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- PDB-5xkt: Klebsiella pneumoniae UreG in complex with GMPPNP and nickel -

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Basic information

Entry
Database: PDB / ID: 5xkt
TitleKlebsiella pneumoniae UreG in complex with GMPPNP and nickel
ComponentsUrease accessory protein UreG
KeywordsHYDROLASE / SIMIBI Class GTPase
Function / homology
Function and homology information


: / nickel cation binding / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Urease accessory protein UreG / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / NICKEL (II) ION / Urease accessory protein UreG
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. rhinoscleromatis SB3432 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFong, Y.H. / Yuen, M.H. / Nim, Y.S. / Lau, P.H. / Wong, K.B.
Funding support Hong Kong, 3items
OrganizationGrant numberCountry
Research Grants Council14117314 Hong Kong
Research Grants CouncilAoE/M-05/12 Hong Kong
The Chinese University of Hong Kong3132814 Hong Kong
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into how GTP-dependent conformational changes in a metallochaperone UreG facilitate urease maturation.
Authors: Yuen, M.H. / Fong, Y.H. / Nim, Y.S. / Lau, P.H. / Wong, K.B.
History
DepositionMay 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,0217
Polymers42,8012
Non-polymers1,2205
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-43 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.553, 49.318, 129.708
Angle α, β, γ (deg.)90.00, 103.16, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Urease accessory protein UreG


Mass: 21400.383 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 5-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. rhinoscleromatis SB3432 (bacteria)
Gene: ureG, KPR_4504 / Production host: Escherichia coli (E. coli) / References: UniProt: R4YE37
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 1.8 M (NH4)2SO4, 3% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19.433 Å / Num. obs: 47816 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.036 / Net I/av σ(I): 15.2 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 4 / Num. unique obs: 8710 / CC1/2: 0.9 / Rpim(I) all: 0.193 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HI0

4hi0


Resolution: 1.8→19.434 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 1998 4.18 %
Rwork0.1563 --
obs0.1578 47816 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 67 488 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143096
X-RAY DIFFRACTIONf_angle_d1.3154212
X-RAY DIFFRACTIONf_dihedral_angle_d10.141850
X-RAY DIFFRACTIONf_chiral_restr0.087488
X-RAY DIFFRACTIONf_plane_restr0.008538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84510.23921400.21183221X-RAY DIFFRACTION100
1.8451-1.89490.24491430.18373285X-RAY DIFFRACTION100
1.8949-1.95060.21431410.17033220X-RAY DIFFRACTION100
1.9506-2.01350.18591430.16213268X-RAY DIFFRACTION100
2.0135-2.08540.21751430.15543259X-RAY DIFFRACTION100
2.0854-2.16880.22011410.15493248X-RAY DIFFRACTION100
2.1688-2.26740.19731430.14893269X-RAY DIFFRACTION100
2.2674-2.38670.19011420.15133260X-RAY DIFFRACTION100
2.3867-2.53590.19191430.14633268X-RAY DIFFRACTION100
2.5359-2.73120.2011430.16043272X-RAY DIFFRACTION100
2.7312-3.00520.19781420.17173281X-RAY DIFFRACTION100
3.0052-3.4380.19261420.16553272X-RAY DIFFRACTION100
3.438-4.32360.14941450.1343312X-RAY DIFFRACTION99
4.3236-19.43560.18311470.15263383X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.6602 Å / Origin y: 8.2038 Å / Origin z: -13.5713 Å
111213212223313233
T0.1041 Å20.0047 Å2-0.0114 Å2-0.0838 Å20.0048 Å2--0.1047 Å2
L0.8542 °20.1014 °2-0.1623 °2-0.3759 °2-0.0025 °2--0.9581 °2
S-0.004 Å °-0.0932 Å °0.002 Å °-0.0064 Å °-0.0206 Å °-0.006 Å °-0.0318 Å °0.1009 Å °0.0237 Å °
Refinement TLS groupSelection details: all

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