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- PDB-3sf5: Crystal Structure of Helicobacter pylori Urease Accessory Protein... -

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Basic information

Entry
Database: PDB / ID: 3sf5
TitleCrystal Structure of Helicobacter pylori Urease Accessory Protein UreF/H complex
Components(Urease accessory protein ...) x 2
KeywordsCHAPERONE / Urease Accessory Protein / UreF / UreH
Function / homology
Function and homology information


metabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease accessory protein UreD / UreD urease accessory protein / Urease accessory protein UreF / Urease accessory protein UreF / Urease accessory protein UreF / UreF domain superfamily / UreF / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Urease accessory protein UreF / Urease accessory protein UreH
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsFong, Y.H. / Chen, Y.W. / Wong, K.B.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Assembly of preactivation complex for urease maturation in Helicobacter pylori: crystal structure of UreF-UreH protein complex
Authors: Fong, Y.H. / Wong, H.C. / Chuck, C.P. / Chen, Y.W. / Sun, H. / Wong, K.B.
History
DepositionJun 12, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Nov 1, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Assembly

Deposited unit
A: Urease accessory protein ureF
B: Urease accessory protein ureH
C: Urease accessory protein ureF
D: Urease accessory protein ureH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,43820
Polymers116,8184
Non-polymers1,62016
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-101 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.653, 70.732, 205.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSERchain A and (resseq 29:254 )AA29 - 25429 - 254
21VALVALSERSERchain C and (resseq 29:254 )CC29 - 25429 - 254
12GLNGLNTHRTHRchain B and (resseq 6:260 )BB6 - 2606 - 260
22GLNGLNTHRTHRchain D and (resseq 6:260 )DD6 - 2606 - 260

NCS ensembles :
ID
1
2

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Components

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Urease accessory protein ... , 2 types, 4 molecules ACBD

#1: Protein Urease accessory protein ureF


Mass: 28651.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureF / Production host: Escherichia coli (E. coli) / References: UniProt: Q09065
#2: Protein Urease accessory protein ureH


Mass: 29757.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureH / Production host: Escherichia coli (E. coli) / References: UniProt: Q09067

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Non-polymers , 4 types, 223 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG 4000, 0.15M ammonium sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 21, 2010
RadiationMonochromator: Ni MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.495→50 Å / Num. all: 36735 / Num. obs: 36388 / % possible obs: 99.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 29.96 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5-2.65195
2.65-2.83199.6
2.83-3.05199.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O1Q

3o1q


Resolution: 2.495→35.827 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8702 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1820 5 %RANDOM
Rwork0.1732 ---
all0.1754 36383 --
obs0.1754 36383 99.08 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.069 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 119.54 Å2 / Biso mean: 31.7302 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.2037 Å20 Å20 Å2
2---1.3273 Å20 Å2
3---2.531 Å2
Refinement stepCycle: LAST / Resolution: 2.495→35.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7746 0 100 207 8053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037975
X-RAY DIFFRACTIONf_angle_d0.69210747
X-RAY DIFFRACTIONf_chiral_restr0.0491225
X-RAY DIFFRACTIONf_plane_restr0.0021373
X-RAY DIFFRACTIONf_dihedral_angle_d13.3163004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1799X-RAY DIFFRACTIONPOSITIONAL0.312
12C1799X-RAY DIFFRACTIONPOSITIONAL0.312
21B2005X-RAY DIFFRACTIONPOSITIONAL0.327
22D2005X-RAY DIFFRACTIONPOSITIONAL0.327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4951-2.56250.29161250.20622380250590
2.5625-2.63790.28221390.20162628276799
2.6379-2.7230.26531380.18662635277399
2.723-2.82030.25481400.175726532793100
2.8203-2.93320.21621380.178226172755100
2.9332-3.06660.22011390.168326512790100
3.0666-3.22820.2271410.177226702811100
3.2282-3.43030.22181390.180226472786100
3.4303-3.69490.1981410.163726822823100
3.6949-4.06630.2041410.160626672808100
4.0663-4.65360.18261430.143627172860100
4.6536-5.85890.21871450.18227582903100
5.8589-35.83040.19921510.185628583009100

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