----7.15 Å2
Refinement stepCycle: LAST / Resolution: 3.09→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 1 0 4774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224847
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9776519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1725592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29224.189222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.6815946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8671536
X-RAY DIFFRACTIONr_chiral_restr0.1360.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213542
X-RAY DIFFRACTIONr_mcbond_it0.8491.52965
X-RAY DIFFRACTIONr_mcangle_it1.62424784
X-RAY DIFFRACTIONr_scbond_it1.95331882
X-RAY DIFFRACTIONr_scangle_it3.6244.51735
LS refinement shellResolution: 3.092→3.172 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 15 -
Rwork0.275 414 -
all-429 -
obs--36.92 %
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)
16.5265-1.06043.00394.1624-0.2452.53920.12960.2439-0.04270.03610.16180.17470.0681-0.2273-0.29140.1984-0.00490.03580.26360.06160.0887-8.725713.7271-2.7572
23.62750.1387-0.74522.4685-0.44275.0378-0.10170.0506-0.0292-0.13470.0604-0.01530.43620.18010.04140.2450.03870.0170.2003-0.02950.03218.22868.403117.1754
35.5542-0.0533-1.54445.33910.17523.804-0.06990.65930.2619-0.18090.1475-0.36490.04650.5047-0.07750.0967-0.0495-0.02230.4830.0240.048711.414435.9477-0.9606
43.3647-1.61790.49072.2924-0.38084.42030.06020.09230.17410.1261-0.0404-0.1039-0.1021-0.4919-0.01980.2223-0.0132-0.01680.2583-0.00940.0573-4.109335.573120.323
56.22240.272-1.42332.4559-1.95437.19580.0141-0.0626-0.13510.2064-0.0290.57020.4771-0.86080.01490.3753-0.1436-0.00040.1602-0.08080.2531-7.726329.452158.3406
62.580.94091.86122.6438-0.0094.04550.04120.00410.00160.38830.04-0.089-0.5318-0.161-0.08110.354-0.0161-0.05040.23980.00320.07895.971837.6736.6168
74.39130.63052.68021.88393.46126.928-0.4315-1.2863-0.0542-0.0220.7393-0.2446-0.23570.7072-0.30780.46770.0363-0.02410.9080.04190.231213.40867.847555.3389
83.1163-1.0948-0.8933.4216-1.45737.2284-0.0629-0.1929-0.0183-0.12180.14510.23520.36-0.3742-0.08220.2556-0.02040.03610.23740.04980.0507-2.29356.622633.9812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 77
2X-RAY DIFFRACTION2A78 - 148
3X-RAY DIFFRACTION3B2 - 77
4X-RAY DIFFRACTION4B78 - 154
5X-RAY DIFFRACTION5C2 - 77
6X-RAY DIFFRACTION6C78 - 149
7X-RAY DIFFRACTION7D2 - 77
8X-RAY DIFFRACTION8D78 - 149

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